Starting phenix.real_space_refine on Thu Sep 26 20:26:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/09_2024/7eq9_31256.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/09_2024/7eq9_31256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/09_2024/7eq9_31256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/09_2024/7eq9_31256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/09_2024/7eq9_31256.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/09_2024/7eq9_31256.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 180 5.16 5 C 39240 2.51 5 N 10740 2.21 5 O 12360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 62520 Number of models: 1 Model: "" Number of chains: 1 Chain: "AA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Restraints were copied for chains: EA, BA, WA, YA, DB, DA, FA, ZA, AB, HB, HA, GA, JA, IB, BB, LA, NA, IA, PA, RA, CB, CA, TA, A, VA, C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T, W, V, Y, X, Z, EB, KA, MA, XA, FB, OA, QA, SA, UA, GB Time building chain proxies: 9.01, per 1000 atoms: 0.14 Number of scatterers: 62520 At special positions: 0 Unit cell: (214.755, 214.755, 214.755, 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 180 16.00 O 12360 8.00 N 10740 7.00 C 39240 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: 11.14 Conformation dependent library (CDL) restraints added in 5.9 seconds 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14880 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 120 sheets defined 47.2% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.51 Creating SS restraints... Processing helix chain 'A' and resid 75 through 116 Processing helix chain 'A' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 116 Processing helix chain 'B' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 116 Processing helix chain 'C' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 116 Processing helix chain 'D' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 116 Processing helix chain 'E' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 116 Processing helix chain 'F' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 116 Processing helix chain 'G' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN G 132 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 116 Processing helix chain 'H' and resid 119 through 136 removed outlier: 4.289A pdb=" N GLN H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 116 Processing helix chain 'I' and resid 119 through 136 removed outlier: 4.289A pdb=" N GLN I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 116 Processing helix chain 'J' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLN J 132 " --> pdb=" O GLU J 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 116 Processing helix chain 'K' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN K 132 " --> pdb=" O GLU K 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 116 Processing helix chain 'L' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 116 Processing helix chain 'M' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN M 132 " --> pdb=" O GLU M 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 116 Processing helix chain 'N' and resid 119 through 136 removed outlier: 4.289A pdb=" N GLN N 132 " --> pdb=" O GLU N 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 116 Processing helix chain 'O' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLN O 132 " --> pdb=" O GLU O 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 116 Processing helix chain 'P' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN P 132 " --> pdb=" O GLU P 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 116 Processing helix chain 'Q' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLN Q 132 " --> pdb=" O GLU Q 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 116 Processing helix chain 'R' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN R 132 " --> pdb=" O GLU R 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 116 Processing helix chain 'S' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN S 132 " --> pdb=" O GLU S 128 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 116 Processing helix chain 'T' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN T 132 " --> pdb=" O GLU T 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 116 Processing helix chain 'V' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN V 132 " --> pdb=" O GLU V 128 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 116 Processing helix chain 'W' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN W 132 " --> pdb=" O GLU W 128 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 116 Processing helix chain 'X' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN X 132 " --> pdb=" O GLU X 128 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 116 Processing helix chain 'Y' and resid 119 through 136 removed outlier: 4.289A pdb=" N GLN Y 132 " --> pdb=" O GLU Y 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 116 Processing helix chain 'Z' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLN Z 132 " --> pdb=" O GLU Z 128 " (cutoff:3.500A) Processing helix chain 'AA' and resid 75 through 116 Processing helix chain 'AA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNAA 132 " --> pdb=" O GLUAA 128 " (cutoff:3.500A) Processing helix chain 'BA' and resid 75 through 116 Processing helix chain 'BA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNBA 132 " --> pdb=" O GLUBA 128 " (cutoff:3.500A) Processing helix chain 'CA' and resid 75 through 116 Processing helix chain 'CA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNCA 132 " --> pdb=" O GLUCA 128 " (cutoff:3.500A) Processing helix chain 'DA' and resid 75 through 116 Processing helix chain 'DA' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLNDA 132 " --> pdb=" O GLUDA 128 " (cutoff:3.500A) Processing helix chain 'EA' and resid 75 through 116 Processing helix chain 'EA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNEA 132 " --> pdb=" O GLUEA 128 " (cutoff:3.500A) Processing helix chain 'FA' and resid 75 through 116 Processing helix chain 'FA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNFA 132 " --> pdb=" O GLUFA 128 " (cutoff:3.500A) Processing helix chain 'GA' and resid 75 through 116 Processing helix chain 'GA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNGA 132 " --> pdb=" O GLUGA 128 " (cutoff:3.500A) Processing helix chain 'HA' and resid 75 through 116 Processing helix chain 'HA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNHA 132 " --> pdb=" O GLUHA 128 " (cutoff:3.500A) Processing helix chain 'IA' and resid 75 through 116 Processing helix chain 'IA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNIA 132 " --> pdb=" O GLUIA 128 " (cutoff:3.500A) Processing helix chain 'JA' and resid 75 through 116 Processing helix chain 'JA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNJA 132 " --> pdb=" O GLUJA 128 " (cutoff:3.500A) Processing helix chain 'KA' and resid 75 through 116 Processing helix chain 'KA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNKA 132 " --> pdb=" O GLUKA 128 " (cutoff:3.500A) Processing helix chain 'LA' and resid 75 through 116 Processing helix chain 'LA' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLNLA 132 " --> pdb=" O GLULA 128 " (cutoff:3.500A) Processing helix chain 'MA' and resid 75 through 116 Processing helix chain 'MA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNMA 132 " --> pdb=" O GLUMA 128 " (cutoff:3.500A) Processing helix chain 'NA' and resid 75 through 116 Processing helix chain 'NA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNNA 132 " --> pdb=" O GLUNA 128 " (cutoff:3.500A) Processing helix chain 'OA' and resid 75 through 116 Processing helix chain 'OA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNOA 132 " --> pdb=" O GLUOA 128 " (cutoff:3.500A) Processing helix chain 'PA' and resid 75 through 116 Processing helix chain 'PA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNPA 132 " --> pdb=" O GLUPA 128 " (cutoff:3.500A) Processing helix chain 'QA' and resid 75 through 116 Processing helix chain 'QA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNQA 132 " --> pdb=" O GLUQA 128 " (cutoff:3.500A) Processing helix chain 'RA' and resid 75 through 116 Processing helix chain 'RA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNRA 132 " --> pdb=" O GLURA 128 " (cutoff:3.500A) Processing helix chain 'SA' and resid 75 through 116 Processing helix chain 'SA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNSA 132 " --> pdb=" O GLUSA 128 " (cutoff:3.500A) Processing helix chain 'TA' and resid 75 through 116 Processing helix chain 'TA' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLNTA 132 " --> pdb=" O GLUTA 128 " (cutoff:3.500A) Processing helix chain 'UA' and resid 75 through 116 Processing helix chain 'UA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNUA 132 " --> pdb=" O GLUUA 128 " (cutoff:3.500A) Processing helix chain 'VA' and resid 75 through 116 Processing helix chain 'VA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNVA 132 " --> pdb=" O GLUVA 128 " (cutoff:3.500A) Processing helix chain 'WA' and resid 75 through 116 Processing helix chain 'WA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNWA 132 " --> pdb=" O GLUWA 128 " (cutoff:3.500A) Processing helix chain 'XA' and resid 75 through 116 Processing helix chain 'XA' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLNXA 132 " --> pdb=" O GLUXA 128 " (cutoff:3.500A) Processing helix chain 'YA' and resid 75 through 116 Processing helix chain 'YA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNYA 132 " --> pdb=" O GLUYA 128 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 75 through 116 Processing helix chain 'ZA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNZA 132 " --> pdb=" O GLUZA 128 " (cutoff:3.500A) Processing helix chain 'AB' and resid 75 through 116 Processing helix chain 'AB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNAB 132 " --> pdb=" O GLUAB 128 " (cutoff:3.500A) Processing helix chain 'BB' and resid 75 through 116 Processing helix chain 'BB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNBB 132 " --> pdb=" O GLUBB 128 " (cutoff:3.500A) Processing helix chain 'CB' and resid 75 through 116 Processing helix chain 'CB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNCB 132 " --> pdb=" O GLUCB 128 " (cutoff:3.500A) Processing helix chain 'DB' and resid 75 through 116 Processing helix chain 'DB' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLNDB 132 " --> pdb=" O GLUDB 128 " (cutoff:3.500A) Processing helix chain 'EB' and resid 75 through 116 Processing helix chain 'EB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNEB 132 " --> pdb=" O GLUEB 128 " (cutoff:3.500A) Processing helix chain 'FB' and resid 75 through 116 Processing helix chain 'FB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNFB 132 " --> pdb=" O GLUFB 128 " (cutoff:3.500A) Processing helix chain 'GB' and resid 75 through 116 Processing helix chain 'GB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNGB 132 " --> pdb=" O GLUGB 128 " (cutoff:3.500A) Processing helix chain 'HB' and resid 75 through 116 Processing helix chain 'HB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNHB 132 " --> pdb=" O GLUHB 128 " (cutoff:3.500A) Processing helix chain 'IB' and resid 75 through 116 Processing helix chain 'IB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNIB 132 " --> pdb=" O GLUIB 128 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA A 31 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 16 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 33 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP A 14 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 6 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE A 71 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG A 8 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 51 Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA B 31 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 16 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 33 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP B 14 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 6 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE B 71 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG B 8 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 48 through 51 Processing sheet with id=AA6, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA C 31 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 16 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL C 33 " --> pdb=" O ASP C 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP C 14 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 6 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE C 71 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG C 8 " --> pdb=" O ILE C 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 48 through 51 Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA D 31 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE D 16 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL D 33 " --> pdb=" O ASP D 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP D 14 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE D 6 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE D 71 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG D 8 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 48 through 51 Processing sheet with id=AB1, first strand: chain 'E' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA E 31 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE E 16 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL E 33 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP E 14 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 6 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE E 71 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG E 8 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 48 through 51 Processing sheet with id=AB3, first strand: chain 'F' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA F 31 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE F 16 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL F 33 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP F 14 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE F 6 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE F 71 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG F 8 " --> pdb=" O ILE F 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 48 through 51 Processing sheet with id=AB5, first strand: chain 'G' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA G 31 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE G 16 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL G 33 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP G 14 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE G 6 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE G 71 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG G 8 " --> pdb=" O ILE G 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 48 through 51 Processing sheet with id=AB7, first strand: chain 'H' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA H 31 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE H 16 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL H 33 " --> pdb=" O ASP H 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP H 14 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE H 6 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE H 71 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG H 8 " --> pdb=" O ILE H 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 48 through 51 Processing sheet with id=AB9, first strand: chain 'I' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA I 31 " --> pdb=" O ILE I 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE I 16 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL I 33 " --> pdb=" O ASP I 14 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASP I 14 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE I 6 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE I 71 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG I 8 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 48 through 51 Processing sheet with id=AC2, first strand: chain 'J' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA J 31 " --> pdb=" O ILE J 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE J 16 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL J 33 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP J 14 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE J 6 " --> pdb=" O ILE J 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE J 71 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG J 8 " --> pdb=" O ILE J 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 48 through 51 Processing sheet with id=AC4, first strand: chain 'K' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA K 31 " --> pdb=" O ILE K 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE K 16 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL K 33 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP K 14 " --> pdb=" O VAL K 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE K 6 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE K 71 " --> pdb=" O ILE K 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG K 8 " --> pdb=" O ILE K 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 48 through 51 Processing sheet with id=AC6, first strand: chain 'L' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA L 31 " --> pdb=" O ILE L 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE L 16 " --> pdb=" O ALA L 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL L 33 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP L 14 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE L 6 " --> pdb=" O ILE L 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE L 71 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG L 8 " --> pdb=" O ILE L 69 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 48 through 51 Processing sheet with id=AC8, first strand: chain 'M' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA M 31 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE M 16 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL M 33 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP M 14 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE M 6 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE M 71 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG M 8 " --> pdb=" O ILE M 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 48 through 51 Processing sheet with id=AD1, first strand: chain 'N' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA N 31 " --> pdb=" O ILE N 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE N 16 " --> pdb=" O ALA N 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL N 33 " --> pdb=" O ASP N 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP N 14 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE N 6 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE N 71 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG N 8 " --> pdb=" O ILE N 69 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 48 through 51 Processing sheet with id=AD3, first strand: chain 'O' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA O 31 " --> pdb=" O ILE O 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE O 16 " --> pdb=" O ALA O 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL O 33 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP O 14 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE O 6 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE O 71 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG O 8 " --> pdb=" O ILE O 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 48 through 51 Processing sheet with id=AD5, first strand: chain 'P' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA P 31 " --> pdb=" O ILE P 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE P 16 " --> pdb=" O ALA P 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL P 33 " --> pdb=" O ASP P 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP P 14 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE P 6 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE P 71 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG P 8 " --> pdb=" O ILE P 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 48 through 51 Processing sheet with id=AD7, first strand: chain 'Q' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA Q 31 " --> pdb=" O ILE Q 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE Q 16 " --> pdb=" O ALA Q 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL Q 33 " --> pdb=" O ASP Q 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP Q 14 " --> pdb=" O VAL Q 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE Q 6 " --> pdb=" O ILE Q 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE Q 71 " --> pdb=" O ILE Q 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG Q 8 " --> pdb=" O ILE Q 69 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 48 through 51 Processing sheet with id=AD9, first strand: chain 'R' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA R 31 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE R 16 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL R 33 " --> pdb=" O ASP R 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP R 14 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE R 6 " --> pdb=" O ILE R 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE R 71 " --> pdb=" O ILE R 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG R 8 " --> pdb=" O ILE R 69 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 48 through 51 Processing sheet with id=AE2, first strand: chain 'S' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA S 31 " --> pdb=" O ILE S 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE S 16 " --> pdb=" O ALA S 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL S 33 " --> pdb=" O ASP S 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP S 14 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE S 6 " --> pdb=" O ILE S 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE S 71 " --> pdb=" O ILE S 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG S 8 " --> pdb=" O ILE S 69 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 48 through 51 Processing sheet with id=AE4, first strand: chain 'T' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA T 31 " --> pdb=" O ILE T 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE T 16 " --> pdb=" O ALA T 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL T 33 " --> pdb=" O ASP T 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP T 14 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE T 6 " --> pdb=" O ILE T 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE T 71 " --> pdb=" O ILE T 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG T 8 " --> pdb=" O ILE T 69 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 48 through 51 Processing sheet with id=AE6, first strand: chain 'V' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA V 31 " --> pdb=" O ILE V 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE V 16 " --> pdb=" O ALA V 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL V 33 " --> pdb=" O ASP V 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP V 14 " --> pdb=" O VAL V 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE V 6 " --> pdb=" O ILE V 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE V 71 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG V 8 " --> pdb=" O ILE V 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 48 through 51 Processing sheet with id=AE8, first strand: chain 'W' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA W 31 " --> pdb=" O ILE W 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE W 16 " --> pdb=" O ALA W 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL W 33 " --> pdb=" O ASP W 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP W 14 " --> pdb=" O VAL W 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE W 6 " --> pdb=" O ILE W 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE W 71 " --> pdb=" O ILE W 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG W 8 " --> pdb=" O ILE W 69 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 48 through 51 Processing sheet with id=AF1, first strand: chain 'X' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA X 31 " --> pdb=" O ILE X 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE X 16 " --> pdb=" O ALA X 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL X 33 " --> pdb=" O ASP X 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP X 14 " --> pdb=" O VAL X 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE X 6 " --> pdb=" O ILE X 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE X 71 " --> pdb=" O ILE X 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG X 8 " --> pdb=" O ILE X 69 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 48 through 51 Processing sheet with id=AF3, first strand: chain 'Y' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA Y 31 " --> pdb=" O ILE Y 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE Y 16 " --> pdb=" O ALA Y 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL Y 33 " --> pdb=" O ASP Y 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP Y 14 " --> pdb=" O VAL Y 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE Y 6 " --> pdb=" O ILE Y 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE Y 71 " --> pdb=" O ILE Y 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG Y 8 " --> pdb=" O ILE Y 69 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 48 through 51 Processing sheet with id=AF5, first strand: chain 'Z' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA Z 31 " --> pdb=" O ILE Z 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE Z 16 " --> pdb=" O ALA Z 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL Z 33 " --> pdb=" O ASP Z 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP Z 14 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE Z 6 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE Z 71 " --> pdb=" O ILE Z 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG Z 8 " --> pdb=" O ILE Z 69 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'AA' and resid 48 through 51 Processing sheet with id=AF7, first strand: chain 'AA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAAA 31 " --> pdb=" O ILEAA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEAA 16 " --> pdb=" O ALAAA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALAA 33 " --> pdb=" O ASPAA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPAA 14 " --> pdb=" O VALAA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEAA 6 " --> pdb=" O ILEAA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEAA 71 " --> pdb=" O ILEAA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGAA 8 " --> pdb=" O ILEAA 69 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'BA' and resid 48 through 51 Processing sheet with id=AF9, first strand: chain 'BA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALABA 31 " --> pdb=" O ILEBA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEBA 16 " --> pdb=" O ALABA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALBA 33 " --> pdb=" O ASPBA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPBA 14 " --> pdb=" O VALBA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEBA 6 " --> pdb=" O ILEBA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEBA 71 " --> pdb=" O ILEBA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGBA 8 " --> pdb=" O ILEBA 69 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'CA' and resid 48 through 51 Processing sheet with id=AG2, first strand: chain 'CA' and resid 48 through 51 removed outlier: 4.346A pdb=" N ALACA 31 " --> pdb=" O ILECA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILECA 16 " --> pdb=" O ALACA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALCA 33 " --> pdb=" O ASPCA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPCA 14 " --> pdb=" O VALCA 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILECA 6 " --> pdb=" O ILECA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILECA 71 " --> pdb=" O ILECA 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARGCA 8 " --> pdb=" O ILECA 69 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'DA' and resid 48 through 51 Processing sheet with id=AG4, first strand: chain 'DA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALADA 31 " --> pdb=" O ILEDA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEDA 16 " --> pdb=" O ALADA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALDA 33 " --> pdb=" O ASPDA 14 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASPDA 14 " --> pdb=" O VALDA 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEDA 6 " --> pdb=" O ILEDA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEDA 71 " --> pdb=" O ILEDA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGDA 8 " --> pdb=" O ILEDA 69 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'EA' and resid 48 through 51 Processing sheet with id=AG6, first strand: chain 'EA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAEA 31 " --> pdb=" O ILEEA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEEA 16 " --> pdb=" O ALAEA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALEA 33 " --> pdb=" O ASPEA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPEA 14 " --> pdb=" O VALEA 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEEA 6 " --> pdb=" O ILEEA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEEA 71 " --> pdb=" O ILEEA 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARGEA 8 " --> pdb=" O ILEEA 69 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'FA' and resid 48 through 51 Processing sheet with id=AG8, first strand: chain 'FA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAFA 31 " --> pdb=" O ILEFA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEFA 16 " --> pdb=" O ALAFA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALFA 33 " --> pdb=" O ASPFA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPFA 14 " --> pdb=" O VALFA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEFA 6 " --> pdb=" O ILEFA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEFA 71 " --> pdb=" O ILEFA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGFA 8 " --> pdb=" O ILEFA 69 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'GA' and resid 48 through 51 Processing sheet with id=AH1, first strand: chain 'GA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAGA 31 " --> pdb=" O ILEGA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEGA 16 " --> pdb=" O ALAGA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALGA 33 " --> pdb=" O ASPGA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPGA 14 " --> pdb=" O VALGA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEGA 6 " --> pdb=" O ILEGA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEGA 71 " --> pdb=" O ILEGA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGGA 8 " --> pdb=" O ILEGA 69 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'HA' and resid 48 through 51 Processing sheet with id=AH3, first strand: chain 'HA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAHA 31 " --> pdb=" O ILEHA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEHA 16 " --> pdb=" O ALAHA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALHA 33 " --> pdb=" O ASPHA 14 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASPHA 14 " --> pdb=" O VALHA 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEHA 6 " --> pdb=" O ILEHA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEHA 71 " --> pdb=" O ILEHA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGHA 8 " --> pdb=" O ILEHA 69 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'IA' and resid 48 through 51 Processing sheet with id=AH5, first strand: chain 'IA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAIA 31 " --> pdb=" O ILEIA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEIA 16 " --> pdb=" O ALAIA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALIA 33 " --> pdb=" O ASPIA 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASPIA 14 " --> pdb=" O VALIA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEIA 6 " --> pdb=" O ILEIA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEIA 71 " --> pdb=" O ILEIA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGIA 8 " --> pdb=" O ILEIA 69 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'JA' and resid 48 through 51 Processing sheet with id=AH7, first strand: chain 'JA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAJA 31 " --> pdb=" O ILEJA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEJA 16 " --> pdb=" O ALAJA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALJA 33 " --> pdb=" O ASPJA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPJA 14 " --> pdb=" O VALJA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEJA 6 " --> pdb=" O ILEJA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEJA 71 " --> pdb=" O ILEJA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGJA 8 " --> pdb=" O ILEJA 69 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'KA' and resid 48 through 51 Processing sheet with id=AH9, first strand: chain 'KA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAKA 31 " --> pdb=" O ILEKA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEKA 16 " --> pdb=" O ALAKA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALKA 33 " --> pdb=" O ASPKA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPKA 14 " --> pdb=" O VALKA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEKA 6 " --> pdb=" O ILEKA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEKA 71 " --> pdb=" O ILEKA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGKA 8 " --> pdb=" O ILEKA 69 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'LA' and resid 48 through 51 Processing sheet with id=AI2, first strand: chain 'LA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALALA 31 " --> pdb=" O ILELA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILELA 16 " --> pdb=" O ALALA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALLA 33 " --> pdb=" O ASPLA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPLA 14 " --> pdb=" O VALLA 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILELA 6 " --> pdb=" O ILELA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILELA 71 " --> pdb=" O ILELA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGLA 8 " --> pdb=" O ILELA 69 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'MA' and resid 48 through 51 Processing sheet with id=AI4, first strand: chain 'MA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAMA 31 " --> pdb=" O ILEMA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEMA 16 " --> pdb=" O ALAMA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALMA 33 " --> pdb=" O ASPMA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPMA 14 " --> pdb=" O VALMA 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILEMA 6 " --> pdb=" O ILEMA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEMA 71 " --> pdb=" O ILEMA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGMA 8 " --> pdb=" O ILEMA 69 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'NA' and resid 48 through 51 Processing sheet with id=AI6, first strand: chain 'NA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALANA 31 " --> pdb=" O ILENA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILENA 16 " --> pdb=" O ALANA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALNA 33 " --> pdb=" O ASPNA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPNA 14 " --> pdb=" O VALNA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILENA 6 " --> pdb=" O ILENA 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILENA 71 " --> pdb=" O ILENA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGNA 8 " --> pdb=" O ILENA 69 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'OA' and resid 48 through 51 Processing sheet with id=AI8, first strand: chain 'OA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAOA 31 " --> pdb=" O ILEOA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEOA 16 " --> pdb=" O ALAOA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALOA 33 " --> pdb=" O ASPOA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPOA 14 " --> pdb=" O VALOA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEOA 6 " --> pdb=" O ILEOA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEOA 71 " --> pdb=" O ILEOA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGOA 8 " --> pdb=" O ILEOA 69 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'PA' and resid 48 through 51 Processing sheet with id=AJ1, first strand: chain 'PA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAPA 31 " --> pdb=" O ILEPA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEPA 16 " --> pdb=" O ALAPA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALPA 33 " --> pdb=" O ASPPA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPPA 14 " --> pdb=" O VALPA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEPA 6 " --> pdb=" O ILEPA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEPA 71 " --> pdb=" O ILEPA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGPA 8 " --> pdb=" O ILEPA 69 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'QA' and resid 48 through 51 Processing sheet with id=AJ3, first strand: chain 'QA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAQA 31 " --> pdb=" O ILEQA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEQA 16 " --> pdb=" O ALAQA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALQA 33 " --> pdb=" O ASPQA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPQA 14 " --> pdb=" O VALQA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEQA 6 " --> pdb=" O ILEQA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEQA 71 " --> pdb=" O ILEQA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGQA 8 " --> pdb=" O ILEQA 69 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'RA' and resid 48 through 51 Processing sheet with id=AJ5, first strand: chain 'RA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALARA 31 " --> pdb=" O ILERA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILERA 16 " --> pdb=" O ALARA 31 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VALRA 33 " --> pdb=" O ASPRA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPRA 14 " --> pdb=" O VALRA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILERA 6 " --> pdb=" O ILERA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILERA 71 " --> pdb=" O ILERA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGRA 8 " --> pdb=" O ILERA 69 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'SA' and resid 48 through 51 Processing sheet with id=AJ7, first strand: chain 'SA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALASA 31 " --> pdb=" O ILESA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILESA 16 " --> pdb=" O ALASA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALSA 33 " --> pdb=" O ASPSA 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASPSA 14 " --> pdb=" O VALSA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILESA 6 " --> pdb=" O ILESA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILESA 71 " --> pdb=" O ILESA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGSA 8 " --> pdb=" O ILESA 69 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'TA' and resid 48 through 51 Processing sheet with id=AJ9, first strand: chain 'TA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALATA 31 " --> pdb=" O ILETA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILETA 16 " --> pdb=" O ALATA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALTA 33 " --> pdb=" O ASPTA 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASPTA 14 " --> pdb=" O VALTA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILETA 6 " --> pdb=" O ILETA 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILETA 71 " --> pdb=" O ILETA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGTA 8 " --> pdb=" O ILETA 69 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'UA' and resid 48 through 51 Processing sheet with id=AK2, first strand: chain 'UA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAUA 31 " --> pdb=" O ILEUA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEUA 16 " --> pdb=" O ALAUA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALUA 33 " --> pdb=" O ASPUA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPUA 14 " --> pdb=" O VALUA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEUA 6 " --> pdb=" O ILEUA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEUA 71 " --> pdb=" O ILEUA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGUA 8 " --> pdb=" O ILEUA 69 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'VA' and resid 48 through 51 Processing sheet with id=AK4, first strand: chain 'VA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAVA 31 " --> pdb=" O ILEVA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEVA 16 " --> pdb=" O ALAVA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALVA 33 " --> pdb=" O ASPVA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPVA 14 " --> pdb=" O VALVA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEVA 6 " --> pdb=" O ILEVA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEVA 71 " --> pdb=" O ILEVA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGVA 8 " --> pdb=" O ILEVA 69 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'WA' and resid 48 through 51 Processing sheet with id=AK6, first strand: chain 'WA' and resid 48 through 51 removed outlier: 4.346A pdb=" N ALAWA 31 " --> pdb=" O ILEWA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEWA 16 " --> pdb=" O ALAWA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALWA 33 " --> pdb=" O ASPWA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPWA 14 " --> pdb=" O VALWA 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEWA 6 " --> pdb=" O ILEWA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEWA 71 " --> pdb=" O ILEWA 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARGWA 8 " --> pdb=" O ILEWA 69 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'XA' and resid 48 through 51 Processing sheet with id=AK8, first strand: chain 'XA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAXA 31 " --> pdb=" O ILEXA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEXA 16 " --> pdb=" O ALAXA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALXA 33 " --> pdb=" O ASPXA 14 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASPXA 14 " --> pdb=" O VALXA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEXA 6 " --> pdb=" O ILEXA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEXA 71 " --> pdb=" O ILEXA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGXA 8 " --> pdb=" O ILEXA 69 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'YA' and resid 48 through 51 Processing sheet with id=AL1, first strand: chain 'YA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAYA 31 " --> pdb=" O ILEYA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEYA 16 " --> pdb=" O ALAYA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALYA 33 " --> pdb=" O ASPYA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPYA 14 " --> pdb=" O VALYA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEYA 6 " --> pdb=" O ILEYA 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILEYA 71 " --> pdb=" O ILEYA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGYA 8 " --> pdb=" O ILEYA 69 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'ZA' and resid 48 through 51 Processing sheet with id=AL3, first strand: chain 'ZA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAZA 31 " --> pdb=" O ILEZA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEZA 16 " --> pdb=" O ALAZA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALZA 33 " --> pdb=" O ASPZA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPZA 14 " --> pdb=" O VALZA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEZA 6 " --> pdb=" O ILEZA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEZA 71 " --> pdb=" O ILEZA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGZA 8 " --> pdb=" O ILEZA 69 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'AB' and resid 48 through 51 Processing sheet with id=AL5, first strand: chain 'AB' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAAB 31 " --> pdb=" O ILEAB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEAB 16 " --> pdb=" O ALAAB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALAB 33 " --> pdb=" O ASPAB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPAB 14 " --> pdb=" O VALAB 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEAB 6 " --> pdb=" O ILEAB 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILEAB 71 " --> pdb=" O ILEAB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGAB 8 " --> pdb=" O ILEAB 69 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'BB' and resid 48 through 51 Processing sheet with id=AL7, first strand: chain 'BB' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALABB 31 " --> pdb=" O ILEBB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEBB 16 " --> pdb=" O ALABB 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALBB 33 " --> pdb=" O ASPBB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPBB 14 " --> pdb=" O VALBB 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILEBB 6 " --> pdb=" O ILEBB 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEBB 71 " --> pdb=" O ILEBB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGBB 8 " --> pdb=" O ILEBB 69 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'CB' and resid 48 through 51 Processing sheet with id=AL9, first strand: chain 'CB' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALACB 31 " --> pdb=" O ILECB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILECB 16 " --> pdb=" O ALACB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALCB 33 " --> pdb=" O ASPCB 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASPCB 14 " --> pdb=" O VALCB 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILECB 6 " --> pdb=" O ILECB 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILECB 71 " --> pdb=" O ILECB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGCB 8 " --> pdb=" O ILECB 69 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'DB' and resid 48 through 51 Processing sheet with id=AM2, first strand: chain 'DB' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALADB 31 " --> pdb=" O ILEDB 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEDB 16 " --> pdb=" O ALADB 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALDB 33 " --> pdb=" O ASPDB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPDB 14 " --> pdb=" O VALDB 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEDB 6 " --> pdb=" O ILEDB 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEDB 71 " --> pdb=" O ILEDB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGDB 8 " --> pdb=" O ILEDB 69 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'EB' and resid 48 through 51 Processing sheet with id=AM4, first strand: chain 'EB' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAEB 31 " --> pdb=" O ILEEB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEEB 16 " --> pdb=" O ALAEB 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALEB 33 " --> pdb=" O ASPEB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPEB 14 " --> pdb=" O VALEB 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEEB 6 " --> pdb=" O ILEEB 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEEB 71 " --> pdb=" O ILEEB 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGEB 8 " --> pdb=" O ILEEB 69 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'FB' and resid 48 through 51 Processing sheet with id=AM6, first strand: chain 'FB' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAFB 31 " --> pdb=" O ILEFB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEFB 16 " --> pdb=" O ALAFB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALFB 33 " --> pdb=" O ASPFB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPFB 14 " --> pdb=" O VALFB 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEFB 6 " --> pdb=" O ILEFB 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEFB 71 " --> pdb=" O ILEFB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGFB 8 " --> pdb=" O ILEFB 69 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'GB' and resid 48 through 51 Processing sheet with id=AM8, first strand: chain 'GB' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAGB 31 " --> pdb=" O ILEGB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEGB 16 " --> pdb=" O ALAGB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALGB 33 " --> pdb=" O ASPGB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPGB 14 " --> pdb=" O VALGB 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILEGB 6 " --> pdb=" O ILEGB 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEGB 71 " --> pdb=" O ILEGB 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARGGB 8 " --> pdb=" O ILEGB 69 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'HB' and resid 48 through 51 Processing sheet with id=AN1, first strand: chain 'HB' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAHB 31 " --> pdb=" O ILEHB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEHB 16 " --> pdb=" O ALAHB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALHB 33 " --> pdb=" O ASPHB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPHB 14 " --> pdb=" O VALHB 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEHB 6 " --> pdb=" O ILEHB 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILEHB 71 " --> pdb=" O ILEHB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGHB 8 " --> pdb=" O ILEHB 69 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'IB' and resid 48 through 51 Processing sheet with id=AN3, first strand: chain 'IB' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAIB 31 " --> pdb=" O ILEIB 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEIB 16 " --> pdb=" O ALAIB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALIB 33 " --> pdb=" O ASPIB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPIB 14 " --> pdb=" O VALIB 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEIB 6 " --> pdb=" O ILEIB 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEIB 71 " --> pdb=" O ILEIB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGIB 8 " --> pdb=" O ILEIB 69 " (cutoff:3.500A) 4320 hydrogen bonds defined for protein. 12420 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: 30.94 Time building geometry restraints manager: 13.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 21119 1.34 - 1.46: 9059 1.46 - 1.58: 32462 1.58 - 1.69: 0 1.69 - 1.81: 360 Bond restraints: 63000 Sorted by residual: bond pdb=" CB ARG T 136 " pdb=" CG ARG T 136 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.21e-01 bond pdb=" CB ARGFB 136 " pdb=" CG ARGFB 136 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.12e-01 bond pdb=" CB ARG Y 136 " pdb=" CG ARG Y 136 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.12e-01 bond pdb=" CB ARGHA 136 " pdb=" CG ARGHA 136 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.08e-01 bond pdb=" CB ARGCA 136 " pdb=" CG ARGCA 136 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.06e-01 ... (remaining 62995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 80677 0.91 - 1.81: 2890 1.81 - 2.72: 564 2.72 - 3.62: 289 3.62 - 4.53: 120 Bond angle restraints: 84540 Sorted by residual: angle pdb=" CB ARGMA 136 " pdb=" CG ARGMA 136 " pdb=" CD ARGMA 136 " ideal model delta sigma weight residual 111.30 115.83 -4.53 2.30e+00 1.89e-01 3.88e+00 angle pdb=" CB ARGFB 136 " pdb=" CG ARGFB 136 " pdb=" CD ARGFB 136 " ideal model delta sigma weight residual 111.30 115.83 -4.53 2.30e+00 1.89e-01 3.87e+00 angle pdb=" CB ARGIA 136 " pdb=" CG ARGIA 136 " pdb=" CD ARGIA 136 " ideal model delta sigma weight residual 111.30 115.83 -4.53 2.30e+00 1.89e-01 3.87e+00 angle pdb=" CB ARGHB 136 " pdb=" CG ARGHB 136 " pdb=" CD ARGHB 136 " ideal model delta sigma weight residual 111.30 115.83 -4.53 2.30e+00 1.89e-01 3.87e+00 angle pdb=" CB ARG H 136 " pdb=" CG ARG H 136 " pdb=" CD ARG H 136 " ideal model delta sigma weight residual 111.30 115.82 -4.52 2.30e+00 1.89e-01 3.86e+00 ... (remaining 84535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 36120 17.34 - 34.69: 3300 34.69 - 52.03: 600 52.03 - 69.37: 300 69.37 - 86.72: 240 Dihedral angle restraints: 40560 sinusoidal: 18060 harmonic: 22500 Sorted by residual: dihedral pdb=" CA ASP L 65 " pdb=" CB ASP L 65 " pdb=" CG ASP L 65 " pdb=" OD1 ASP L 65 " ideal model delta sinusoidal sigma weight residual -30.00 -85.48 55.48 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA ASPAB 65 " pdb=" CB ASPAB 65 " pdb=" CG ASPAB 65 " pdb=" OD1 ASPAB 65 " ideal model delta sinusoidal sigma weight residual -30.00 -85.47 55.47 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA ASPBB 65 " pdb=" CB ASPBB 65 " pdb=" CG ASPBB 65 " pdb=" OD1 ASPBB 65 " ideal model delta sinusoidal sigma weight residual -30.00 -85.47 55.47 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 40557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 6116 0.026 - 0.051: 2114 0.051 - 0.077: 1010 0.077 - 0.102: 245 0.102 - 0.128: 595 Chirality restraints: 10080 Sorted by residual: chirality pdb=" CA ILEIA 28 " pdb=" N ILEIA 28 " pdb=" C ILEIA 28 " pdb=" CB ILEIA 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILECA 28 " pdb=" N ILECA 28 " pdb=" C ILECA 28 " pdb=" CB ILECA 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE X 28 " pdb=" N ILE X 28 " pdb=" C ILE X 28 " pdb=" CB ILE X 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 10077 not shown) Planarity restraints: 10740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGJA 109 " 0.059 9.50e-02 1.11e+02 2.69e-02 6.18e-01 pdb=" NE ARGJA 109 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARGJA 109 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARGJA 109 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGJA 109 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 109 " 0.060 9.50e-02 1.11e+02 2.70e-02 6.16e-01 pdb=" NE ARG Y 109 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG Y 109 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 109 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 109 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGDB 109 " 0.059 9.50e-02 1.11e+02 2.69e-02 6.14e-01 pdb=" NE ARGDB 109 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARGDB 109 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARGDB 109 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGDB 109 " -0.000 2.00e-02 2.50e+03 ... (remaining 10737 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 11521 2.79 - 3.32: 60913 3.32 - 3.85: 96525 3.85 - 4.37: 104987 4.37 - 4.90: 187453 Nonbonded interactions: 461399 Sorted by model distance: nonbonded pdb=" OG SER D 122 " pdb=" OE2 GLURA 90 " model vdw 2.267 3.040 nonbonded pdb=" OG SER I 122 " pdb=" OE2 GLUGB 90 " model vdw 2.267 3.040 nonbonded pdb=" OE2 GLU H 90 " pdb=" OG SERIA 122 " model vdw 2.267 3.040 nonbonded pdb=" OG SERKA 122 " pdb=" OE2 GLUIB 90 " model vdw 2.267 3.040 nonbonded pdb=" OG SER F 122 " pdb=" OE2 GLU Z 90 " model vdw 2.267 3.040 ... (remaining 461394 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' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'PA' selection = chain 'Q' selection = chain 'QA' selection = chain 'R' selection = chain 'RA' selection = chain 'S' selection = chain 'SA' selection = chain 'T' selection = chain 'TA' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' } 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=1.00 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: 0.010 Normalize map: mean=0, sd=1: 0.400 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: 0.040 Extract box with map and model: 1.780 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 97.240 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.920 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: 0.020 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5094 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 : 0.002 0.024 63000 Z= 0.144 Angle : 0.472 4.531 84540 Z= 0.238 Chirality : 0.042 0.128 10080 Planarity : 0.003 0.027 10740 Dihedral : 15.652 86.717 25680 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.10), residues: 7380 helix: 3.18 (0.08), residues: 3540 sheet: 0.27 (0.11), residues: 2160 loop : -1.93 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRPJA 52 HIS 0.002 0.001 HISFB 85 PHE 0.003 0.001 PHECB 32 TYR 0.004 0.001 TYRVA 82 ARG 0.007 0.001 ARGQA 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1504 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1504 time to evaluate : 5.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.4870 (tt0) cc_final: 0.4654 (tm-30) REVERT: A 99 ARG cc_start: 0.4598 (tmm-80) cc_final: 0.4356 (tmm-80) REVERT: A 110 MET cc_start: 0.3916 (tmm) cc_final: 0.3461 (ttt) REVERT: B 110 MET cc_start: 0.4087 (tmm) cc_final: 0.3827 (ttt) REVERT: C 23 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8663 (tm-30) REVERT: C 110 MET cc_start: 0.5331 (tmm) cc_final: 0.5116 (ttp) REVERT: D 36 PRO cc_start: 0.8784 (Cg_endo) cc_final: 0.8466 (Cg_exo) REVERT: D 57 ASP cc_start: 0.6310 (m-30) cc_final: 0.6046 (m-30) REVERT: D 95 GLU cc_start: 0.5297 (tt0) cc_final: 0.4942 (tm-30) REVERT: D 110 MET cc_start: 0.4508 (tmm) cc_final: 0.4276 (ttt) REVERT: E 23 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8145 (tm-30) REVERT: E 57 ASP cc_start: 0.7018 (m-30) cc_final: 0.6807 (m-30) REVERT: E 65 ASP cc_start: 0.7197 (p0) cc_final: 0.6731 (p0) REVERT: E 95 GLU cc_start: 0.5668 (tt0) cc_final: 0.5322 (tm-30) REVERT: E 110 MET cc_start: 0.4106 (tmm) cc_final: 0.3895 (tmm) REVERT: F 95 GLU cc_start: 0.4836 (tt0) cc_final: 0.4630 (tm-30) REVERT: F 99 ARG cc_start: 0.4658 (tmm-80) cc_final: 0.4418 (tmm-80) REVERT: F 110 MET cc_start: 0.4085 (tmm) cc_final: 0.3625 (ttt) REVERT: G 110 MET cc_start: 0.4199 (tmm) cc_final: 0.3941 (ttt) REVERT: H 25 LEU cc_start: 0.7986 (mt) cc_final: 0.7783 (mt) REVERT: H 110 MET cc_start: 0.5287 (tmm) cc_final: 0.5007 (ttp) REVERT: I 36 PRO cc_start: 0.8800 (Cg_endo) cc_final: 0.8492 (Cg_exo) REVERT: I 95 GLU cc_start: 0.5258 (tt0) cc_final: 0.4913 (tm-30) REVERT: I 110 MET cc_start: 0.4557 (tmm) cc_final: 0.4332 (ttt) REVERT: J 23 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8218 (tm-30) REVERT: J 65 ASP cc_start: 0.7175 (p0) cc_final: 0.6705 (p0) REVERT: J 95 GLU cc_start: 0.5686 (tt0) cc_final: 0.5345 (tm-30) REVERT: J 110 MET cc_start: 0.4159 (tmm) cc_final: 0.3952 (tmm) REVERT: K 95 GLU cc_start: 0.4787 (tt0) cc_final: 0.4581 (tm-30) REVERT: K 99 ARG cc_start: 0.4654 (tmm-80) cc_final: 0.4412 (tmm-80) REVERT: K 110 MET cc_start: 0.4190 (tmm) cc_final: 0.3721 (ttt) REVERT: L 110 MET cc_start: 0.4117 (tmm) cc_final: 0.3873 (ttt) REVERT: M 25 LEU cc_start: 0.7948 (mt) cc_final: 0.7740 (mt) REVERT: N 36 PRO cc_start: 0.8829 (Cg_endo) cc_final: 0.8527 (Cg_exo) REVERT: N 57 ASP cc_start: 0.6288 (m-30) cc_final: 0.6028 (m-30) REVERT: N 95 GLU cc_start: 0.5238 (tt0) cc_final: 0.4896 (tm-30) REVERT: N 110 MET cc_start: 0.4562 (tmm) cc_final: 0.4333 (ttt) REVERT: O 23 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8191 (tm-30) REVERT: O 57 ASP cc_start: 0.7000 (m-30) cc_final: 0.6790 (m-30) REVERT: O 65 ASP cc_start: 0.7194 (p0) cc_final: 0.6719 (p0) REVERT: O 95 GLU cc_start: 0.5670 (tt0) cc_final: 0.5331 (tm-30) REVERT: O 110 MET cc_start: 0.4106 (tmm) cc_final: 0.3891 (tmm) REVERT: P 95 GLU cc_start: 0.4769 (tt0) cc_final: 0.4560 (tm-30) REVERT: P 99 ARG cc_start: 0.4538 (tmm-80) cc_final: 0.4306 (tmm-80) REVERT: P 110 MET cc_start: 0.4001 (tmm) cc_final: 0.3552 (ttt) REVERT: Q 110 MET cc_start: 0.4170 (tmm) cc_final: 0.3911 (ttt) REVERT: R 25 LEU cc_start: 0.7978 (mt) cc_final: 0.7771 (mt) REVERT: R 110 MET cc_start: 0.5327 (tmm) cc_final: 0.5115 (ttp) REVERT: S 36 PRO cc_start: 0.8793 (Cg_endo) cc_final: 0.8483 (Cg_exo) REVERT: S 57 ASP cc_start: 0.6306 (m-30) cc_final: 0.6041 (m-30) REVERT: S 95 GLU cc_start: 0.5235 (tt0) cc_final: 0.4892 (tm-30) REVERT: S 110 MET cc_start: 0.4629 (tmm) cc_final: 0.4210 (ttt) REVERT: T 23 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8183 (tm-30) REVERT: T 65 ASP cc_start: 0.7175 (p0) cc_final: 0.6712 (p0) REVERT: T 95 GLU cc_start: 0.5723 (tt0) cc_final: 0.5360 (tm-30) REVERT: T 110 MET cc_start: 0.4175 (tmm) cc_final: 0.3970 (tmm) REVERT: V 95 GLU cc_start: 0.4771 (tt0) cc_final: 0.4561 (tm-30) REVERT: V 99 ARG cc_start: 0.4526 (tmm-80) cc_final: 0.4294 (tmm-80) REVERT: V 110 MET cc_start: 0.4006 (tmm) cc_final: 0.3558 (ttt) REVERT: W 110 MET cc_start: 0.4172 (tmm) cc_final: 0.3914 (ttt) REVERT: X 25 LEU cc_start: 0.7971 (mt) cc_final: 0.7766 (mt) REVERT: X 110 MET cc_start: 0.5339 (tmm) cc_final: 0.5124 (ttp) REVERT: Y 36 PRO cc_start: 0.8778 (Cg_endo) cc_final: 0.8469 (Cg_exo) REVERT: Y 57 ASP cc_start: 0.6298 (m-30) cc_final: 0.6032 (m-30) REVERT: Y 95 GLU cc_start: 0.5230 (tt0) cc_final: 0.4889 (tm-30) REVERT: Y 110 MET cc_start: 0.4637 (tmm) cc_final: 0.4210 (ttt) REVERT: Z 23 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8155 (tm-30) REVERT: Z 65 ASP cc_start: 0.7172 (p0) cc_final: 0.6709 (p0) REVERT: Z 95 GLU cc_start: 0.5707 (tt0) cc_final: 0.5364 (tm-30) REVERT: Z 110 MET cc_start: 0.4174 (tmm) cc_final: 0.3968 (tmm) REVERT: AA 95 GLU cc_start: 0.4804 (tt0) cc_final: 0.4596 (tm-30) REVERT: AA 99 ARG cc_start: 0.4661 (tmm-80) cc_final: 0.4418 (tmm-80) REVERT: AA 110 MET cc_start: 0.4188 (tmm) cc_final: 0.3719 (ttt) REVERT: BA 110 MET cc_start: 0.3999 (tmm) cc_final: 0.3740 (ttt) REVERT: CA 25 LEU cc_start: 0.7950 (mt) cc_final: 0.7742 (mt) REVERT: DA 36 PRO cc_start: 0.8818 (Cg_endo) cc_final: 0.8513 (Cg_exo) REVERT: DA 57 ASP cc_start: 0.6284 (m-30) cc_final: 0.6024 (m-30) REVERT: DA 95 GLU cc_start: 0.5224 (tt0) cc_final: 0.4880 (tm-30) REVERT: DA 110 MET cc_start: 0.4555 (tmm) cc_final: 0.4327 (ttt) REVERT: EA 23 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8189 (tm-30) REVERT: EA 65 ASP cc_start: 0.7189 (p0) cc_final: 0.6716 (p0) REVERT: EA 95 GLU cc_start: 0.5684 (tt0) cc_final: 0.5347 (tm-30) REVERT: EA 110 MET cc_start: 0.4114 (tmm) cc_final: 0.3899 (tmm) REVERT: FA 95 GLU cc_start: 0.4834 (tt0) cc_final: 0.4628 (tm-30) REVERT: FA 99 ARG cc_start: 0.4653 (tmm-80) cc_final: 0.4411 (tmm-80) REVERT: FA 110 MET cc_start: 0.4079 (tmm) cc_final: 0.3620 (ttt) REVERT: GA 110 MET cc_start: 0.4191 (tmm) cc_final: 0.3940 (ttt) REVERT: HA 23 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8641 (tm-30) REVERT: HA 110 MET cc_start: 0.5274 (tmm) cc_final: 0.4999 (ttp) REVERT: IA 36 PRO cc_start: 0.8798 (Cg_endo) cc_final: 0.8488 (Cg_exo) REVERT: IA 95 GLU cc_start: 0.5244 (tt0) cc_final: 0.4902 (tm-30) REVERT: IA 110 MET cc_start: 0.4561 (tmm) cc_final: 0.4333 (ttt) REVERT: JA 23 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8238 (tm-30) REVERT: JA 65 ASP cc_start: 0.7175 (p0) cc_final: 0.6705 (p0) REVERT: JA 95 GLU cc_start: 0.5694 (tt0) cc_final: 0.5356 (tm-30) REVERT: JA 110 MET cc_start: 0.4152 (tmm) cc_final: 0.3947 (tmm) REVERT: KA 95 GLU cc_start: 0.4875 (tt0) cc_final: 0.4656 (tm-30) REVERT: KA 99 ARG cc_start: 0.4593 (tmm-80) cc_final: 0.4353 (tmm-80) REVERT: KA 110 MET cc_start: 0.3915 (tmm) cc_final: 0.3460 (ttt) REVERT: LA 110 MET cc_start: 0.4201 (tmm) cc_final: 0.3960 (ttt) REVERT: MA 23 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8666 (tm-30) REVERT: MA 110 MET cc_start: 0.5326 (tmm) cc_final: 0.5116 (ttp) REVERT: NA 36 PRO cc_start: 0.8796 (Cg_endo) cc_final: 0.8479 (Cg_exo) REVERT: NA 57 ASP cc_start: 0.6318 (m-30) cc_final: 0.6053 (m-30) REVERT: NA 95 GLU cc_start: 0.5322 (tt0) cc_final: 0.4963 (tm-30) REVERT: NA 110 MET cc_start: 0.4503 (tmm) cc_final: 0.4256 (ttt) REVERT: OA 23 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8131 (tm-30) REVERT: OA 57 ASP cc_start: 0.7024 (m-30) cc_final: 0.6812 (m-30) REVERT: OA 65 ASP cc_start: 0.7188 (p0) cc_final: 0.6721 (p0) REVERT: OA 95 GLU cc_start: 0.5649 (tt0) cc_final: 0.5306 (tm-30) REVERT: OA 110 MET cc_start: 0.4099 (tmm) cc_final: 0.3887 (tmm) REVERT: PA 95 GLU cc_start: 0.4801 (tt0) cc_final: 0.4592 (tm-30) REVERT: PA 99 ARG cc_start: 0.4656 (tmm-80) cc_final: 0.4414 (tmm-80) REVERT: PA 110 MET cc_start: 0.4186 (tmm) cc_final: 0.3717 (ttt) REVERT: QA 110 MET cc_start: 0.3976 (tmm) cc_final: 0.3720 (ttt) REVERT: RA 25 LEU cc_start: 0.7949 (mt) cc_final: 0.7742 (mt) REVERT: SA 36 PRO cc_start: 0.8801 (Cg_endo) cc_final: 0.8493 (Cg_exo) REVERT: SA 57 ASP cc_start: 0.6291 (m-30) cc_final: 0.6031 (m-30) REVERT: SA 95 GLU cc_start: 0.5240 (tt0) cc_final: 0.4901 (tm-30) REVERT: SA 110 MET cc_start: 0.4566 (tmm) cc_final: 0.4334 (ttt) REVERT: TA 23 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8182 (tm-30) REVERT: TA 57 ASP cc_start: 0.7003 (m-30) cc_final: 0.6795 (m-30) REVERT: TA 65 ASP cc_start: 0.7188 (p0) cc_final: 0.6719 (p0) REVERT: TA 95 GLU cc_start: 0.5673 (tt0) cc_final: 0.5316 (tm-30) REVERT: TA 110 MET cc_start: 0.4106 (tmm) cc_final: 0.3892 (tmm) REVERT: UA 99 ARG cc_start: 0.4539 (tmm-80) cc_final: 0.4307 (tmm-80) REVERT: UA 110 MET cc_start: 0.4005 (tmm) cc_final: 0.3555 (ttt) REVERT: VA 110 MET cc_start: 0.4115 (tmm) cc_final: 0.3859 (ttt) REVERT: WA 25 LEU cc_start: 0.7978 (mt) cc_final: 0.7774 (mt) REVERT: WA 110 MET cc_start: 0.5333 (tmm) cc_final: 0.5122 (ttp) REVERT: XA 36 PRO cc_start: 0.8792 (Cg_endo) cc_final: 0.8480 (Cg_exo) REVERT: XA 57 ASP cc_start: 0.6300 (m-30) cc_final: 0.6035 (m-30) REVERT: XA 95 GLU cc_start: 0.5243 (tt0) cc_final: 0.4901 (tm-30) REVERT: XA 110 MET cc_start: 0.4626 (tmm) cc_final: 0.4204 (ttt) REVERT: YA 23 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8178 (tm-30) REVERT: YA 65 ASP cc_start: 0.7174 (p0) cc_final: 0.6709 (p0) REVERT: YA 95 GLU cc_start: 0.5712 (tt0) cc_final: 0.5366 (tm-30) REVERT: YA 110 MET cc_start: 0.4185 (tmm) cc_final: 0.3982 (tmm) REVERT: ZA 95 GLU cc_start: 0.4872 (tt0) cc_final: 0.4654 (tm-30) REVERT: ZA 99 ARG cc_start: 0.4598 (tmm-80) cc_final: 0.4357 (tmm-80) REVERT: ZA 110 MET cc_start: 0.3915 (tmm) cc_final: 0.3459 (ttt) REVERT: AB 110 MET cc_start: 0.4203 (tmm) cc_final: 0.3960 (ttt) REVERT: BB 23 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8675 (tm-30) REVERT: BB 110 MET cc_start: 0.5326 (tmm) cc_final: 0.5113 (ttp) REVERT: CB 36 PRO cc_start: 0.8791 (Cg_endo) cc_final: 0.8472 (Cg_exo) REVERT: CB 57 ASP cc_start: 0.6302 (m-30) cc_final: 0.6038 (m-30) REVERT: CB 95 GLU cc_start: 0.5302 (tt0) cc_final: 0.4945 (tm-30) REVERT: CB 110 MET cc_start: 0.4507 (tmm) cc_final: 0.4279 (ttt) REVERT: DB 23 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8158 (tm-30) REVERT: DB 57 ASP cc_start: 0.7027 (m-30) cc_final: 0.6814 (m-30) REVERT: DB 65 ASP cc_start: 0.7196 (p0) cc_final: 0.6732 (p0) REVERT: DB 95 GLU cc_start: 0.5655 (tt0) cc_final: 0.5309 (tm-30) REVERT: DB 110 MET cc_start: 0.4112 (tmm) cc_final: 0.3904 (tmm) REVERT: EB 95 GLU cc_start: 0.4822 (tt0) cc_final: 0.4614 (tm-30) REVERT: EB 99 ARG cc_start: 0.4654 (tmm-80) cc_final: 0.4413 (tmm-80) REVERT: EB 110 MET cc_start: 0.4077 (tmm) cc_final: 0.3618 (ttt) REVERT: FB 110 MET cc_start: 0.4196 (tmm) cc_final: 0.3940 (ttt) REVERT: GB 23 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8631 (tm-30) REVERT: GB 110 MET cc_start: 0.5275 (tmm) cc_final: 0.5003 (ttp) REVERT: HB 57 ASP cc_start: 0.6361 (m-30) cc_final: 0.6093 (m-30) REVERT: HB 95 GLU cc_start: 0.5238 (tt0) cc_final: 0.4894 (tm-30) REVERT: HB 110 MET cc_start: 0.4563 (tmm) cc_final: 0.4335 (ttt) REVERT: IB 23 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8233 (tm-30) REVERT: IB 65 ASP cc_start: 0.7181 (p0) cc_final: 0.6711 (p0) REVERT: IB 95 GLU cc_start: 0.5713 (tt0) cc_final: 0.5356 (tm-30) REVERT: IB 110 MET cc_start: 0.4151 (tmm) cc_final: 0.3945 (tmm) outliers start: 0 outliers final: 0 residues processed: 1504 average time/residue: 0.6213 time to fit residues: 1534.6028 Evaluate side-chains 1042 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1042 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 0.8980 chunk 545 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 chunk 291 optimal weight: 0.0980 chunk 564 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 343 optimal weight: 0.8980 chunk 420 optimal weight: 8.9990 chunk 653 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5179 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 63000 Z= 0.192 Angle : 0.481 3.842 84540 Z= 0.253 Chirality : 0.044 0.136 10080 Planarity : 0.003 0.021 10740 Dihedral : 3.190 11.299 8100 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.73 % Allowed : 6.91 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.10), residues: 7380 helix: 3.61 (0.08), residues: 3540 sheet: 0.32 (0.11), residues: 2160 loop : -1.66 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPDB 52 HIS 0.001 0.000 HISLA 85 PHE 0.004 0.001 PHEGB 32 TYR 0.011 0.002 TYR K 82 ARG 0.005 0.000 ARGAA 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1295 time to evaluate : 5.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.4635 (tmm-80) cc_final: 0.4370 (tmm-80) REVERT: A 127 GLN cc_start: 0.7377 (mm-40) cc_final: 0.7127 (mp10) REVERT: C 127 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6971 (mm-40) REVERT: C 134 LEU cc_start: 0.7658 (tt) cc_final: 0.7435 (pp) REVERT: D 36 PRO cc_start: 0.8817 (Cg_endo) cc_final: 0.8471 (Cg_exo) REVERT: D 46 GLN cc_start: 0.6472 (tp-100) cc_final: 0.6137 (tp-100) REVERT: D 95 GLU cc_start: 0.5184 (tt0) cc_final: 0.4802 (tm-30) REVERT: E 23 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8226 (tm-30) REVERT: E 58 ASP cc_start: 0.7326 (m-30) cc_final: 0.6953 (t0) REVERT: E 65 ASP cc_start: 0.7171 (p0) cc_final: 0.6659 (p0) REVERT: E 95 GLU cc_start: 0.5584 (tt0) cc_final: 0.5362 (tm-30) REVERT: E 127 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7325 (mm-40) REVERT: F 99 ARG cc_start: 0.4697 (tmm-80) cc_final: 0.4437 (tmm-80) REVERT: F 127 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7112 (mp10) REVERT: H 127 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6978 (mm-40) REVERT: H 134 LEU cc_start: 0.7624 (tt) cc_final: 0.7400 (pp) REVERT: I 36 PRO cc_start: 0.8831 (Cg_endo) cc_final: 0.8542 (Cg_exo) REVERT: I 95 GLU cc_start: 0.5146 (tt0) cc_final: 0.4775 (tm-30) REVERT: J 23 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8287 (tm-30) REVERT: J 58 ASP cc_start: 0.7335 (m-30) cc_final: 0.6954 (t0) REVERT: J 65 ASP cc_start: 0.7603 (p0) cc_final: 0.7115 (p0) REVERT: J 95 GLU cc_start: 0.5544 (tt0) cc_final: 0.5318 (tm-30) REVERT: J 127 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7417 (mm-40) REVERT: K 99 ARG cc_start: 0.4693 (tmm-80) cc_final: 0.4430 (tmm-80) REVERT: M 127 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6936 (mm-40) REVERT: M 134 LEU cc_start: 0.7543 (tt) cc_final: 0.7318 (pp) REVERT: N 36 PRO cc_start: 0.8855 (Cg_endo) cc_final: 0.8531 (Cg_exo) REVERT: N 46 GLN cc_start: 0.6438 (tp-100) cc_final: 0.6162 (tp-100) REVERT: N 95 GLU cc_start: 0.5124 (tt0) cc_final: 0.4755 (tm-30) REVERT: O 23 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8267 (tm-30) REVERT: O 58 ASP cc_start: 0.7278 (m-30) cc_final: 0.6906 (t0) REVERT: O 65 ASP cc_start: 0.7637 (p0) cc_final: 0.7144 (p0) REVERT: O 95 GLU cc_start: 0.5594 (tt0) cc_final: 0.5380 (tm-30) REVERT: O 127 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7298 (mm-40) REVERT: P 99 ARG cc_start: 0.4576 (tmm-80) cc_final: 0.4323 (tmm-80) REVERT: R 127 GLN cc_start: 0.7128 (mm-40) cc_final: 0.6916 (mm-40) REVERT: R 134 LEU cc_start: 0.7588 (tt) cc_final: 0.7355 (pp) REVERT: S 36 PRO cc_start: 0.8822 (Cg_endo) cc_final: 0.8536 (Cg_exo) REVERT: S 95 GLU cc_start: 0.5113 (tt0) cc_final: 0.4752 (tm-30) REVERT: S 106 ASP cc_start: 0.4834 (t0) cc_final: 0.4333 (t0) REVERT: S 109 ARG cc_start: 0.6178 (tmm-80) cc_final: 0.5971 (ttp80) REVERT: S 110 MET cc_start: 0.4552 (tmm) cc_final: 0.4309 (ttt) REVERT: T 23 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8261 (tm-30) REVERT: T 58 ASP cc_start: 0.7334 (m-30) cc_final: 0.6960 (t0) REVERT: T 65 ASP cc_start: 0.7150 (p0) cc_final: 0.6642 (p0) REVERT: T 127 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7400 (mm-40) REVERT: V 99 ARG cc_start: 0.4563 (tmm-80) cc_final: 0.4310 (tmm-80) REVERT: X 127 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6971 (mm-40) REVERT: X 134 LEU cc_start: 0.7648 (tt) cc_final: 0.7419 (pp) REVERT: Y 36 PRO cc_start: 0.8807 (Cg_endo) cc_final: 0.8521 (Cg_exo) REVERT: Y 95 GLU cc_start: 0.5108 (tt0) cc_final: 0.4749 (tm-30) REVERT: Y 106 ASP cc_start: 0.4718 (t0) cc_final: 0.4225 (t0) REVERT: Y 109 ARG cc_start: 0.6177 (tmm-80) cc_final: 0.5967 (ttp80) REVERT: Y 110 MET cc_start: 0.4562 (tmm) cc_final: 0.4293 (ttt) REVERT: Z 23 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8233 (tm-30) REVERT: Z 58 ASP cc_start: 0.7317 (m-30) cc_final: 0.6944 (t0) REVERT: Z 65 ASP cc_start: 0.7032 (p0) cc_final: 0.6502 (p0) REVERT: Z 95 GLU cc_start: 0.5624 (tt0) cc_final: 0.5406 (tm-30) REVERT: Z 127 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7405 (mm-40) REVERT: AA 99 ARG cc_start: 0.4701 (tmm-80) cc_final: 0.4437 (tmm-80) REVERT: CA 127 GLN cc_start: 0.7153 (mm-40) cc_final: 0.6931 (mm-40) REVERT: CA 134 LEU cc_start: 0.7492 (tt) cc_final: 0.7257 (pp) REVERT: DA 36 PRO cc_start: 0.8846 (Cg_endo) cc_final: 0.8518 (Cg_exo) REVERT: DA 46 GLN cc_start: 0.6425 (tp-100) cc_final: 0.6151 (tp-100) REVERT: DA 95 GLU cc_start: 0.5107 (tt0) cc_final: 0.4740 (tm-30) REVERT: EA 23 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8264 (tm-30) REVERT: EA 58 ASP cc_start: 0.7295 (m-30) cc_final: 0.6922 (t0) REVERT: EA 65 ASP cc_start: 0.7632 (p0) cc_final: 0.7141 (p0) REVERT: EA 95 GLU cc_start: 0.5607 (tt0) cc_final: 0.5396 (tm-30) REVERT: EA 127 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7391 (mm-40) REVERT: FA 99 ARG cc_start: 0.4690 (tmm-80) cc_final: 0.4428 (tmm-80) REVERT: FA 127 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7132 (mp10) REVERT: HA 127 GLN cc_start: 0.7142 (mm-40) cc_final: 0.6918 (mm-40) REVERT: HA 134 LEU cc_start: 0.7590 (tt) cc_final: 0.7353 (pp) REVERT: IA 36 PRO cc_start: 0.8828 (Cg_endo) cc_final: 0.8538 (Cg_exo) REVERT: IA 95 GLU cc_start: 0.5130 (tt0) cc_final: 0.4760 (tm-30) REVERT: JA 23 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8308 (tm-30) REVERT: JA 58 ASP cc_start: 0.7377 (m-30) cc_final: 0.6999 (t0) REVERT: JA 65 ASP cc_start: 0.7607 (p0) cc_final: 0.7118 (p0) REVERT: JA 95 GLU cc_start: 0.5612 (tt0) cc_final: 0.5400 (tm-30) REVERT: JA 127 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7358 (mm-40) REVERT: KA 99 ARG cc_start: 0.4631 (tmm-80) cc_final: 0.4368 (tmm-80) REVERT: MA 46 GLN cc_start: 0.7589 (tp40) cc_final: 0.7353 (tp-100) REVERT: MA 127 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6983 (mm-40) REVERT: MA 134 LEU cc_start: 0.7696 (tt) cc_final: 0.7467 (pp) REVERT: NA 36 PRO cc_start: 0.8828 (Cg_endo) cc_final: 0.8482 (Cg_exo) REVERT: NA 46 GLN cc_start: 0.6454 (tp-100) cc_final: 0.6123 (tp-100) REVERT: NA 95 GLU cc_start: 0.5210 (tt0) cc_final: 0.4823 (tm-30) REVERT: OA 23 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8212 (tm-30) REVERT: OA 58 ASP cc_start: 0.7330 (m-30) cc_final: 0.6958 (t0) REVERT: OA 65 ASP cc_start: 0.7048 (p0) cc_final: 0.6513 (p0) REVERT: OA 95 GLU cc_start: 0.5571 (tt0) cc_final: 0.5351 (tm-30) REVERT: OA 127 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7384 (mm-40) REVERT: PA 99 ARG cc_start: 0.4696 (tmm-80) cc_final: 0.4433 (tmm-80) REVERT: PA 127 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7186 (mp10) REVERT: RA 127 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6941 (mm-40) REVERT: RA 134 LEU cc_start: 0.7537 (tt) cc_final: 0.7306 (pp) REVERT: SA 95 GLU cc_start: 0.5123 (tt0) cc_final: 0.4761 (tm-30) REVERT: TA 23 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8257 (tm-30) REVERT: TA 58 ASP cc_start: 0.7284 (m-30) cc_final: 0.6911 (t0) REVERT: TA 65 ASP cc_start: 0.7634 (p0) cc_final: 0.7146 (p0) REVERT: TA 95 GLU cc_start: 0.5582 (tt0) cc_final: 0.5372 (tm-30) REVERT: TA 127 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7388 (mm-40) REVERT: WA 127 GLN cc_start: 0.7121 (mm-40) cc_final: 0.6910 (mm-40) REVERT: WA 134 LEU cc_start: 0.7585 (tt) cc_final: 0.7349 (pp) REVERT: XA 36 PRO cc_start: 0.8820 (Cg_endo) cc_final: 0.8534 (Cg_exo) REVERT: XA 95 GLU cc_start: 0.5123 (tt0) cc_final: 0.4761 (tm-30) REVERT: XA 106 ASP cc_start: 0.4843 (t0) cc_final: 0.4344 (t0) REVERT: XA 109 ARG cc_start: 0.6177 (tmm-80) cc_final: 0.5970 (ttp80) REVERT: XA 110 MET cc_start: 0.4550 (tmm) cc_final: 0.4305 (ttt) REVERT: YA 23 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8254 (tm-30) REVERT: YA 58 ASP cc_start: 0.7339 (m-30) cc_final: 0.6966 (t0) REVERT: YA 65 ASP cc_start: 0.7036 (p0) cc_final: 0.6504 (p0) REVERT: YA 95 GLU cc_start: 0.5632 (tt0) cc_final: 0.5412 (tm-30) REVERT: YA 127 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7483 (mm-40) REVERT: ZA 99 ARG cc_start: 0.4635 (tmm-80) cc_final: 0.4371 (tmm-80) REVERT: ZA 127 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7143 (mp10) REVERT: BB 46 GLN cc_start: 0.7636 (tp40) cc_final: 0.7395 (tp-100) REVERT: BB 127 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6987 (mm-40) REVERT: BB 134 LEU cc_start: 0.7691 (tt) cc_final: 0.7458 (pp) REVERT: CB 36 PRO cc_start: 0.8823 (Cg_endo) cc_final: 0.8476 (Cg_exo) REVERT: CB 46 GLN cc_start: 0.6449 (tp-100) cc_final: 0.6119 (tp-100) REVERT: CB 95 GLU cc_start: 0.5187 (tt0) cc_final: 0.4804 (tm-30) REVERT: DB 23 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8233 (tm-30) REVERT: DB 58 ASP cc_start: 0.7331 (m-30) cc_final: 0.6961 (t0) REVERT: DB 65 ASP cc_start: 0.7632 (p0) cc_final: 0.7146 (p0) REVERT: DB 95 GLU cc_start: 0.5570 (tt0) cc_final: 0.5350 (tm-30) REVERT: DB 127 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7409 (mm-40) REVERT: EB 99 ARG cc_start: 0.4692 (tmm-80) cc_final: 0.4431 (tmm-80) REVERT: GB 46 GLN cc_start: 0.7581 (tp40) cc_final: 0.7341 (tp-100) REVERT: GB 127 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6930 (mm-40) REVERT: GB 134 LEU cc_start: 0.7558 (tt) cc_final: 0.7326 (pp) REVERT: HB 95 GLU cc_start: 0.5125 (tt0) cc_final: 0.4754 (tm-30) REVERT: IB 23 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8301 (tm-30) REVERT: IB 58 ASP cc_start: 0.7368 (m-30) cc_final: 0.6982 (t0) REVERT: IB 65 ASP cc_start: 0.7612 (p0) cc_final: 0.7123 (p0) REVERT: IB 127 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7446 (mm-40) outliers start: 127 outliers final: 101 residues processed: 1357 average time/residue: 0.6006 time to fit residues: 1341.9380 Evaluate side-chains 1200 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1099 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain AA residue 11 THR Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain BA residue 98 LEU Chi-restraints excluded: chain CA residue 94 VAL Chi-restraints excluded: chain DA residue 25 LEU Chi-restraints excluded: chain EA residue 25 LEU Chi-restraints excluded: chain EA residue 27 THR Chi-restraints excluded: chain FA residue 11 THR Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 98 LEU Chi-restraints excluded: chain HA residue 25 LEU Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 25 LEU Chi-restraints excluded: chain JA residue 25 LEU Chi-restraints excluded: chain JA residue 27 THR Chi-restraints excluded: chain KA residue 11 THR Chi-restraints excluded: chain KA residue 68 VAL Chi-restraints excluded: chain LA residue 68 VAL Chi-restraints excluded: chain LA residue 98 LEU Chi-restraints excluded: chain MA residue 25 LEU Chi-restraints excluded: chain MA residue 94 VAL Chi-restraints excluded: chain NA residue 25 LEU Chi-restraints excluded: chain OA residue 25 LEU Chi-restraints excluded: chain OA residue 27 THR Chi-restraints excluded: chain PA residue 11 THR Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain QA residue 98 LEU Chi-restraints excluded: chain RA residue 94 VAL Chi-restraints excluded: chain SA residue 25 LEU Chi-restraints excluded: chain TA residue 25 LEU Chi-restraints excluded: chain TA residue 27 THR Chi-restraints excluded: chain UA residue 11 THR Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 94 VAL Chi-restraints excluded: chain VA residue 68 VAL Chi-restraints excluded: chain VA residue 98 LEU Chi-restraints excluded: chain WA residue 94 VAL Chi-restraints excluded: chain XA residue 25 LEU Chi-restraints excluded: chain YA residue 25 LEU Chi-restraints excluded: chain YA residue 27 THR Chi-restraints excluded: chain ZA residue 11 THR Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain AB residue 68 VAL Chi-restraints excluded: chain AB residue 98 LEU Chi-restraints excluded: chain BB residue 25 LEU Chi-restraints excluded: chain BB residue 94 VAL Chi-restraints excluded: chain CB residue 25 LEU Chi-restraints excluded: chain DB residue 25 LEU Chi-restraints excluded: chain DB residue 27 THR Chi-restraints excluded: chain EB residue 11 THR Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain FB residue 68 VAL Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain GB residue 25 LEU Chi-restraints excluded: chain GB residue 94 VAL Chi-restraints excluded: chain HB residue 25 LEU Chi-restraints excluded: chain IB residue 25 LEU Chi-restraints excluded: chain IB residue 27 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 363 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 544 optimal weight: 9.9990 chunk 445 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 655 optimal weight: 6.9990 chunk 707 optimal weight: 8.9990 chunk 583 optimal weight: 6.9990 chunk 649 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 525 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS B 85 HIS C 85 HIS D 85 HIS F 85 HIS G 85 HIS H 85 HIS I 85 HIS K 85 HIS L 85 HIS M 85 HIS N 85 HIS P 85 HIS Q 85 HIS R 85 HIS S 85 HIS V 85 HIS W 85 HIS X 85 HIS Y 85 HIS AA 85 HIS BA 85 HIS CA 85 HIS DA 85 HIS FA 85 HIS GA 85 HIS HA 46 GLN HA 85 HIS IA 85 HIS KA 85 HIS LA 85 HIS MA 85 HIS NA 85 HIS PA 85 HIS QA 85 HIS RA 85 HIS SA 85 HIS UA 85 HIS VA 85 HIS WA 85 HIS XA 85 HIS ZA 85 HIS AB 85 HIS BB 85 HIS CB 85 HIS EB 85 HIS FB 85 HIS GB 85 HIS HB 85 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5241 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 63000 Z= 0.572 Angle : 0.732 7.435 84540 Z= 0.387 Chirality : 0.051 0.203 10080 Planarity : 0.005 0.033 10740 Dihedral : 4.173 16.100 8100 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.51 % Allowed : 9.07 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.09), residues: 7380 helix: 2.54 (0.07), residues: 3600 sheet: -0.67 (0.12), residues: 1800 loop : -1.26 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRPTA 52 HIS 0.004 0.001 HIS W 85 PHE 0.019 0.004 PHEMA 32 TYR 0.020 0.004 TYRLA 55 ARG 0.008 0.001 ARGCB 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1130 time to evaluate : 5.861 Fit side-chains REVERT: C 46 GLN cc_start: 0.7478 (tp40) cc_final: 0.7156 (tp-100) REVERT: C 127 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7296 (mm-40) REVERT: C 134 LEU cc_start: 0.7741 (tt) cc_final: 0.7508 (pp) REVERT: D 26 ILE cc_start: 0.3479 (OUTLIER) cc_final: 0.3253 (pt) REVERT: D 95 GLU cc_start: 0.5498 (tt0) cc_final: 0.5169 (tm-30) REVERT: E 23 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8267 (tm-30) REVERT: E 65 ASP cc_start: 0.7107 (p0) cc_final: 0.6304 (p0) REVERT: E 95 GLU cc_start: 0.5491 (tt0) cc_final: 0.5185 (tm-30) REVERT: H 30 LYS cc_start: 0.6090 (mttt) cc_final: 0.5397 (mtmm) REVERT: H 46 GLN cc_start: 0.7380 (tp40) cc_final: 0.7061 (tp-100) REVERT: H 127 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7245 (mm-40) REVERT: H 134 LEU cc_start: 0.7721 (tt) cc_final: 0.7488 (pp) REVERT: I 26 ILE cc_start: 0.3546 (OUTLIER) cc_final: 0.3332 (pt) REVERT: I 95 GLU cc_start: 0.5458 (tt0) cc_final: 0.5139 (tm-30) REVERT: J 23 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8313 (tm-30) REVERT: J 65 ASP cc_start: 0.7080 (p0) cc_final: 0.6275 (p0) REVERT: J 95 GLU cc_start: 0.5545 (tt0) cc_final: 0.5240 (tm-30) REVERT: L 23 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7954 (tm-30) REVERT: M 127 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7205 (mm-40) REVERT: M 134 LEU cc_start: 0.7635 (tt) cc_final: 0.7400 (pp) REVERT: N 26 ILE cc_start: 0.3495 (OUTLIER) cc_final: 0.3267 (pt) REVERT: N 95 GLU cc_start: 0.5475 (tt0) cc_final: 0.5059 (tm-30) REVERT: O 23 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8301 (tm-30) REVERT: O 65 ASP cc_start: 0.7106 (p0) cc_final: 0.6299 (p0) REVERT: O 95 GLU cc_start: 0.5525 (tt0) cc_final: 0.5229 (tm-30) REVERT: Q 23 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7993 (tm-30) REVERT: Q 58 ASP cc_start: 0.7489 (m-30) cc_final: 0.7282 (m-30) REVERT: R 46 GLN cc_start: 0.7451 (tp40) cc_final: 0.7141 (tp-100) REVERT: R 127 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7193 (mm-40) REVERT: R 134 LEU cc_start: 0.7696 (tt) cc_final: 0.7453 (pp) REVERT: S 26 ILE cc_start: 0.3475 (OUTLIER) cc_final: 0.3245 (pt) REVERT: S 36 PRO cc_start: 0.8790 (Cg_endo) cc_final: 0.8509 (Cg_exo) REVERT: S 95 GLU cc_start: 0.5419 (tt0) cc_final: 0.5110 (tm-30) REVERT: T 23 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8293 (tm-30) REVERT: T 65 ASP cc_start: 0.7089 (p0) cc_final: 0.6291 (p0) REVERT: W 23 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7994 (tm-30) REVERT: X 46 GLN cc_start: 0.7440 (tp40) cc_final: 0.7128 (tp-100) REVERT: X 127 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7255 (mm-40) REVERT: X 134 LEU cc_start: 0.7737 (tt) cc_final: 0.7498 (pp) REVERT: Y 26 ILE cc_start: 0.3478 (OUTLIER) cc_final: 0.3263 (pt) REVERT: Y 36 PRO cc_start: 0.8780 (Cg_endo) cc_final: 0.8499 (Cg_exo) REVERT: Y 95 GLU cc_start: 0.5419 (tt0) cc_final: 0.5110 (tm-30) REVERT: Z 23 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8261 (tm-30) REVERT: Z 65 ASP cc_start: 0.7074 (p0) cc_final: 0.6277 (p0) REVERT: Z 95 GLU cc_start: 0.5553 (tt0) cc_final: 0.5247 (tm-30) REVERT: BA 23 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7951 (tm-30) REVERT: CA 127 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7213 (mm-40) REVERT: CA 134 LEU cc_start: 0.7582 (tt) cc_final: 0.7334 (pp) REVERT: DA 26 ILE cc_start: 0.3489 (OUTLIER) cc_final: 0.3277 (pt) REVERT: DA 95 GLU cc_start: 0.5415 (tt0) cc_final: 0.5101 (tm-30) REVERT: EA 23 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8297 (tm-30) REVERT: EA 65 ASP cc_start: 0.7098 (p0) cc_final: 0.6293 (p0) REVERT: EA 95 GLU cc_start: 0.5521 (tt0) cc_final: 0.5227 (tm-30) REVERT: GA 23 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7961 (tm-30) REVERT: HA 30 LYS cc_start: 0.6090 (mttt) cc_final: 0.5401 (mtmm) REVERT: HA 127 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7187 (mm-40) REVERT: HA 134 LEU cc_start: 0.7685 (tt) cc_final: 0.7437 (pp) REVERT: IA 26 ILE cc_start: 0.3556 (OUTLIER) cc_final: 0.3340 (pt) REVERT: IA 95 GLU cc_start: 0.5405 (tt0) cc_final: 0.4968 (tm-30) REVERT: JA 23 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8335 (tm-30) REVERT: JA 65 ASP cc_start: 0.7084 (p0) cc_final: 0.6329 (p0) REVERT: JA 95 GLU cc_start: 0.5538 (tt0) cc_final: 0.5244 (tm-30) REVERT: MA 127 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7307 (mm-40) REVERT: MA 134 LEU cc_start: 0.7773 (tt) cc_final: 0.7533 (pp) REVERT: NA 26 ILE cc_start: 0.3481 (OUTLIER) cc_final: 0.3267 (pt) REVERT: NA 95 GLU cc_start: 0.5523 (tt0) cc_final: 0.5190 (tm-30) REVERT: NA 109 ARG cc_start: 0.5573 (tmm-80) cc_final: 0.5319 (ttp-170) REVERT: OA 23 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8250 (tm-30) REVERT: OA 65 ASP cc_start: 0.7096 (p0) cc_final: 0.6289 (p0) REVERT: OA 95 GLU cc_start: 0.5480 (tt0) cc_final: 0.5182 (tm-30) REVERT: QA 23 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7955 (tm-30) REVERT: RA 127 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7219 (mm-40) REVERT: RA 134 LEU cc_start: 0.7632 (tt) cc_final: 0.7390 (pp) REVERT: SA 26 ILE cc_start: 0.3491 (OUTLIER) cc_final: 0.3264 (pt) REVERT: SA 95 GLU cc_start: 0.5423 (tt0) cc_final: 0.5024 (tm-30) REVERT: SA 109 ARG cc_start: 0.5574 (tmm-80) cc_final: 0.5314 (ttp-170) REVERT: TA 23 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8292 (tm-30) REVERT: TA 46 GLN cc_start: 0.7344 (tp-100) cc_final: 0.7025 (tp-100) REVERT: TA 65 ASP cc_start: 0.7096 (p0) cc_final: 0.6292 (p0) REVERT: TA 95 GLU cc_start: 0.5503 (tt0) cc_final: 0.5225 (tm-30) REVERT: VA 23 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7986 (tm-30) REVERT: VA 58 ASP cc_start: 0.7512 (m-30) cc_final: 0.7306 (m-30) REVERT: WA 127 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7186 (mm-40) REVERT: WA 134 LEU cc_start: 0.7684 (tt) cc_final: 0.7439 (pp) REVERT: XA 26 ILE cc_start: 0.3477 (OUTLIER) cc_final: 0.3245 (pt) REVERT: XA 36 PRO cc_start: 0.8785 (Cg_endo) cc_final: 0.8504 (Cg_exo) REVERT: XA 95 GLU cc_start: 0.5429 (tt0) cc_final: 0.5119 (tm-30) REVERT: YA 23 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8281 (tm-30) REVERT: YA 65 ASP cc_start: 0.7079 (p0) cc_final: 0.6282 (p0) REVERT: YA 95 GLU cc_start: 0.5556 (tt0) cc_final: 0.5248 (tm-30) REVERT: BB 127 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7311 (mm-40) REVERT: BB 134 LEU cc_start: 0.7770 (tt) cc_final: 0.7527 (pp) REVERT: CB 26 ILE cc_start: 0.3483 (OUTLIER) cc_final: 0.3273 (pt) REVERT: CB 95 GLU cc_start: 0.5499 (tt0) cc_final: 0.5169 (tm-30) REVERT: DB 23 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8272 (tm-30) REVERT: DB 65 ASP cc_start: 0.7107 (p0) cc_final: 0.6303 (p0) REVERT: DB 95 GLU cc_start: 0.5475 (tt0) cc_final: 0.5172 (tm-30) REVERT: FB 23 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7946 (tm-30) REVERT: GB 30 LYS cc_start: 0.6099 (mttt) cc_final: 0.5407 (mtmm) REVERT: GB 127 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7195 (mm-40) REVERT: GB 134 LEU cc_start: 0.7651 (tt) cc_final: 0.7409 (pp) REVERT: HB 26 ILE cc_start: 0.3553 (OUTLIER) cc_final: 0.3337 (pt) REVERT: HB 95 GLU cc_start: 0.5436 (tt0) cc_final: 0.5119 (tm-30) REVERT: IB 23 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8326 (tm-30) REVERT: IB 65 ASP cc_start: 0.7083 (p0) cc_final: 0.6280 (p0) outliers start: 257 outliers final: 176 residues processed: 1287 average time/residue: 0.5728 time to fit residues: 1241.8033 Evaluate side-chains 1164 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 976 time to evaluate : 5.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain Q residue 37 MET Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 58 ASP Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 134 LEU Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain W residue 37 MET Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain W residue 110 MET Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain AA residue 11 THR Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain AA residue 94 VAL Chi-restraints excluded: chain BA residue 37 MET Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain BA residue 110 MET Chi-restraints excluded: chain CA residue 25 LEU Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 94 VAL Chi-restraints excluded: chain DA residue 25 LEU Chi-restraints excluded: chain DA residue 26 ILE Chi-restraints excluded: chain DA residue 58 ASP Chi-restraints excluded: chain EA residue 25 LEU Chi-restraints excluded: chain EA residue 58 ASP Chi-restraints excluded: chain EA residue 134 LEU Chi-restraints excluded: chain FA residue 11 THR Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain FA residue 94 VAL Chi-restraints excluded: chain FA residue 132 GLN Chi-restraints excluded: chain GA residue 37 MET Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 98 LEU Chi-restraints excluded: chain GA residue 110 MET Chi-restraints excluded: chain HA residue 25 LEU Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 25 LEU Chi-restraints excluded: chain IA residue 26 ILE Chi-restraints excluded: chain IA residue 58 ASP Chi-restraints excluded: chain JA residue 25 LEU Chi-restraints excluded: chain JA residue 58 ASP Chi-restraints excluded: chain KA residue 11 THR Chi-restraints excluded: chain KA residue 68 VAL Chi-restraints excluded: chain KA residue 94 VAL Chi-restraints excluded: chain LA residue 37 MET Chi-restraints excluded: chain LA residue 68 VAL Chi-restraints excluded: chain LA residue 110 MET Chi-restraints excluded: chain MA residue 25 LEU Chi-restraints excluded: chain MA residue 70 THR Chi-restraints excluded: chain MA residue 94 VAL Chi-restraints excluded: chain NA residue 25 LEU Chi-restraints excluded: chain NA residue 26 ILE Chi-restraints excluded: chain NA residue 58 ASP Chi-restraints excluded: chain OA residue 25 LEU Chi-restraints excluded: chain OA residue 58 ASP Chi-restraints excluded: chain OA residue 134 LEU Chi-restraints excluded: chain PA residue 11 THR Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain PA residue 94 VAL Chi-restraints excluded: chain QA residue 37 MET Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain QA residue 94 VAL Chi-restraints excluded: chain QA residue 98 LEU Chi-restraints excluded: chain QA residue 110 MET Chi-restraints excluded: chain RA residue 25 LEU Chi-restraints excluded: chain RA residue 70 THR Chi-restraints excluded: chain RA residue 94 VAL Chi-restraints excluded: chain SA residue 25 LEU Chi-restraints excluded: chain SA residue 26 ILE Chi-restraints excluded: chain SA residue 58 ASP Chi-restraints excluded: chain TA residue 25 LEU Chi-restraints excluded: chain TA residue 58 ASP Chi-restraints excluded: chain TA residue 134 LEU Chi-restraints excluded: chain UA residue 11 THR Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 94 VAL Chi-restraints excluded: chain VA residue 37 MET Chi-restraints excluded: chain VA residue 68 VAL Chi-restraints excluded: chain VA residue 110 MET Chi-restraints excluded: chain WA residue 25 LEU Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain WA residue 94 VAL Chi-restraints excluded: chain XA residue 25 LEU Chi-restraints excluded: chain XA residue 26 ILE Chi-restraints excluded: chain XA residue 58 ASP Chi-restraints excluded: chain YA residue 25 LEU Chi-restraints excluded: chain YA residue 58 ASP Chi-restraints excluded: chain YA residue 134 LEU Chi-restraints excluded: chain ZA residue 11 THR Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain ZA residue 94 VAL Chi-restraints excluded: chain AB residue 68 VAL Chi-restraints excluded: chain AB residue 98 LEU Chi-restraints excluded: chain AB residue 110 MET Chi-restraints excluded: chain BB residue 25 LEU Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain BB residue 94 VAL Chi-restraints excluded: chain BB residue 106 ASP Chi-restraints excluded: chain CB residue 25 LEU Chi-restraints excluded: chain CB residue 26 ILE Chi-restraints excluded: chain CB residue 58 ASP Chi-restraints excluded: chain DB residue 25 LEU Chi-restraints excluded: chain DB residue 58 ASP Chi-restraints excluded: chain DB residue 134 LEU Chi-restraints excluded: chain EB residue 11 THR Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain EB residue 94 VAL Chi-restraints excluded: chain FB residue 37 MET Chi-restraints excluded: chain FB residue 68 VAL Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain FB residue 110 MET Chi-restraints excluded: chain GB residue 25 LEU Chi-restraints excluded: chain GB residue 70 THR Chi-restraints excluded: chain GB residue 94 VAL Chi-restraints excluded: chain HB residue 25 LEU Chi-restraints excluded: chain HB residue 26 ILE Chi-restraints excluded: chain HB residue 58 ASP Chi-restraints excluded: chain IB residue 25 LEU Chi-restraints excluded: chain IB residue 58 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 647 optimal weight: 0.0070 chunk 492 optimal weight: 4.9990 chunk 339 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 439 optimal weight: 1.9990 chunk 657 optimal weight: 4.9990 chunk 695 optimal weight: 8.9990 chunk 343 optimal weight: 2.9990 chunk 623 optimal weight: 20.0000 chunk 187 optimal weight: 0.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 85 HIS OA 85 HIS DB 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5197 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 63000 Z= 0.178 Angle : 0.514 8.868 84540 Z= 0.264 Chirality : 0.044 0.140 10080 Planarity : 0.003 0.030 10740 Dihedral : 3.377 13.342 8100 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.05 % Allowed : 11.30 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.10), residues: 7380 helix: 3.75 (0.08), residues: 3540 sheet: -0.23 (0.12), residues: 1800 loop : -1.13 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRPAB 52 HIS 0.002 0.001 HISCA 85 PHE 0.002 0.000 PHE R 32 TYR 0.005 0.001 TYRRA 82 ARG 0.008 0.001 ARGEB 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1210 time to evaluate : 5.913 Fit side-chains REVERT: A 4 ILE cc_start: 0.7107 (mt) cc_final: 0.6866 (tt) REVERT: B 23 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7712 (tm-30) REVERT: C 46 GLN cc_start: 0.7484 (tp40) cc_final: 0.7177 (tp-100) REVERT: C 127 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7351 (mm-40) REVERT: C 134 LEU cc_start: 0.7733 (tt) cc_final: 0.7495 (pp) REVERT: D 95 GLU cc_start: 0.5504 (tt0) cc_final: 0.5076 (tm-30) REVERT: E 7 MET cc_start: 0.5757 (mtp) cc_final: 0.5508 (mtp) REVERT: E 23 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8222 (tm-30) REVERT: E 65 ASP cc_start: 0.7132 (p0) cc_final: 0.6474 (p0) REVERT: E 95 GLU cc_start: 0.5537 (tt0) cc_final: 0.5243 (tm-30) REVERT: G 23 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7785 (tm-30) REVERT: H 46 GLN cc_start: 0.7387 (tp40) cc_final: 0.7086 (tp-100) REVERT: H 127 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7299 (mm-40) REVERT: H 134 LEU cc_start: 0.7712 (tt) cc_final: 0.7473 (pp) REVERT: I 37 MET cc_start: 0.7224 (ppp) cc_final: 0.6763 (ppp) REVERT: I 95 GLU cc_start: 0.5464 (tt0) cc_final: 0.5046 (tm-30) REVERT: J 7 MET cc_start: 0.5918 (mtp) cc_final: 0.5623 (mtp) REVERT: J 23 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8247 (tm-30) REVERT: J 65 ASP cc_start: 0.7111 (p0) cc_final: 0.6451 (p0) REVERT: J 95 GLU cc_start: 0.5554 (tt0) cc_final: 0.5265 (tm-30) REVERT: L 23 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7783 (tm-30) REVERT: M 127 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7255 (mm-40) REVERT: M 134 LEU cc_start: 0.7517 (tt) cc_final: 0.7277 (pp) REVERT: N 95 GLU cc_start: 0.5219 (tt0) cc_final: 0.4856 (tm-30) REVERT: O 7 MET cc_start: 0.5775 (mtp) cc_final: 0.5500 (mtp) REVERT: O 23 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8234 (tm-30) REVERT: O 65 ASP cc_start: 0.7131 (p0) cc_final: 0.6468 (p0) REVERT: O 95 GLU cc_start: 0.5544 (tt0) cc_final: 0.5257 (tm-30) REVERT: P 4 ILE cc_start: 0.7109 (mt) cc_final: 0.6862 (tt) REVERT: Q 23 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7822 (tm-30) REVERT: R 46 GLN cc_start: 0.7459 (tp40) cc_final: 0.7168 (tp-100) REVERT: R 127 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7243 (mm-40) REVERT: R 134 LEU cc_start: 0.7687 (tt) cc_final: 0.7440 (pp) REVERT: S 37 MET cc_start: 0.7233 (ppp) cc_final: 0.6779 (ppp) REVERT: S 95 GLU cc_start: 0.5431 (tt0) cc_final: 0.5027 (tm-30) REVERT: T 7 MET cc_start: 0.5746 (mtp) cc_final: 0.5525 (mtp) REVERT: T 23 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8225 (tm-30) REVERT: T 65 ASP cc_start: 0.7118 (p0) cc_final: 0.6465 (p0) REVERT: V 4 ILE cc_start: 0.7110 (mt) cc_final: 0.6859 (tt) REVERT: W 23 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7820 (tm-30) REVERT: X 46 GLN cc_start: 0.7442 (tp40) cc_final: 0.7154 (tp-100) REVERT: X 127 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7307 (mm-40) REVERT: X 134 LEU cc_start: 0.7728 (tt) cc_final: 0.7484 (pp) REVERT: Y 37 MET cc_start: 0.7247 (ppp) cc_final: 0.6786 (ppp) REVERT: Y 95 GLU cc_start: 0.5429 (tt0) cc_final: 0.5026 (tm-30) REVERT: Z 7 MET cc_start: 0.5737 (mtp) cc_final: 0.5508 (mtp) REVERT: Z 23 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8193 (tm-30) REVERT: Z 65 ASP cc_start: 0.7111 (p0) cc_final: 0.6458 (p0) REVERT: Z 95 GLU cc_start: 0.5581 (tt0) cc_final: 0.5287 (tm-30) REVERT: BA 23 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7777 (tm-30) REVERT: CA 127 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7308 (mm-40) REVERT: CA 134 LEU cc_start: 0.7577 (tt) cc_final: 0.7323 (pp) REVERT: DA 95 GLU cc_start: 0.5421 (tt0) cc_final: 0.5010 (tm-30) REVERT: EA 7 MET cc_start: 0.5763 (mtp) cc_final: 0.5486 (mtp) REVERT: EA 23 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8228 (tm-30) REVERT: EA 65 ASP cc_start: 0.7126 (p0) cc_final: 0.6463 (p0) REVERT: EA 95 GLU cc_start: 0.5552 (tt0) cc_final: 0.5272 (tm-30) REVERT: HA 127 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7288 (mm-40) REVERT: HA 134 LEU cc_start: 0.7678 (tt) cc_final: 0.7424 (pp) REVERT: IA 37 MET cc_start: 0.7226 (ppp) cc_final: 0.6766 (ppp) REVERT: IA 95 GLU cc_start: 0.5236 (tt0) cc_final: 0.4867 (tm-30) REVERT: JA 7 MET cc_start: 0.5760 (mtp) cc_final: 0.5501 (mtp) REVERT: JA 23 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8262 (tm-30) REVERT: JA 65 ASP cc_start: 0.7113 (p0) cc_final: 0.6457 (p0) REVERT: JA 95 GLU cc_start: 0.5574 (tt0) cc_final: 0.5279 (tm-30) REVERT: LA 23 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7727 (tm-30) REVERT: MA 46 GLN cc_start: 0.7362 (tp40) cc_final: 0.7060 (tp-100) REVERT: MA 127 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7364 (mm-40) REVERT: MA 134 LEU cc_start: 0.7765 (tt) cc_final: 0.7520 (pp) REVERT: NA 95 GLU cc_start: 0.5529 (tt0) cc_final: 0.5096 (tm-30) REVERT: OA 7 MET cc_start: 0.5766 (mtp) cc_final: 0.5508 (mtp) REVERT: OA 23 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8202 (tm-30) REVERT: OA 65 ASP cc_start: 0.7125 (p0) cc_final: 0.6463 (p0) REVERT: OA 95 GLU cc_start: 0.5532 (tt0) cc_final: 0.5232 (tm-30) REVERT: QA 23 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7788 (tm-30) REVERT: RA 127 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7317 (mm-40) REVERT: RA 134 LEU cc_start: 0.7627 (tt) cc_final: 0.7379 (pp) REVERT: SA 95 GLU cc_start: 0.5226 (tt0) cc_final: 0.4867 (tm-30) REVERT: TA 7 MET cc_start: 0.5768 (mtp) cc_final: 0.5509 (mtp) REVERT: TA 23 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8222 (tm-30) REVERT: TA 65 ASP cc_start: 0.7126 (p0) cc_final: 0.6465 (p0) REVERT: TA 95 GLU cc_start: 0.5562 (tt0) cc_final: 0.5275 (tm-30) REVERT: UA 4 ILE cc_start: 0.7111 (mt) cc_final: 0.6862 (tt) REVERT: VA 23 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7809 (tm-30) REVERT: WA 127 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7237 (mm-40) REVERT: WA 134 LEU cc_start: 0.7675 (tt) cc_final: 0.7425 (pp) REVERT: XA 37 MET cc_start: 0.7225 (ppp) cc_final: 0.6788 (ppp) REVERT: XA 95 GLU cc_start: 0.5442 (tt0) cc_final: 0.5036 (tm-30) REVERT: YA 7 MET cc_start: 0.5746 (mtp) cc_final: 0.5506 (mtp) REVERT: YA 23 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8214 (tm-30) REVERT: YA 65 ASP cc_start: 0.7114 (p0) cc_final: 0.6460 (p0) REVERT: YA 95 GLU cc_start: 0.5585 (tt0) cc_final: 0.5289 (tm-30) REVERT: AB 23 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7721 (tm-30) REVERT: BB 46 GLN cc_start: 0.7406 (tp40) cc_final: 0.7097 (tp-100) REVERT: BB 127 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7367 (mm-40) REVERT: BB 134 LEU cc_start: 0.7762 (tt) cc_final: 0.7514 (pp) REVERT: CB 95 GLU cc_start: 0.5504 (tt0) cc_final: 0.5074 (tm-30) REVERT: DB 7 MET cc_start: 0.5898 (mtp) cc_final: 0.5596 (mtp) REVERT: DB 23 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8226 (tm-30) REVERT: DB 65 ASP cc_start: 0.7131 (p0) cc_final: 0.6475 (p0) REVERT: DB 95 GLU cc_start: 0.5519 (tt0) cc_final: 0.5230 (tm-30) REVERT: GB 46 GLN cc_start: 0.7341 (tp40) cc_final: 0.7032 (tp-100) REVERT: GB 127 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7252 (mm-40) REVERT: GB 134 LEU cc_start: 0.7645 (tt) cc_final: 0.7397 (pp) REVERT: HB 95 GLU cc_start: 0.5441 (tt0) cc_final: 0.5025 (tm-30) REVERT: IB 7 MET cc_start: 0.5928 (mtp) cc_final: 0.5530 (mtp) REVERT: IB 23 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8281 (tm-30) REVERT: IB 65 ASP cc_start: 0.7118 (p0) cc_final: 0.6460 (p0) outliers start: 150 outliers final: 97 residues processed: 1295 average time/residue: 0.5959 time to fit residues: 1288.0048 Evaluate side-chains 1179 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1082 time to evaluate : 5.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain T residue 19 ILE Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 68 VAL Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain BA residue 98 LEU Chi-restraints excluded: chain CA residue 94 VAL Chi-restraints excluded: chain DA residue 25 LEU Chi-restraints excluded: chain EA residue 19 ILE Chi-restraints excluded: chain EA residue 25 LEU Chi-restraints excluded: chain EA residue 68 VAL Chi-restraints excluded: chain EA residue 97 ILE Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 98 LEU Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 25 LEU Chi-restraints excluded: chain JA residue 19 ILE Chi-restraints excluded: chain JA residue 25 LEU Chi-restraints excluded: chain JA residue 68 VAL Chi-restraints excluded: chain JA residue 97 ILE Chi-restraints excluded: chain KA residue 68 VAL Chi-restraints excluded: chain LA residue 68 VAL Chi-restraints excluded: chain LA residue 98 LEU Chi-restraints excluded: chain MA residue 94 VAL Chi-restraints excluded: chain NA residue 25 LEU Chi-restraints excluded: chain OA residue 19 ILE Chi-restraints excluded: chain OA residue 25 LEU Chi-restraints excluded: chain OA residue 68 VAL Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain QA residue 98 LEU Chi-restraints excluded: chain SA residue 25 LEU Chi-restraints excluded: chain TA residue 19 ILE Chi-restraints excluded: chain TA residue 25 LEU Chi-restraints excluded: chain TA residue 68 VAL Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain VA residue 68 VAL Chi-restraints excluded: chain VA residue 98 LEU Chi-restraints excluded: chain WA residue 94 VAL Chi-restraints excluded: chain XA residue 25 LEU Chi-restraints excluded: chain YA residue 19 ILE Chi-restraints excluded: chain YA residue 25 LEU Chi-restraints excluded: chain YA residue 68 VAL Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain AB residue 68 VAL Chi-restraints excluded: chain AB residue 98 LEU Chi-restraints excluded: chain BB residue 94 VAL Chi-restraints excluded: chain CB residue 25 LEU Chi-restraints excluded: chain DB residue 19 ILE Chi-restraints excluded: chain DB residue 25 LEU Chi-restraints excluded: chain DB residue 68 VAL Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain FB residue 68 VAL Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain GB residue 94 VAL Chi-restraints excluded: chain HB residue 25 LEU Chi-restraints excluded: chain IB residue 19 ILE Chi-restraints excluded: chain IB residue 25 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 579 optimal weight: 10.0000 chunk 395 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 518 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 593 optimal weight: 4.9990 chunk 481 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 355 optimal weight: 0.9980 chunk 624 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN D 23 GLN G 113 GLN I 23 GLN N 23 GLN S 23 GLN Y 23 GLN DA 23 GLN FA 23 GLN GA 23 GLN GA 113 GLN IA 23 GLN LA 113 GLN NA 23 GLN SA 23 GLN XA 23 GLN AB 113 GLN CB 23 GLN FB 113 GLN HB 23 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5194 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 63000 Z= 0.189 Angle : 0.521 8.859 84540 Z= 0.268 Chirality : 0.043 0.136 10080 Planarity : 0.003 0.029 10740 Dihedral : 3.191 12.029 8100 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.57 % Allowed : 12.39 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.10), residues: 7380 helix: 4.07 (0.08), residues: 3540 sheet: -0.07 (0.12), residues: 1800 loop : -1.09 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRPFB 52 HIS 0.002 0.001 HIS Y 85 PHE 0.002 0.001 PHE I 32 TYR 0.008 0.001 TYR Z 82 ARG 0.008 0.000 ARG S 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1122 time to evaluate : 5.851 Fit side-chains REVERT: B 23 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7806 (tm-30) REVERT: C 127 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7258 (mm-40) REVERT: C 134 LEU cc_start: 0.7733 (tt) cc_final: 0.7492 (pp) REVERT: D 95 GLU cc_start: 0.5301 (tt0) cc_final: 0.4902 (tm-30) REVERT: E 23 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8259 (tm-30) REVERT: E 65 ASP cc_start: 0.7134 (p0) cc_final: 0.6466 (p0) REVERT: E 95 GLU cc_start: 0.5542 (tt0) cc_final: 0.5246 (tm-30) REVERT: G 23 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7816 (tm-30) REVERT: H 46 GLN cc_start: 0.7383 (tp40) cc_final: 0.7106 (tp-100) REVERT: H 127 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7343 (mm-40) REVERT: H 134 LEU cc_start: 0.7714 (tt) cc_final: 0.7472 (pp) REVERT: I 37 MET cc_start: 0.7314 (ppp) cc_final: 0.6925 (ppp) REVERT: I 95 GLU cc_start: 0.5262 (tt0) cc_final: 0.4874 (tm-30) REVERT: J 23 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8284 (tm-30) REVERT: J 65 ASP cc_start: 0.7110 (p0) cc_final: 0.6463 (p0) REVERT: J 95 GLU cc_start: 0.5772 (tt0) cc_final: 0.5409 (tm-30) REVERT: M 127 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7236 (mm-40) REVERT: M 134 LEU cc_start: 0.7518 (tt) cc_final: 0.7275 (pp) REVERT: N 95 GLU cc_start: 0.5168 (tt0) cc_final: 0.4780 (tm-30) REVERT: O 23 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8267 (tm-30) REVERT: O 65 ASP cc_start: 0.7131 (p0) cc_final: 0.6479 (p0) REVERT: O 95 GLU cc_start: 0.5770 (tt0) cc_final: 0.5407 (tm-30) REVERT: O 134 LEU cc_start: 0.7328 (tp) cc_final: 0.7093 (pp) REVERT: R 46 GLN cc_start: 0.7454 (tp40) cc_final: 0.7172 (tp-100) REVERT: R 127 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7288 (mm-40) REVERT: R 134 LEU cc_start: 0.7688 (tt) cc_final: 0.7437 (pp) REVERT: S 37 MET cc_start: 0.7229 (ppp) cc_final: 0.6826 (ppp) REVERT: S 95 GLU cc_start: 0.5232 (tt0) cc_final: 0.4855 (tm-30) REVERT: T 23 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8265 (tm-30) REVERT: T 65 ASP cc_start: 0.7114 (p0) cc_final: 0.6451 (p0) REVERT: T 134 LEU cc_start: 0.7343 (tp) cc_final: 0.7109 (pp) REVERT: X 46 GLN cc_start: 0.7438 (tp40) cc_final: 0.7155 (tp-100) REVERT: X 127 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7353 (mm-40) REVERT: X 134 LEU cc_start: 0.7625 (tt) cc_final: 0.7376 (pp) REVERT: Y 37 MET cc_start: 0.7244 (ppp) cc_final: 0.6835 (ppp) REVERT: Y 95 GLU cc_start: 0.5230 (tt0) cc_final: 0.4854 (tm-30) REVERT: Z 23 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8234 (tm-30) REVERT: Z 65 ASP cc_start: 0.7108 (p0) cc_final: 0.6444 (p0) REVERT: Z 95 GLU cc_start: 0.5800 (tt0) cc_final: 0.5431 (tm-30) REVERT: CA 127 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7136 (mm-40) REVERT: CA 134 LEU cc_start: 0.7578 (tt) cc_final: 0.7320 (pp) REVERT: DA 95 GLU cc_start: 0.5220 (tt0) cc_final: 0.4839 (tm-30) REVERT: EA 23 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8262 (tm-30) REVERT: EA 65 ASP cc_start: 0.7124 (p0) cc_final: 0.6475 (p0) REVERT: EA 95 GLU cc_start: 0.5780 (tt0) cc_final: 0.5422 (tm-30) REVERT: GA 23 GLN cc_start: 0.8271 (tm130) cc_final: 0.7772 (tm-30) REVERT: HA 127 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7116 (mm-40) REVERT: HA 134 LEU cc_start: 0.7681 (tt) cc_final: 0.7423 (pp) REVERT: IA 37 MET cc_start: 0.7218 (ppp) cc_final: 0.6856 (ppp) REVERT: IA 95 GLU cc_start: 0.5189 (tt0) cc_final: 0.4788 (tm-30) REVERT: JA 23 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8304 (tm-30) REVERT: JA 65 ASP cc_start: 0.7106 (p0) cc_final: 0.6464 (p0) REVERT: JA 95 GLU cc_start: 0.5786 (tt0) cc_final: 0.5423 (tm-30) REVERT: LA 23 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7820 (tm-30) REVERT: MA 127 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7271 (mm-40) REVERT: MA 134 LEU cc_start: 0.7765 (tt) cc_final: 0.7517 (pp) REVERT: NA 95 GLU cc_start: 0.5326 (tt0) cc_final: 0.4922 (tm-30) REVERT: OA 23 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8241 (tm-30) REVERT: OA 65 ASP cc_start: 0.7126 (p0) cc_final: 0.6454 (p0) REVERT: OA 95 GLU cc_start: 0.5534 (tt0) cc_final: 0.5242 (tm-30) REVERT: OA 134 LEU cc_start: 0.7254 (tp) cc_final: 0.7000 (pp) REVERT: RA 127 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7244 (mm-40) REVERT: RA 134 LEU cc_start: 0.7629 (tt) cc_final: 0.7377 (pp) REVERT: SA 95 GLU cc_start: 0.5176 (tt0) cc_final: 0.4786 (tm-30) REVERT: TA 23 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8257 (tm-30) REVERT: TA 65 ASP cc_start: 0.7125 (p0) cc_final: 0.6476 (p0) REVERT: TA 95 GLU cc_start: 0.5568 (tt0) cc_final: 0.5284 (tm-30) REVERT: TA 134 LEU cc_start: 0.7329 (tp) cc_final: 0.7106 (pp) REVERT: UA 134 LEU cc_start: 0.7568 (tp) cc_final: 0.7331 (pp) REVERT: WA 127 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7278 (mm-40) REVERT: WA 134 LEU cc_start: 0.7676 (tt) cc_final: 0.7423 (pp) REVERT: XA 37 MET cc_start: 0.7222 (ppp) cc_final: 0.6833 (ppp) REVERT: XA 95 GLU cc_start: 0.5243 (tt0) cc_final: 0.4863 (tm-30) REVERT: YA 23 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8256 (tm-30) REVERT: YA 65 ASP cc_start: 0.7110 (p0) cc_final: 0.6447 (p0) REVERT: YA 95 GLU cc_start: 0.5804 (tt0) cc_final: 0.5437 (tm-30) REVERT: YA 134 LEU cc_start: 0.7472 (tp) cc_final: 0.7269 (pp) REVERT: AB 23 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7814 (tm-30) REVERT: BB 127 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7274 (mm-40) REVERT: BB 134 LEU cc_start: 0.7762 (tt) cc_final: 0.7511 (pp) REVERT: CB 95 GLU cc_start: 0.5301 (tt0) cc_final: 0.4901 (tm-30) REVERT: DB 23 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8264 (tm-30) REVERT: DB 65 ASP cc_start: 0.7131 (p0) cc_final: 0.6484 (p0) REVERT: DB 95 GLU cc_start: 0.5530 (tt0) cc_final: 0.5235 (tm-30) REVERT: DB 134 LEU cc_start: 0.7337 (tp) cc_final: 0.7116 (pp) REVERT: FB 23 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7682 (tm-30) REVERT: GB 127 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7225 (mm-40) REVERT: GB 134 LEU cc_start: 0.7534 (tt) cc_final: 0.7282 (pp) REVERT: HB 95 GLU cc_start: 0.5240 (tt0) cc_final: 0.4852 (tm-30) REVERT: IB 23 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8319 (tm-30) REVERT: IB 65 ASP cc_start: 0.7114 (p0) cc_final: 0.6444 (p0) outliers start: 188 outliers final: 138 residues processed: 1197 average time/residue: 0.5718 time to fit residues: 1148.5865 Evaluate side-chains 1213 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1075 time to evaluate : 5.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 58 ASP Chi-restraints excluded: chain T residue 19 ILE Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain AA residue 11 THR Chi-restraints excluded: chain AA residue 25 LEU Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain CA residue 25 LEU Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 94 VAL Chi-restraints excluded: chain DA residue 25 LEU Chi-restraints excluded: chain EA residue 19 ILE Chi-restraints excluded: chain EA residue 25 LEU Chi-restraints excluded: chain EA residue 97 ILE Chi-restraints excluded: chain FA residue 11 THR Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 134 LEU Chi-restraints excluded: chain HA residue 25 LEU Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 25 LEU Chi-restraints excluded: chain IA residue 58 ASP Chi-restraints excluded: chain JA residue 19 ILE Chi-restraints excluded: chain JA residue 25 LEU Chi-restraints excluded: chain KA residue 11 THR Chi-restraints excluded: chain KA residue 25 LEU Chi-restraints excluded: chain KA residue 68 VAL Chi-restraints excluded: chain LA residue 68 VAL Chi-restraints excluded: chain MA residue 25 LEU Chi-restraints excluded: chain MA residue 70 THR Chi-restraints excluded: chain MA residue 94 VAL Chi-restraints excluded: chain NA residue 25 LEU Chi-restraints excluded: chain OA residue 19 ILE Chi-restraints excluded: chain OA residue 25 LEU Chi-restraints excluded: chain OA residue 27 THR Chi-restraints excluded: chain PA residue 11 THR Chi-restraints excluded: chain PA residue 25 LEU Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain RA residue 70 THR Chi-restraints excluded: chain RA residue 94 VAL Chi-restraints excluded: chain SA residue 25 LEU Chi-restraints excluded: chain TA residue 19 ILE Chi-restraints excluded: chain TA residue 25 LEU Chi-restraints excluded: chain UA residue 11 THR Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 94 VAL Chi-restraints excluded: chain VA residue 58 ASP Chi-restraints excluded: chain VA residue 68 VAL Chi-restraints excluded: chain VA residue 134 LEU Chi-restraints excluded: chain WA residue 25 LEU Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain WA residue 94 VAL Chi-restraints excluded: chain XA residue 25 LEU Chi-restraints excluded: chain XA residue 58 ASP Chi-restraints excluded: chain YA residue 19 ILE Chi-restraints excluded: chain YA residue 25 LEU Chi-restraints excluded: chain ZA residue 11 THR Chi-restraints excluded: chain ZA residue 25 LEU Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain AB residue 68 VAL Chi-restraints excluded: chain BB residue 25 LEU Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain BB residue 94 VAL Chi-restraints excluded: chain CB residue 25 LEU Chi-restraints excluded: chain CB residue 58 ASP Chi-restraints excluded: chain DB residue 19 ILE Chi-restraints excluded: chain DB residue 25 LEU Chi-restraints excluded: chain EB residue 11 THR Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain FB residue 68 VAL Chi-restraints excluded: chain FB residue 94 VAL Chi-restraints excluded: chain FB residue 134 LEU Chi-restraints excluded: chain GB residue 25 LEU Chi-restraints excluded: chain GB residue 70 THR Chi-restraints excluded: chain GB residue 94 VAL Chi-restraints excluded: chain HB residue 25 LEU Chi-restraints excluded: chain HB residue 58 ASP Chi-restraints excluded: chain IB residue 19 ILE Chi-restraints excluded: chain IB residue 25 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 4.9990 chunk 626 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 408 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 696 optimal weight: 7.9990 chunk 578 optimal weight: 8.9990 chunk 322 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 365 optimal weight: 1.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN D 23 GLN E 113 GLN F 23 GLN I 23 GLN J 113 GLN K 23 GLN L 23 GLN N 23 GLN O 113 GLN Q 23 GLN S 23 GLN T 113 GLN V 23 GLN W 23 GLN Y 23 GLN Z 113 GLN AA 23 GLN BA 23 GLN DA 23 GLN EA 113 GLN FA 23 GLN GA 23 GLN IA 23 GLN JA 113 GLN KA 23 GLN NA 23 GLN OA 113 GLN QA 23 GLN TA 113 GLN UA 23 GLN UA 124 GLN VA 23 GLN XA 23 GLN YA 113 GLN ZA 23 GLN CB 23 GLN DB 113 GLN EB 23 GLN HB 23 GLN IB 113 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 63000 Z= 0.389 Angle : 0.633 9.052 84540 Z= 0.330 Chirality : 0.047 0.170 10080 Planarity : 0.004 0.031 10740 Dihedral : 3.697 13.692 8100 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.89 % Allowed : 13.32 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.10), residues: 7380 helix: 3.49 (0.08), residues: 3540 sheet: -0.31 (0.12), residues: 1800 loop : -1.16 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 52 HIS 0.004 0.001 HISDB 85 PHE 0.012 0.003 PHE H 32 TYR 0.014 0.003 TYR A 82 ARG 0.008 0.001 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1331 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1046 time to evaluate : 5.893 Fit side-chains REVERT: B 23 GLN cc_start: 0.8398 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 58 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6668 (m-30) REVERT: D 95 GLU cc_start: 0.5508 (tt0) cc_final: 0.5136 (tm-30) REVERT: E 23 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8216 (tm-30) REVERT: E 65 ASP cc_start: 0.7107 (p0) cc_final: 0.6321 (p0) REVERT: E 95 GLU cc_start: 0.5602 (tt0) cc_final: 0.5321 (tm-30) REVERT: H 127 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7312 (mm-40) REVERT: H 134 LEU cc_start: 0.7730 (tt) cc_final: 0.7477 (pp) REVERT: I 37 MET cc_start: 0.7359 (ppp) cc_final: 0.7150 (ppp) REVERT: I 95 GLU cc_start: 0.5473 (tt0) cc_final: 0.5109 (tm-30) REVERT: J 23 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8254 (tm-30) REVERT: J 65 ASP cc_start: 0.7110 (p0) cc_final: 0.6326 (p0) REVERT: J 95 GLU cc_start: 0.5839 (tt0) cc_final: 0.5487 (tm-30) REVERT: L 23 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: N 95 GLU cc_start: 0.5405 (tt0) cc_final: 0.4961 (tm-30) REVERT: O 23 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8243 (tm-30) REVERT: O 65 ASP cc_start: 0.7134 (p0) cc_final: 0.6348 (p0) REVERT: O 95 GLU cc_start: 0.5831 (tt0) cc_final: 0.5480 (tm-30) REVERT: P 134 LEU cc_start: 0.7487 (tp) cc_final: 0.7257 (pp) REVERT: Q 23 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: R 127 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7265 (mm-40) REVERT: S 37 MET cc_start: 0.7399 (ppp) cc_final: 0.7091 (ppp) REVERT: S 95 GLU cc_start: 0.5436 (tt0) cc_final: 0.5082 (tm-30) REVERT: T 23 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8220 (tm-30) REVERT: T 65 ASP cc_start: 0.7084 (p0) cc_final: 0.6304 (p0) REVERT: V 134 LEU cc_start: 0.7471 (tp) cc_final: 0.7243 (pp) REVERT: W 23 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: Y 37 MET cc_start: 0.7412 (ppp) cc_final: 0.7102 (ppp) REVERT: Y 95 GLU cc_start: 0.5436 (tt0) cc_final: 0.5081 (tm-30) REVERT: Z 23 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8183 (tm-30) REVERT: Z 65 ASP cc_start: 0.7076 (p0) cc_final: 0.6294 (p0) REVERT: Z 95 GLU cc_start: 0.5866 (tt0) cc_final: 0.5510 (tm-30) REVERT: BA 23 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: CA 127 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7211 (mm-40) REVERT: DA 95 GLU cc_start: 0.5428 (tt0) cc_final: 0.5072 (tm-30) REVERT: EA 23 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8238 (tm-30) REVERT: EA 65 ASP cc_start: 0.7127 (p0) cc_final: 0.6341 (p0) REVERT: EA 95 GLU cc_start: 0.5841 (tt0) cc_final: 0.5559 (tm-30) REVERT: FA 46 GLN cc_start: 0.7209 (tp-100) cc_final: 0.7004 (tp-100) REVERT: GA 23 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7982 (tm-30) REVERT: HA 134 LEU cc_start: 0.7696 (tt) cc_final: 0.7429 (pp) REVERT: IA 37 MET cc_start: 0.7390 (ppp) cc_final: 0.7179 (ppp) REVERT: IA 95 GLU cc_start: 0.5443 (tt0) cc_final: 0.4988 (tm-30) REVERT: JA 23 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8273 (tm-30) REVERT: JA 65 ASP cc_start: 0.7113 (p0) cc_final: 0.6309 (p0) REVERT: JA 95 GLU cc_start: 0.5850 (tt0) cc_final: 0.5498 (tm-30) REVERT: LA 23 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8003 (tm-30) REVERT: MA 58 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6708 (m-30) REVERT: NA 95 GLU cc_start: 0.5533 (tt0) cc_final: 0.5159 (tm-30) REVERT: OA 23 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8194 (tm-30) REVERT: OA 65 ASP cc_start: 0.7094 (p0) cc_final: 0.6304 (p0) REVERT: OA 95 GLU cc_start: 0.5594 (tt0) cc_final: 0.5315 (tm-30) REVERT: QA 23 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: RA 127 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7287 (mm-40) REVERT: RA 134 LEU cc_start: 0.7642 (tt) cc_final: 0.7383 (pp) REVERT: SA 95 GLU cc_start: 0.5408 (tt0) cc_final: 0.4969 (tm-30) REVERT: TA 23 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8233 (tm-30) REVERT: TA 65 ASP cc_start: 0.7125 (p0) cc_final: 0.6341 (p0) REVERT: TA 95 GLU cc_start: 0.5626 (tt0) cc_final: 0.5354 (tm-30) REVERT: VA 23 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: XA 37 MET cc_start: 0.7390 (ppp) cc_final: 0.7099 (ppp) REVERT: XA 95 GLU cc_start: 0.5446 (tt0) cc_final: 0.5092 (tm-30) REVERT: YA 23 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8207 (tm-30) REVERT: YA 65 ASP cc_start: 0.7077 (p0) cc_final: 0.6296 (p0) REVERT: YA 95 GLU cc_start: 0.5873 (tt0) cc_final: 0.5581 (tm-30) REVERT: AB 23 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7993 (tm-30) REVERT: BB 58 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6716 (m-30) REVERT: CB 95 GLU cc_start: 0.5508 (tt0) cc_final: 0.5136 (tm-30) REVERT: DB 23 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8237 (tm-30) REVERT: DB 65 ASP cc_start: 0.7129 (p0) cc_final: 0.6347 (p0) REVERT: DB 95 GLU cc_start: 0.5587 (tt0) cc_final: 0.5308 (tm-30) REVERT: FB 23 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7975 (tm-30) REVERT: GB 134 LEU cc_start: 0.7662 (tt) cc_final: 0.7402 (pp) REVERT: HB 95 GLU cc_start: 0.5450 (tt0) cc_final: 0.5085 (tm-30) REVERT: IB 23 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8276 (tm-30) REVERT: IB 65 ASP cc_start: 0.7078 (p0) cc_final: 0.6291 (p0) outliers start: 285 outliers final: 215 residues processed: 1201 average time/residue: 0.5724 time to fit residues: 1153.4196 Evaluate side-chains 1238 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1014 time to evaluate : 5.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 23 GLN Chi-restraints excluded: chain L residue 37 MET Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 23 GLN Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 58 ASP Chi-restraints excluded: chain T residue 19 ILE Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain T residue 97 ILE Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain W residue 23 GLN Chi-restraints excluded: chain W residue 58 ASP Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 110 MET Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 68 VAL Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain AA residue 11 THR Chi-restraints excluded: chain AA residue 25 LEU Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain BA residue 23 GLN Chi-restraints excluded: chain BA residue 37 MET Chi-restraints excluded: chain BA residue 58 ASP Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain BA residue 94 VAL Chi-restraints excluded: chain BA residue 98 LEU Chi-restraints excluded: chain BA residue 134 LEU Chi-restraints excluded: chain CA residue 26 ILE Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 94 VAL Chi-restraints excluded: chain DA residue 25 LEU Chi-restraints excluded: chain DA residue 58 ASP Chi-restraints excluded: chain EA residue 19 ILE Chi-restraints excluded: chain EA residue 25 LEU Chi-restraints excluded: chain EA residue 58 ASP Chi-restraints excluded: chain EA residue 68 VAL Chi-restraints excluded: chain FA residue 11 THR Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain GA residue 58 ASP Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 94 VAL Chi-restraints excluded: chain GA residue 98 LEU Chi-restraints excluded: chain GA residue 134 LEU Chi-restraints excluded: chain HA residue 25 LEU Chi-restraints excluded: chain HA residue 26 ILE Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 25 LEU Chi-restraints excluded: chain IA residue 58 ASP Chi-restraints excluded: chain JA residue 19 ILE Chi-restraints excluded: chain JA residue 25 LEU Chi-restraints excluded: chain JA residue 58 ASP Chi-restraints excluded: chain JA residue 68 VAL Chi-restraints excluded: chain KA residue 11 THR Chi-restraints excluded: chain KA residue 25 LEU Chi-restraints excluded: chain KA residue 68 VAL Chi-restraints excluded: chain LA residue 58 ASP Chi-restraints excluded: chain LA residue 68 VAL Chi-restraints excluded: chain LA residue 94 VAL Chi-restraints excluded: chain MA residue 25 LEU Chi-restraints excluded: chain MA residue 26 ILE Chi-restraints excluded: chain MA residue 58 ASP Chi-restraints excluded: chain MA residue 70 THR Chi-restraints excluded: chain MA residue 94 VAL Chi-restraints excluded: chain NA residue 25 LEU Chi-restraints excluded: chain NA residue 58 ASP Chi-restraints excluded: chain OA residue 19 ILE Chi-restraints excluded: chain OA residue 26 ILE Chi-restraints excluded: chain OA residue 68 VAL Chi-restraints excluded: chain OA residue 97 ILE Chi-restraints excluded: chain PA residue 11 THR Chi-restraints excluded: chain PA residue 25 LEU Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 23 GLN Chi-restraints excluded: chain QA residue 58 ASP Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain QA residue 94 VAL Chi-restraints excluded: chain QA residue 134 LEU Chi-restraints excluded: chain RA residue 26 ILE Chi-restraints excluded: chain RA residue 70 THR Chi-restraints excluded: chain RA residue 94 VAL Chi-restraints excluded: chain SA residue 25 LEU Chi-restraints excluded: chain SA residue 58 ASP Chi-restraints excluded: chain TA residue 19 ILE Chi-restraints excluded: chain TA residue 25 LEU Chi-restraints excluded: chain TA residue 58 ASP Chi-restraints excluded: chain TA residue 68 VAL Chi-restraints excluded: chain TA residue 97 ILE Chi-restraints excluded: chain UA residue 11 THR Chi-restraints excluded: chain UA residue 25 LEU Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 94 VAL Chi-restraints excluded: chain UA residue 124 GLN Chi-restraints excluded: chain VA residue 23 GLN Chi-restraints excluded: chain VA residue 58 ASP Chi-restraints excluded: chain VA residue 68 VAL Chi-restraints excluded: chain VA residue 94 VAL Chi-restraints excluded: chain VA residue 134 LEU Chi-restraints excluded: chain WA residue 26 ILE Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain WA residue 94 VAL Chi-restraints excluded: chain XA residue 25 LEU Chi-restraints excluded: chain XA residue 58 ASP Chi-restraints excluded: chain YA residue 19 ILE Chi-restraints excluded: chain YA residue 26 ILE Chi-restraints excluded: chain YA residue 58 ASP Chi-restraints excluded: chain YA residue 68 VAL Chi-restraints excluded: chain ZA residue 11 THR Chi-restraints excluded: chain ZA residue 25 LEU Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain AB residue 58 ASP Chi-restraints excluded: chain AB residue 68 VAL Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 134 LEU Chi-restraints excluded: chain BB residue 25 LEU Chi-restraints excluded: chain BB residue 26 ILE Chi-restraints excluded: chain BB residue 58 ASP Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain BB residue 94 VAL Chi-restraints excluded: chain BB residue 106 ASP Chi-restraints excluded: chain CB residue 25 LEU Chi-restraints excluded: chain CB residue 58 ASP Chi-restraints excluded: chain DB residue 19 ILE Chi-restraints excluded: chain DB residue 25 LEU Chi-restraints excluded: chain DB residue 68 VAL Chi-restraints excluded: chain DB residue 97 ILE Chi-restraints excluded: chain EB residue 11 THR Chi-restraints excluded: chain EB residue 25 LEU Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain FB residue 58 ASP Chi-restraints excluded: chain FB residue 68 VAL Chi-restraints excluded: chain FB residue 94 VAL Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain FB residue 134 LEU Chi-restraints excluded: chain GB residue 25 LEU Chi-restraints excluded: chain GB residue 26 ILE Chi-restraints excluded: chain GB residue 70 THR Chi-restraints excluded: chain GB residue 94 VAL Chi-restraints excluded: chain HB residue 25 LEU Chi-restraints excluded: chain HB residue 58 ASP Chi-restraints excluded: chain IB residue 19 ILE Chi-restraints excluded: chain IB residue 26 ILE Chi-restraints excluded: chain IB residue 58 ASP Chi-restraints excluded: chain IB residue 68 VAL Chi-restraints excluded: chain IB residue 97 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 671 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 396 optimal weight: 5.9990 chunk 508 optimal weight: 4.9990 chunk 394 optimal weight: 10.0000 chunk 586 optimal weight: 0.5980 chunk 389 optimal weight: 7.9990 chunk 693 optimal weight: 5.9990 chunk 434 optimal weight: 2.9990 chunk 423 optimal weight: 4.9990 chunk 320 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN D 23 GLN F 23 GLN G 23 GLN I 23 GLN K 23 GLN N 23 GLN S 23 GLN V 23 GLN Y 23 GLN AA 23 GLN DA 23 GLN FA 23 GLN IA 23 GLN KA 23 GLN NA 23 GLN SA 23 GLN UA 23 GLN XA 23 GLN ZA 23 GLN EB 23 GLN HB 23 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5226 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 63000 Z= 0.345 Angle : 0.618 9.764 84540 Z= 0.321 Chirality : 0.046 0.142 10080 Planarity : 0.004 0.031 10740 Dihedral : 3.640 13.360 8100 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.77 % Allowed : 13.77 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.10), residues: 7380 helix: 3.44 (0.08), residues: 3540 sheet: -0.40 (0.12), residues: 1800 loop : -1.11 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP W 52 HIS 0.003 0.001 HISDB 85 PHE 0.011 0.002 PHERA 32 TYR 0.011 0.002 TYR T 82 ARG 0.008 0.001 ARG V 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1049 time to evaluate : 5.878 Fit side-chains REVERT: B 23 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8111 (tm-30) REVERT: C 46 GLN cc_start: 0.7718 (tp40) cc_final: 0.7502 (tp-100) REVERT: C 58 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: D 95 GLU cc_start: 0.5510 (tt0) cc_final: 0.5146 (tm-30) REVERT: E 23 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8192 (tm-30) REVERT: E 65 ASP cc_start: 0.7113 (p0) cc_final: 0.6343 (p0) REVERT: E 95 GLU cc_start: 0.5601 (tt0) cc_final: 0.5320 (tm-30) REVERT: G 23 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7721 (tm130) REVERT: I 95 GLU cc_start: 0.5473 (tt0) cc_final: 0.5119 (tm-30) REVERT: J 23 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8249 (tm-30) REVERT: J 65 ASP cc_start: 0.7099 (p0) cc_final: 0.6331 (p0) REVERT: J 95 GLU cc_start: 0.5846 (tt0) cc_final: 0.5493 (tm-30) REVERT: N 95 GLU cc_start: 0.5495 (tt0) cc_final: 0.5076 (tm-30) REVERT: O 23 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8246 (tm-30) REVERT: O 65 ASP cc_start: 0.7123 (p0) cc_final: 0.6350 (p0) REVERT: O 95 GLU cc_start: 0.5839 (tt0) cc_final: 0.5487 (tm-30) REVERT: P 134 LEU cc_start: 0.7470 (tp) cc_final: 0.7241 (pp) REVERT: S 95 GLU cc_start: 0.5432 (tt0) cc_final: 0.5086 (tm-30) REVERT: T 23 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8230 (tm-30) REVERT: T 65 ASP cc_start: 0.7091 (p0) cc_final: 0.6372 (p0) REVERT: V 134 LEU cc_start: 0.7456 (tp) cc_final: 0.7230 (pp) REVERT: Y 95 GLU cc_start: 0.5431 (tt0) cc_final: 0.5085 (tm-30) REVERT: Z 23 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8197 (tm-30) REVERT: Z 65 ASP cc_start: 0.7084 (p0) cc_final: 0.6364 (p0) REVERT: Z 95 GLU cc_start: 0.5872 (tt0) cc_final: 0.5517 (tm-30) REVERT: DA 95 GLU cc_start: 0.5429 (tt0) cc_final: 0.5081 (tm-30) REVERT: EA 23 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8240 (tm-30) REVERT: EA 65 ASP cc_start: 0.7116 (p0) cc_final: 0.6344 (p0) REVERT: EA 95 GLU cc_start: 0.5844 (tt0) cc_final: 0.5494 (tm-30) REVERT: FA 46 GLN cc_start: 0.7218 (tp-100) cc_final: 0.7008 (tp-100) REVERT: GA 23 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7934 (tm-30) REVERT: IA 37 MET cc_start: 0.7408 (ppp) cc_final: 0.7205 (ppp) REVERT: IA 95 GLU cc_start: 0.5444 (tt0) cc_final: 0.4999 (tm-30) REVERT: JA 23 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8275 (tm-30) REVERT: JA 65 ASP cc_start: 0.7101 (p0) cc_final: 0.6382 (p0) REVERT: JA 95 GLU cc_start: 0.5858 (tt0) cc_final: 0.5504 (tm-30) REVERT: LA 23 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8129 (tm-30) REVERT: MA 58 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6689 (m-30) REVERT: NA 95 GLU cc_start: 0.5535 (tt0) cc_final: 0.5169 (tm-30) REVERT: OA 23 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8178 (tm-30) REVERT: OA 65 ASP cc_start: 0.7097 (p0) cc_final: 0.6368 (p0) REVERT: OA 95 GLU cc_start: 0.5575 (tt0) cc_final: 0.5296 (tm-30) REVERT: SA 95 GLU cc_start: 0.5493 (tt0) cc_final: 0.5080 (tm-30) REVERT: TA 23 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8207 (tm-30) REVERT: TA 65 ASP cc_start: 0.7114 (p0) cc_final: 0.6343 (p0) REVERT: TA 95 GLU cc_start: 0.5609 (tt0) cc_final: 0.5336 (tm-30) REVERT: XA 95 GLU cc_start: 0.5442 (tt0) cc_final: 0.5095 (tm-30) REVERT: YA 23 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8218 (tm-30) REVERT: YA 65 ASP cc_start: 0.7084 (p0) cc_final: 0.6364 (p0) REVERT: YA 95 GLU cc_start: 0.5879 (tt0) cc_final: 0.5519 (tm-30) REVERT: AB 23 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8119 (tm-30) REVERT: BB 58 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6700 (m-30) REVERT: CB 95 GLU cc_start: 0.5511 (tt0) cc_final: 0.5146 (tm-30) REVERT: DB 23 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8249 (tm-30) REVERT: DB 65 ASP cc_start: 0.7117 (p0) cc_final: 0.6350 (p0) REVERT: DB 95 GLU cc_start: 0.5570 (tt0) cc_final: 0.5292 (tm-30) REVERT: FB 23 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7946 (tm-30) REVERT: HB 95 GLU cc_start: 0.5450 (tt0) cc_final: 0.5096 (tm-30) REVERT: IB 23 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8247 (tm-30) REVERT: IB 65 ASP cc_start: 0.7085 (p0) cc_final: 0.6357 (p0) outliers start: 276 outliers final: 233 residues processed: 1195 average time/residue: 0.5707 time to fit residues: 1144.0582 Evaluate side-chains 1264 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1027 time to evaluate : 5.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 23 GLN Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 58 ASP Chi-restraints excluded: chain T residue 19 ILE Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 97 ILE Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 23 GLN Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain W residue 58 ASP Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 26 ILE Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 68 VAL Chi-restraints excluded: chain AA residue 11 THR Chi-restraints excluded: chain AA residue 23 GLN Chi-restraints excluded: chain AA residue 25 LEU Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain BA residue 58 ASP Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain BA residue 94 VAL Chi-restraints excluded: chain BA residue 98 LEU Chi-restraints excluded: chain BA residue 134 LEU Chi-restraints excluded: chain CA residue 25 LEU Chi-restraints excluded: chain CA residue 26 ILE Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 94 VAL Chi-restraints excluded: chain DA residue 25 LEU Chi-restraints excluded: chain DA residue 58 ASP Chi-restraints excluded: chain EA residue 19 ILE Chi-restraints excluded: chain EA residue 25 LEU Chi-restraints excluded: chain EA residue 58 ASP Chi-restraints excluded: chain EA residue 68 VAL Chi-restraints excluded: chain FA residue 11 THR Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain GA residue 58 ASP Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 94 VAL Chi-restraints excluded: chain GA residue 98 LEU Chi-restraints excluded: chain GA residue 110 MET Chi-restraints excluded: chain GA residue 134 LEU Chi-restraints excluded: chain HA residue 25 LEU Chi-restraints excluded: chain HA residue 26 ILE Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 25 LEU Chi-restraints excluded: chain IA residue 58 ASP Chi-restraints excluded: chain JA residue 19 ILE Chi-restraints excluded: chain JA residue 25 LEU Chi-restraints excluded: chain JA residue 58 ASP Chi-restraints excluded: chain KA residue 11 THR Chi-restraints excluded: chain KA residue 23 GLN Chi-restraints excluded: chain KA residue 25 LEU Chi-restraints excluded: chain KA residue 68 VAL Chi-restraints excluded: chain KA residue 94 VAL Chi-restraints excluded: chain LA residue 58 ASP Chi-restraints excluded: chain LA residue 68 VAL Chi-restraints excluded: chain LA residue 94 VAL Chi-restraints excluded: chain LA residue 98 LEU Chi-restraints excluded: chain MA residue 25 LEU Chi-restraints excluded: chain MA residue 26 ILE Chi-restraints excluded: chain MA residue 58 ASP Chi-restraints excluded: chain MA residue 70 THR Chi-restraints excluded: chain MA residue 94 VAL Chi-restraints excluded: chain NA residue 25 LEU Chi-restraints excluded: chain NA residue 58 ASP Chi-restraints excluded: chain OA residue 19 ILE Chi-restraints excluded: chain OA residue 25 LEU Chi-restraints excluded: chain OA residue 26 ILE Chi-restraints excluded: chain OA residue 58 ASP Chi-restraints excluded: chain OA residue 68 VAL Chi-restraints excluded: chain OA residue 97 ILE Chi-restraints excluded: chain PA residue 11 THR Chi-restraints excluded: chain PA residue 25 LEU Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 58 ASP Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain QA residue 94 VAL Chi-restraints excluded: chain QA residue 98 LEU Chi-restraints excluded: chain QA residue 110 MET Chi-restraints excluded: chain QA residue 134 LEU Chi-restraints excluded: chain RA residue 26 ILE Chi-restraints excluded: chain RA residue 70 THR Chi-restraints excluded: chain RA residue 94 VAL Chi-restraints excluded: chain SA residue 25 LEU Chi-restraints excluded: chain SA residue 58 ASP Chi-restraints excluded: chain TA residue 19 ILE Chi-restraints excluded: chain TA residue 25 LEU Chi-restraints excluded: chain TA residue 97 ILE Chi-restraints excluded: chain UA residue 11 THR Chi-restraints excluded: chain UA residue 23 GLN Chi-restraints excluded: chain UA residue 25 LEU Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 94 VAL Chi-restraints excluded: chain UA residue 124 GLN Chi-restraints excluded: chain VA residue 58 ASP Chi-restraints excluded: chain VA residue 68 VAL Chi-restraints excluded: chain VA residue 94 VAL Chi-restraints excluded: chain VA residue 110 MET Chi-restraints excluded: chain VA residue 134 LEU Chi-restraints excluded: chain WA residue 25 LEU Chi-restraints excluded: chain WA residue 26 ILE Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain WA residue 94 VAL Chi-restraints excluded: chain XA residue 25 LEU Chi-restraints excluded: chain XA residue 58 ASP Chi-restraints excluded: chain YA residue 19 ILE Chi-restraints excluded: chain YA residue 25 LEU Chi-restraints excluded: chain YA residue 26 ILE Chi-restraints excluded: chain YA residue 58 ASP Chi-restraints excluded: chain ZA residue 11 THR Chi-restraints excluded: chain ZA residue 23 GLN Chi-restraints excluded: chain ZA residue 25 LEU Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain ZA residue 94 VAL Chi-restraints excluded: chain AB residue 58 ASP Chi-restraints excluded: chain AB residue 68 VAL Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 98 LEU Chi-restraints excluded: chain AB residue 110 MET Chi-restraints excluded: chain AB residue 134 LEU Chi-restraints excluded: chain BB residue 25 LEU Chi-restraints excluded: chain BB residue 26 ILE Chi-restraints excluded: chain BB residue 58 ASP Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain BB residue 94 VAL Chi-restraints excluded: chain BB residue 106 ASP Chi-restraints excluded: chain CB residue 25 LEU Chi-restraints excluded: chain CB residue 58 ASP Chi-restraints excluded: chain DB residue 19 ILE Chi-restraints excluded: chain DB residue 25 LEU Chi-restraints excluded: chain DB residue 58 ASP Chi-restraints excluded: chain DB residue 68 VAL Chi-restraints excluded: chain DB residue 97 ILE Chi-restraints excluded: chain EB residue 11 THR Chi-restraints excluded: chain EB residue 23 GLN Chi-restraints excluded: chain EB residue 25 LEU Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain FB residue 58 ASP Chi-restraints excluded: chain FB residue 68 VAL Chi-restraints excluded: chain FB residue 94 VAL Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain FB residue 134 LEU Chi-restraints excluded: chain GB residue 25 LEU Chi-restraints excluded: chain GB residue 26 ILE Chi-restraints excluded: chain GB residue 70 THR Chi-restraints excluded: chain GB residue 94 VAL Chi-restraints excluded: chain HB residue 25 LEU Chi-restraints excluded: chain HB residue 58 ASP Chi-restraints excluded: chain IB residue 19 ILE Chi-restraints excluded: chain IB residue 25 LEU Chi-restraints excluded: chain IB residue 26 ILE Chi-restraints excluded: chain IB residue 58 ASP Chi-restraints excluded: chain IB residue 68 VAL Chi-restraints excluded: chain IB residue 97 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 429 optimal weight: 7.9990 chunk 277 optimal weight: 10.0000 chunk 414 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 441 optimal weight: 0.8980 chunk 472 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 545 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN D 23 GLN F 23 GLN G 23 GLN I 23 GLN K 23 GLN L 23 GLN N 23 GLN Q 23 GLN S 23 GLN V 23 GLN W 23 GLN Y 23 GLN AA 23 GLN BA 23 GLN DA 23 GLN FA 23 GLN IA 23 GLN KA 23 GLN NA 23 GLN QA 23 GLN SA 23 GLN UA 23 GLN UA 124 GLN VA 23 GLN XA 23 GLN ZA 23 GLN CB 23 GLN EB 23 GLN HB 23 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5199 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 63000 Z= 0.198 Angle : 0.563 10.943 84540 Z= 0.291 Chirality : 0.044 0.139 10080 Planarity : 0.004 0.032 10740 Dihedral : 3.241 11.269 8100 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.49 % Allowed : 15.20 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.10), residues: 7380 helix: 3.97 (0.08), residues: 3540 sheet: -0.11 (0.12), residues: 1800 loop : -1.04 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRPTA 52 HIS 0.001 0.001 HIS Y 85 PHE 0.004 0.001 PHEHA 32 TYR 0.007 0.001 TYROA 82 ARG 0.009 0.001 ARG K 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1148 time to evaluate : 5.783 Fit side-chains REVERT: B 4 ILE cc_start: 0.7045 (mt) cc_final: 0.6836 (tt) REVERT: C 46 GLN cc_start: 0.7661 (tp40) cc_final: 0.7451 (tp-100) REVERT: C 127 GLN cc_start: 0.7453 (mm-40) cc_final: 0.7232 (mm-40) REVERT: D 95 GLU cc_start: 0.5533 (tt0) cc_final: 0.5098 (tm-30) REVERT: E 23 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8187 (tm-30) REVERT: E 65 ASP cc_start: 0.7100 (p0) cc_final: 0.6438 (p0) REVERT: E 95 GLU cc_start: 0.5596 (tt0) cc_final: 0.5306 (tm-30) REVERT: E 134 LEU cc_start: 0.7337 (tp) cc_final: 0.7101 (pp) REVERT: H 46 GLN cc_start: 0.7644 (tp40) cc_final: 0.7433 (tp-100) REVERT: H 127 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7238 (mm-40) REVERT: I 95 GLU cc_start: 0.5472 (tt0) cc_final: 0.5016 (tm-30) REVERT: J 23 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8209 (tm-30) REVERT: J 65 ASP cc_start: 0.6953 (p0) cc_final: 0.6268 (p0) REVERT: J 95 GLU cc_start: 0.5826 (tt0) cc_final: 0.5464 (tm-30) REVERT: J 134 LEU cc_start: 0.7521 (tp) cc_final: 0.7313 (pp) REVERT: L 4 ILE cc_start: 0.7039 (mt) cc_final: 0.6834 (tt) REVERT: L 23 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: M 127 GLN cc_start: 0.7401 (mm-40) cc_final: 0.7201 (mm-40) REVERT: N 95 GLU cc_start: 0.5300 (tt0) cc_final: 0.4920 (tm-30) REVERT: O 23 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8178 (tm-30) REVERT: O 65 ASP cc_start: 0.7094 (p0) cc_final: 0.6428 (p0) REVERT: O 95 GLU cc_start: 0.5825 (tt0) cc_final: 0.5466 (tm-30) REVERT: O 134 LEU cc_start: 0.7286 (tp) cc_final: 0.7065 (pp) REVERT: Q 23 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: R 127 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7196 (mm-40) REVERT: S 95 GLU cc_start: 0.5468 (tt0) cc_final: 0.5054 (tm-30) REVERT: T 23 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8253 (tm-30) REVERT: T 65 ASP cc_start: 0.7082 (p0) cc_final: 0.6425 (p0) REVERT: T 134 LEU cc_start: 0.7344 (tp) cc_final: 0.7085 (pp) REVERT: W 23 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: Y 28 ILE cc_start: 0.6421 (mt) cc_final: 0.6174 (tt) REVERT: Y 95 GLU cc_start: 0.5469 (tt0) cc_final: 0.5054 (tm-30) REVERT: Z 23 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8222 (tm-30) REVERT: Z 65 ASP cc_start: 0.7074 (p0) cc_final: 0.6416 (p0) REVERT: Z 95 GLU cc_start: 0.5853 (tt0) cc_final: 0.5487 (tm-30) REVERT: Z 134 LEU cc_start: 0.7330 (tp) cc_final: 0.7130 (pp) REVERT: BA 4 ILE cc_start: 0.7032 (mt) cc_final: 0.6822 (tt) REVERT: BA 23 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: CA 127 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7218 (mm-40) REVERT: DA 95 GLU cc_start: 0.5451 (tt0) cc_final: 0.5034 (tm-30) REVERT: EA 23 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8172 (tm-30) REVERT: EA 65 ASP cc_start: 0.7089 (p0) cc_final: 0.6422 (p0) REVERT: EA 95 GLU cc_start: 0.5834 (tt0) cc_final: 0.5474 (tm-30) REVERT: EA 134 LEU cc_start: 0.7237 (tp) cc_final: 0.7020 (pp) REVERT: HA 127 GLN cc_start: 0.7390 (mm-40) cc_final: 0.7176 (mm-40) REVERT: IA 95 GLU cc_start: 0.5323 (tt0) cc_final: 0.4936 (tm-30) REVERT: JA 23 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8237 (tm-30) REVERT: JA 65 ASP cc_start: 0.6953 (p0) cc_final: 0.6269 (p0) REVERT: JA 95 GLU cc_start: 0.5837 (tt0) cc_final: 0.5475 (tm-30) REVERT: JA 134 LEU cc_start: 0.7511 (tp) cc_final: 0.7304 (pp) REVERT: MA 127 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7318 (mm-40) REVERT: NA 28 ILE cc_start: 0.6404 (mt) cc_final: 0.6130 (tt) REVERT: NA 95 GLU cc_start: 0.5554 (tt0) cc_final: 0.5116 (tm-30) REVERT: OA 23 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8140 (tm-30) REVERT: OA 65 ASP cc_start: 0.7087 (p0) cc_final: 0.6421 (p0) REVERT: OA 95 GLU cc_start: 0.5588 (tt0) cc_final: 0.5300 (tm-30) REVERT: OA 134 LEU cc_start: 0.7252 (tp) cc_final: 0.6976 (pp) REVERT: QA 23 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7730 (tm-30) REVERT: RA 127 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7227 (mm-40) REVERT: SA 95 GLU cc_start: 0.5313 (tt0) cc_final: 0.4933 (tm-30) REVERT: TA 23 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8179 (tm-30) REVERT: TA 65 ASP cc_start: 0.7086 (p0) cc_final: 0.6414 (p0) REVERT: TA 95 GLU cc_start: 0.5621 (tt0) cc_final: 0.5340 (tm-30) REVERT: TA 134 LEU cc_start: 0.7288 (tp) cc_final: 0.7082 (pp) REVERT: VA 23 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: WA 127 GLN cc_start: 0.7382 (mm-40) cc_final: 0.7179 (mm-40) REVERT: XA 95 GLU cc_start: 0.5478 (tt0) cc_final: 0.5062 (tm-30) REVERT: YA 23 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8242 (tm-30) REVERT: YA 65 ASP cc_start: 0.7075 (p0) cc_final: 0.6417 (p0) REVERT: YA 95 GLU cc_start: 0.5859 (tt0) cc_final: 0.5491 (tm-30) REVERT: YA 134 LEU cc_start: 0.7325 (tp) cc_final: 0.7097 (pp) REVERT: BB 127 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7324 (mm-40) REVERT: CB 95 GLU cc_start: 0.5533 (tt0) cc_final: 0.5097 (tm-30) REVERT: DB 23 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8191 (tm-30) REVERT: DB 65 ASP cc_start: 0.6975 (p0) cc_final: 0.6290 (p0) REVERT: DB 95 GLU cc_start: 0.5581 (tt0) cc_final: 0.5292 (tm-30) REVERT: DB 134 LEU cc_start: 0.7183 (tp) cc_final: 0.6939 (pp) REVERT: FB 4 ILE cc_start: 0.7023 (mt) cc_final: 0.6809 (tt) REVERT: FB 23 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8033 (tm-30) REVERT: GB 58 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6527 (m-30) REVERT: HB 95 GLU cc_start: 0.5450 (tt0) cc_final: 0.4995 (tm-30) REVERT: IB 23 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8279 (tm-30) REVERT: IB 65 ASP cc_start: 0.7067 (p0) cc_final: 0.6424 (p0) outliers start: 182 outliers final: 152 residues processed: 1232 average time/residue: 0.5654 time to fit residues: 1174.8829 Evaluate side-chains 1242 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1083 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain L residue 23 GLN Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 23 GLN Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain T residue 19 ILE Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain W residue 23 GLN Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain Y residue 23 GLN Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain AA residue 11 THR Chi-restraints excluded: chain AA residue 25 LEU Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain BA residue 23 GLN Chi-restraints excluded: chain BA residue 58 ASP Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain BA residue 94 VAL Chi-restraints excluded: chain BA residue 98 LEU Chi-restraints excluded: chain BA residue 134 LEU Chi-restraints excluded: chain CA residue 94 VAL Chi-restraints excluded: chain DA residue 23 GLN Chi-restraints excluded: chain DA residue 25 LEU Chi-restraints excluded: chain EA residue 19 ILE Chi-restraints excluded: chain EA residue 25 LEU Chi-restraints excluded: chain FA residue 11 THR Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 94 VAL Chi-restraints excluded: chain GA residue 98 LEU Chi-restraints excluded: chain GA residue 134 LEU Chi-restraints excluded: chain HA residue 25 LEU Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 23 GLN Chi-restraints excluded: chain IA residue 25 LEU Chi-restraints excluded: chain IA residue 58 ASP Chi-restraints excluded: chain JA residue 19 ILE Chi-restraints excluded: chain JA residue 25 LEU Chi-restraints excluded: chain KA residue 11 THR Chi-restraints excluded: chain KA residue 25 LEU Chi-restraints excluded: chain KA residue 68 VAL Chi-restraints excluded: chain LA residue 68 VAL Chi-restraints excluded: chain LA residue 94 VAL Chi-restraints excluded: chain LA residue 98 LEU Chi-restraints excluded: chain MA residue 25 LEU Chi-restraints excluded: chain MA residue 94 VAL Chi-restraints excluded: chain NA residue 7 MET Chi-restraints excluded: chain NA residue 58 ASP Chi-restraints excluded: chain OA residue 19 ILE Chi-restraints excluded: chain OA residue 25 LEU Chi-restraints excluded: chain PA residue 11 THR Chi-restraints excluded: chain PA residue 25 LEU Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 23 GLN Chi-restraints excluded: chain QA residue 58 ASP Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain QA residue 94 VAL Chi-restraints excluded: chain QA residue 98 LEU Chi-restraints excluded: chain QA residue 134 LEU Chi-restraints excluded: chain RA residue 94 VAL Chi-restraints excluded: chain SA residue 25 LEU Chi-restraints excluded: chain TA residue 19 ILE Chi-restraints excluded: chain TA residue 25 LEU Chi-restraints excluded: chain UA residue 11 THR Chi-restraints excluded: chain UA residue 25 LEU Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 94 VAL Chi-restraints excluded: chain UA residue 124 GLN Chi-restraints excluded: chain VA residue 23 GLN Chi-restraints excluded: chain VA residue 58 ASP Chi-restraints excluded: chain VA residue 68 VAL Chi-restraints excluded: chain VA residue 94 VAL Chi-restraints excluded: chain VA residue 134 LEU Chi-restraints excluded: chain WA residue 28 ILE Chi-restraints excluded: chain WA residue 94 VAL Chi-restraints excluded: chain XA residue 7 MET Chi-restraints excluded: chain XA residue 23 GLN Chi-restraints excluded: chain XA residue 58 ASP Chi-restraints excluded: chain YA residue 19 ILE Chi-restraints excluded: chain YA residue 25 LEU Chi-restraints excluded: chain ZA residue 11 THR Chi-restraints excluded: chain ZA residue 25 LEU Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain AB residue 68 VAL Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 98 LEU Chi-restraints excluded: chain BB residue 25 LEU Chi-restraints excluded: chain BB residue 94 VAL Chi-restraints excluded: chain CB residue 23 GLN Chi-restraints excluded: chain CB residue 25 LEU Chi-restraints excluded: chain CB residue 58 ASP Chi-restraints excluded: chain DB residue 19 ILE Chi-restraints excluded: chain DB residue 25 LEU Chi-restraints excluded: chain EB residue 11 THR Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain FB residue 68 VAL Chi-restraints excluded: chain FB residue 94 VAL Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain FB residue 134 LEU Chi-restraints excluded: chain GB residue 25 LEU Chi-restraints excluded: chain GB residue 58 ASP Chi-restraints excluded: chain GB residue 94 VAL Chi-restraints excluded: chain HB residue 25 LEU Chi-restraints excluded: chain HB residue 58 ASP Chi-restraints excluded: chain IB residue 19 ILE Chi-restraints excluded: chain IB residue 25 LEU Chi-restraints excluded: chain IB residue 68 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 631 optimal weight: 8.9990 chunk 664 optimal weight: 0.4980 chunk 606 optimal weight: 2.9990 chunk 646 optimal weight: 9.9990 chunk 389 optimal weight: 5.9990 chunk 281 optimal weight: 7.9990 chunk 507 optimal weight: 8.9990 chunk 198 optimal weight: 8.9990 chunk 584 optimal weight: 3.9990 chunk 611 optimal weight: 9.9990 chunk 644 optimal weight: 10.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN B 23 GLN B 113 GLN D 23 GLN F 23 GLN G 23 GLN G 113 GLN I 23 GLN K 23 GLN L 23 GLN L 113 GLN N 23 GLN Q 23 GLN S 23 GLN V 23 GLN W 23 GLN Y 23 GLN AA 23 GLN BA 23 GLN BA 113 GLN DA 23 GLN FA 23 GLN GA 23 GLN KA 23 GLN LA 23 GLN LA 113 GLN NA 23 GLN QA 23 GLN QA 113 GLN SA 23 GLN UA 23 GLN VA 23 GLN XA 23 GLN ZA 23 GLN AB 23 GLN AB 113 GLN CB 23 GLN EB 23 GLN FB 113 GLN HB 23 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5227 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 63000 Z= 0.389 Angle : 0.675 12.031 84540 Z= 0.349 Chirality : 0.047 0.189 10080 Planarity : 0.004 0.032 10740 Dihedral : 3.650 13.202 8100 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.79 % Allowed : 15.52 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.10), residues: 7380 helix: 3.48 (0.08), residues: 3540 sheet: -0.30 (0.12), residues: 1800 loop : -1.12 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPYA 52 HIS 0.004 0.001 HISVA 85 PHE 0.013 0.003 PHEGB 32 TYR 0.016 0.003 TYRAB 82 ARG 0.008 0.001 ARG P 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1052 time to evaluate : 5.830 Fit side-chains REVERT: C 58 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6323 (m-30) REVERT: D 95 GLU cc_start: 0.5512 (tt0) cc_final: 0.5144 (tm-30) REVERT: E 23 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8178 (tm-30) REVERT: E 65 ASP cc_start: 0.7092 (p0) cc_final: 0.6315 (p0) REVERT: E 95 GLU cc_start: 0.5602 (tt0) cc_final: 0.5323 (tm-30) REVERT: I 95 GLU cc_start: 0.5476 (tt0) cc_final: 0.5124 (tm-30) REVERT: J 23 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8220 (tm-30) REVERT: J 65 ASP cc_start: 0.7089 (p0) cc_final: 0.6319 (p0) REVERT: J 95 GLU cc_start: 0.5846 (tt0) cc_final: 0.5490 (tm-30) REVERT: L 23 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: M 7 MET cc_start: 0.6079 (mtp) cc_final: 0.5872 (mtt) REVERT: M 46 GLN cc_start: 0.7449 (tp40) cc_final: 0.7218 (tp-100) REVERT: N 95 GLU cc_start: 0.5432 (tt0) cc_final: 0.4989 (tm-30) REVERT: O 23 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8189 (tm-30) REVERT: O 65 ASP cc_start: 0.7114 (p0) cc_final: 0.6340 (p0) REVERT: O 95 GLU cc_start: 0.5839 (tt0) cc_final: 0.5485 (tm-30) REVERT: O 134 LEU cc_start: 0.7291 (tp) cc_final: 0.7083 (pp) REVERT: Q 23 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: R 7 MET cc_start: 0.6082 (mtp) cc_final: 0.5610 (mtt) REVERT: S 95 GLU cc_start: 0.5436 (tt0) cc_final: 0.5087 (tm-30) REVERT: T 23 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8183 (tm-30) REVERT: T 65 ASP cc_start: 0.7065 (p0) cc_final: 0.6339 (p0) REVERT: W 23 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: X 7 MET cc_start: 0.6070 (mtp) cc_final: 0.5601 (mtt) REVERT: Y 95 GLU cc_start: 0.5435 (tt0) cc_final: 0.5086 (tm-30) REVERT: Z 23 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8149 (tm-30) REVERT: Z 65 ASP cc_start: 0.7058 (p0) cc_final: 0.6327 (p0) REVERT: Z 95 GLU cc_start: 0.5869 (tt0) cc_final: 0.5510 (tm-30) REVERT: AA 134 LEU cc_start: 0.7487 (tp) cc_final: 0.7249 (pp) REVERT: BA 23 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: CA 7 MET cc_start: 0.6065 (mtp) cc_final: 0.5595 (mtt) REVERT: DA 95 GLU cc_start: 0.5433 (tt0) cc_final: 0.5081 (tm-30) REVERT: EA 23 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8187 (tm-30) REVERT: EA 65 ASP cc_start: 0.7109 (p0) cc_final: 0.6336 (p0) REVERT: EA 95 GLU cc_start: 0.5848 (tt0) cc_final: 0.5494 (tm-30) REVERT: FA 134 LEU cc_start: 0.7334 (tp) cc_final: 0.7089 (pp) REVERT: IA 95 GLU cc_start: 0.5238 (tt0) cc_final: 0.4826 (tm-30) REVERT: JA 23 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8219 (tm-30) REVERT: JA 65 ASP cc_start: 0.7091 (p0) cc_final: 0.6372 (p0) REVERT: JA 95 GLU cc_start: 0.5857 (tt0) cc_final: 0.5501 (tm-30) REVERT: KA 134 LEU cc_start: 0.7392 (tp) cc_final: 0.7150 (pp) REVERT: MA 58 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6307 (m-30) REVERT: NA 95 GLU cc_start: 0.5535 (tt0) cc_final: 0.5166 (tm-30) REVERT: OA 23 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8157 (tm-30) REVERT: OA 65 ASP cc_start: 0.7074 (p0) cc_final: 0.6293 (p0) REVERT: OA 95 GLU cc_start: 0.5595 (tt0) cc_final: 0.5317 (tm-30) REVERT: PA 134 LEU cc_start: 0.7562 (tp) cc_final: 0.7303 (pp) REVERT: QA 23 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: SA 95 GLU cc_start: 0.5434 (tt0) cc_final: 0.4997 (tm-30) REVERT: TA 23 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8186 (tm-30) REVERT: TA 65 ASP cc_start: 0.7107 (p0) cc_final: 0.6331 (p0) REVERT: TA 95 GLU cc_start: 0.5629 (tt0) cc_final: 0.5358 (tm-30) REVERT: VA 23 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: WA 7 MET cc_start: 0.6106 (mtp) cc_final: 0.5843 (mtt) REVERT: XA 95 GLU cc_start: 0.5445 (tt0) cc_final: 0.5096 (tm-30) REVERT: YA 23 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8171 (tm-30) REVERT: YA 65 ASP cc_start: 0.7060 (p0) cc_final: 0.6310 (p0) REVERT: YA 95 GLU cc_start: 0.5877 (tt0) cc_final: 0.5515 (tm-30) REVERT: BB 58 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6455 (m-30) REVERT: CB 95 GLU cc_start: 0.5512 (tt0) cc_final: 0.5144 (tm-30) REVERT: DB 23 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8196 (tm-30) REVERT: DB 65 ASP cc_start: 0.7108 (p0) cc_final: 0.6339 (p0) REVERT: DB 95 GLU cc_start: 0.5587 (tt0) cc_final: 0.5309 (tm-30) REVERT: DB 134 LEU cc_start: 0.7222 (tp) cc_final: 0.6938 (pp) REVERT: EB 134 LEU cc_start: 0.7319 (tp) cc_final: 0.7092 (pp) REVERT: FB 23 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8038 (tm-30) REVERT: HB 95 GLU cc_start: 0.5452 (tt0) cc_final: 0.5099 (tm-30) REVERT: IB 23 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8239 (tm-30) REVERT: IB 65 ASP cc_start: 0.6949 (p0) cc_final: 0.6191 (p0) outliers start: 204 outliers final: 179 residues processed: 1159 average time/residue: 0.5754 time to fit residues: 1114.8357 Evaluate side-chains 1230 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1042 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 23 GLN Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain L residue 23 GLN Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 23 GLN Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 7 MET Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 58 ASP Chi-restraints excluded: chain T residue 19 ILE Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 23 GLN Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain W residue 23 GLN Chi-restraints excluded: chain W residue 58 ASP Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain Y residue 23 GLN Chi-restraints excluded: chain Y residue 58 ASP Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain AA residue 11 THR Chi-restraints excluded: chain AA residue 23 GLN Chi-restraints excluded: chain AA residue 25 LEU Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain BA residue 23 GLN Chi-restraints excluded: chain BA residue 58 ASP Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain BA residue 94 VAL Chi-restraints excluded: chain BA residue 98 LEU Chi-restraints excluded: chain BA residue 134 LEU Chi-restraints excluded: chain CA residue 25 LEU Chi-restraints excluded: chain CA residue 94 VAL Chi-restraints excluded: chain DA residue 23 GLN Chi-restraints excluded: chain DA residue 25 LEU Chi-restraints excluded: chain DA residue 58 ASP Chi-restraints excluded: chain EA residue 19 ILE Chi-restraints excluded: chain EA residue 25 LEU Chi-restraints excluded: chain FA residue 11 THR Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain GA residue 23 GLN Chi-restraints excluded: chain GA residue 58 ASP Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 94 VAL Chi-restraints excluded: chain GA residue 134 LEU Chi-restraints excluded: chain HA residue 25 LEU Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 25 LEU Chi-restraints excluded: chain IA residue 58 ASP Chi-restraints excluded: chain JA residue 19 ILE Chi-restraints excluded: chain JA residue 25 LEU Chi-restraints excluded: chain KA residue 11 THR Chi-restraints excluded: chain KA residue 23 GLN Chi-restraints excluded: chain KA residue 68 VAL Chi-restraints excluded: chain LA residue 23 GLN Chi-restraints excluded: chain LA residue 58 ASP Chi-restraints excluded: chain LA residue 68 VAL Chi-restraints excluded: chain LA residue 94 VAL Chi-restraints excluded: chain MA residue 58 ASP Chi-restraints excluded: chain MA residue 94 VAL Chi-restraints excluded: chain NA residue 7 MET Chi-restraints excluded: chain NA residue 23 GLN Chi-restraints excluded: chain NA residue 25 LEU Chi-restraints excluded: chain NA residue 58 ASP Chi-restraints excluded: chain OA residue 19 ILE Chi-restraints excluded: chain OA residue 25 LEU Chi-restraints excluded: chain OA residue 58 ASP Chi-restraints excluded: chain OA residue 97 ILE Chi-restraints excluded: chain PA residue 11 THR Chi-restraints excluded: chain PA residue 25 LEU Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 23 GLN Chi-restraints excluded: chain QA residue 58 ASP Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain QA residue 94 VAL Chi-restraints excluded: chain QA residue 134 LEU Chi-restraints excluded: chain RA residue 94 VAL Chi-restraints excluded: chain SA residue 23 GLN Chi-restraints excluded: chain SA residue 25 LEU Chi-restraints excluded: chain SA residue 58 ASP Chi-restraints excluded: chain TA residue 19 ILE Chi-restraints excluded: chain TA residue 25 LEU Chi-restraints excluded: chain UA residue 11 THR Chi-restraints excluded: chain UA residue 23 GLN Chi-restraints excluded: chain UA residue 25 LEU Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 94 VAL Chi-restraints excluded: chain UA residue 124 GLN Chi-restraints excluded: chain VA residue 23 GLN Chi-restraints excluded: chain VA residue 58 ASP Chi-restraints excluded: chain VA residue 68 VAL Chi-restraints excluded: chain VA residue 94 VAL Chi-restraints excluded: chain VA residue 134 LEU Chi-restraints excluded: chain WA residue 94 VAL Chi-restraints excluded: chain XA residue 7 MET Chi-restraints excluded: chain XA residue 23 GLN Chi-restraints excluded: chain XA residue 58 ASP Chi-restraints excluded: chain YA residue 19 ILE Chi-restraints excluded: chain ZA residue 11 THR Chi-restraints excluded: chain ZA residue 23 GLN Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain AB residue 23 GLN Chi-restraints excluded: chain AB residue 58 ASP Chi-restraints excluded: chain AB residue 68 VAL Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 134 LEU Chi-restraints excluded: chain BB residue 25 LEU Chi-restraints excluded: chain BB residue 58 ASP Chi-restraints excluded: chain BB residue 94 VAL Chi-restraints excluded: chain CB residue 23 GLN Chi-restraints excluded: chain CB residue 25 LEU Chi-restraints excluded: chain CB residue 58 ASP Chi-restraints excluded: chain DB residue 19 ILE Chi-restraints excluded: chain DB residue 25 LEU Chi-restraints excluded: chain DB residue 58 ASP Chi-restraints excluded: chain EB residue 11 THR Chi-restraints excluded: chain EB residue 23 GLN Chi-restraints excluded: chain EB residue 25 LEU Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain FB residue 68 VAL Chi-restraints excluded: chain FB residue 94 VAL Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain FB residue 134 LEU Chi-restraints excluded: chain GB residue 94 VAL Chi-restraints excluded: chain HB residue 23 GLN Chi-restraints excluded: chain HB residue 25 LEU Chi-restraints excluded: chain HB residue 58 ASP Chi-restraints excluded: chain IB residue 19 ILE Chi-restraints excluded: chain IB residue 25 LEU Chi-restraints excluded: chain IB residue 68 VAL Chi-restraints excluded: chain IB residue 97 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 424 optimal weight: 2.9990 chunk 683 optimal weight: 0.9980 chunk 417 optimal weight: 9.9990 chunk 324 optimal weight: 0.9990 chunk 475 optimal weight: 7.9990 chunk 717 optimal weight: 10.0000 chunk 660 optimal weight: 5.9990 chunk 571 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 441 optimal weight: 0.7980 chunk 350 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN B 23 GLN D 23 GLN F 23 GLN G 23 GLN I 23 GLN K 23 GLN L 23 GLN N 23 GLN Q 23 GLN S 23 GLN V 23 GLN V 124 GLN W 23 GLN Y 23 GLN AA 23 GLN BA 23 GLN DA 23 GLN FA 23 GLN GA 23 GLN IA 23 GLN KA 23 GLN LA 23 GLN NA 23 GLN QA 23 GLN SA 23 GLN UA 23 GLN UA 124 GLN VA 23 GLN XA 23 GLN ZA 23 GLN AB 23 GLN CB 23 GLN EB 23 GLN HB 23 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 63000 Z= 0.235 Angle : 0.599 12.870 84540 Z= 0.311 Chirality : 0.044 0.138 10080 Planarity : 0.004 0.033 10740 Dihedral : 3.410 13.232 8100 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.40 % Allowed : 15.90 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.10), residues: 7380 helix: 3.82 (0.08), residues: 3540 sheet: -0.15 (0.12), residues: 1800 loop : -1.00 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRPQA 52 HIS 0.001 0.001 HISDA 85 PHE 0.005 0.001 PHEGB 32 TYR 0.016 0.002 TYRLA 82 ARG 0.009 0.001 ARG P 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1087 time to evaluate : 5.863 Fit side-chains REVERT: B 23 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: C 46 GLN cc_start: 0.7622 (tp40) cc_final: 0.7370 (tp-100) REVERT: C 127 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7300 (mm-40) REVERT: D 95 GLU cc_start: 0.5511 (tt0) cc_final: 0.5044 (tm-30) REVERT: E 23 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8187 (tm-30) REVERT: E 65 ASP cc_start: 0.7076 (p0) cc_final: 0.6397 (p0) REVERT: E 95 GLU cc_start: 0.5605 (tt0) cc_final: 0.5317 (tm-30) REVERT: E 134 LEU cc_start: 0.7306 (tp) cc_final: 0.7106 (pp) REVERT: G 23 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: I 95 GLU cc_start: 0.5476 (tt0) cc_final: 0.5125 (tm-30) REVERT: J 23 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8205 (tm-30) REVERT: J 65 ASP cc_start: 0.7102 (p0) cc_final: 0.6403 (p0) REVERT: J 95 GLU cc_start: 0.5840 (tt0) cc_final: 0.5477 (tm-30) REVERT: N 95 GLU cc_start: 0.5315 (tt0) cc_final: 0.4933 (tm-30) REVERT: O 23 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8172 (tm-30) REVERT: O 65 ASP cc_start: 0.7126 (p0) cc_final: 0.6424 (p0) REVERT: O 95 GLU cc_start: 0.5835 (tt0) cc_final: 0.5477 (tm-30) REVERT: O 134 LEU cc_start: 0.7283 (tp) cc_final: 0.7061 (pp) REVERT: P 4 ILE cc_start: 0.6828 (mt) cc_final: 0.6576 (tt) REVERT: R 7 MET cc_start: 0.6102 (mtp) cc_final: 0.5591 (mtt) REVERT: R 46 GLN cc_start: 0.7519 (tp40) cc_final: 0.7287 (tp-100) REVERT: S 95 GLU cc_start: 0.5443 (tt0) cc_final: 0.5094 (tm-30) REVERT: T 23 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8251 (tm-30) REVERT: T 65 ASP cc_start: 0.7105 (p0) cc_final: 0.6408 (p0) REVERT: X 7 MET cc_start: 0.5927 (mtp) cc_final: 0.5650 (mtp) REVERT: X 46 GLN cc_start: 0.7512 (tp40) cc_final: 0.7280 (tp-100) REVERT: Y 95 GLU cc_start: 0.5442 (tt0) cc_final: 0.5094 (tm-30) REVERT: Z 23 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8218 (tm-30) REVERT: Z 65 ASP cc_start: 0.7095 (p0) cc_final: 0.6396 (p0) REVERT: Z 95 GLU cc_start: 0.5863 (tt0) cc_final: 0.5499 (tm-30) REVERT: Z 134 LEU cc_start: 0.7335 (tp) cc_final: 0.7115 (pp) REVERT: AA 134 LEU cc_start: 0.7467 (tp) cc_final: 0.7233 (pp) REVERT: CA 7 MET cc_start: 0.5894 (mtp) cc_final: 0.5633 (mtp) REVERT: CA 127 GLN cc_start: 0.7343 (mm-40) cc_final: 0.7140 (mm-40) REVERT: DA 95 GLU cc_start: 0.5433 (tt0) cc_final: 0.5082 (tm-30) REVERT: EA 23 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8170 (tm-30) REVERT: EA 65 ASP cc_start: 0.7122 (p0) cc_final: 0.6418 (p0) REVERT: EA 95 GLU cc_start: 0.5843 (tt0) cc_final: 0.5485 (tm-30) REVERT: EA 134 LEU cc_start: 0.7233 (tp) cc_final: 0.7025 (pp) REVERT: FA 131 ASP cc_start: 0.5659 (p0) cc_final: 0.5459 (p0) REVERT: FA 134 LEU cc_start: 0.7317 (tp) cc_final: 0.7062 (pp) REVERT: GA 23 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: IA 95 GLU cc_start: 0.5239 (tt0) cc_final: 0.4838 (tm-30) REVERT: JA 23 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8230 (tm-30) REVERT: JA 65 ASP cc_start: 0.7101 (p0) cc_final: 0.6406 (p0) REVERT: JA 95 GLU cc_start: 0.5850 (tt0) cc_final: 0.5489 (tm-30) REVERT: KA 134 LEU cc_start: 0.7364 (tp) cc_final: 0.7130 (pp) REVERT: LA 23 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: NA 95 GLU cc_start: 0.5535 (tt0) cc_final: 0.5167 (tm-30) REVERT: OA 23 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8168 (tm-30) REVERT: OA 65 ASP cc_start: 0.7064 (p0) cc_final: 0.6382 (p0) REVERT: OA 95 GLU cc_start: 0.5597 (tt0) cc_final: 0.5311 (tm-30) REVERT: OA 134 LEU cc_start: 0.7374 (tp) cc_final: 0.7135 (pp) REVERT: PA 4 ILE cc_start: 0.6844 (mt) cc_final: 0.6590 (tt) REVERT: PA 134 LEU cc_start: 0.7535 (tp) cc_final: 0.7285 (pp) REVERT: SA 95 GLU cc_start: 0.5311 (tt0) cc_final: 0.4927 (tm-30) REVERT: TA 23 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8167 (tm-30) REVERT: TA 65 ASP cc_start: 0.7120 (p0) cc_final: 0.6413 (p0) REVERT: TA 95 GLU cc_start: 0.5632 (tt0) cc_final: 0.5352 (tm-30) REVERT: TA 134 LEU cc_start: 0.7288 (tp) cc_final: 0.7080 (pp) REVERT: XA 95 GLU cc_start: 0.5452 (tt0) cc_final: 0.5102 (tm-30) REVERT: YA 23 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8238 (tm-30) REVERT: YA 65 ASP cc_start: 0.7095 (p0) cc_final: 0.6399 (p0) REVERT: YA 95 GLU cc_start: 0.5873 (tt0) cc_final: 0.5505 (tm-30) REVERT: AB 23 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: CB 95 GLU cc_start: 0.5512 (tt0) cc_final: 0.5045 (tm-30) REVERT: DB 23 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8209 (tm-30) REVERT: DB 65 ASP cc_start: 0.7115 (p0) cc_final: 0.6419 (p0) REVERT: DB 95 GLU cc_start: 0.5592 (tt0) cc_final: 0.5304 (tm-30) REVERT: DB 134 LEU cc_start: 0.7184 (tp) cc_final: 0.6937 (pp) REVERT: EB 134 LEU cc_start: 0.7304 (tp) cc_final: 0.7068 (pp) REVERT: FB 23 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7955 (tm-30) REVERT: HB 95 GLU cc_start: 0.5452 (tt0) cc_final: 0.5101 (tm-30) REVERT: IB 23 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8247 (tm-30) REVERT: IB 65 ASP cc_start: 0.6958 (p0) cc_final: 0.6229 (p0) outliers start: 176 outliers final: 164 residues processed: 1161 average time/residue: 0.5716 time to fit residues: 1113.1719 Evaluate side-chains 1231 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1062 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 23 GLN Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain L residue 58 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain S residue 7 MET Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 58 ASP Chi-restraints excluded: chain T residue 19 ILE Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 23 GLN Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 68 VAL Chi-restraints excluded: chain V residue 124 GLN Chi-restraints excluded: chain W residue 58 ASP Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 94 VAL Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 94 VAL Chi-restraints excluded: chain Y residue 7 MET Chi-restraints excluded: chain Y residue 23 GLN Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain AA residue 11 THR Chi-restraints excluded: chain AA residue 23 GLN Chi-restraints excluded: chain AA residue 25 LEU Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain BA residue 58 ASP Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain BA residue 94 VAL Chi-restraints excluded: chain BA residue 98 LEU Chi-restraints excluded: chain BA residue 134 LEU Chi-restraints excluded: chain CA residue 94 VAL Chi-restraints excluded: chain DA residue 23 GLN Chi-restraints excluded: chain DA residue 25 LEU Chi-restraints excluded: chain EA residue 19 ILE Chi-restraints excluded: chain EA residue 25 LEU Chi-restraints excluded: chain FA residue 11 THR Chi-restraints excluded: chain FA residue 23 GLN Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain GA residue 23 GLN Chi-restraints excluded: chain GA residue 58 ASP Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 94 VAL Chi-restraints excluded: chain GA residue 98 LEU Chi-restraints excluded: chain GA residue 134 LEU Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 23 GLN Chi-restraints excluded: chain IA residue 25 LEU Chi-restraints excluded: chain IA residue 58 ASP Chi-restraints excluded: chain JA residue 19 ILE Chi-restraints excluded: chain JA residue 25 LEU Chi-restraints excluded: chain KA residue 11 THR Chi-restraints excluded: chain KA residue 23 GLN Chi-restraints excluded: chain KA residue 68 VAL Chi-restraints excluded: chain LA residue 23 GLN Chi-restraints excluded: chain LA residue 58 ASP Chi-restraints excluded: chain LA residue 68 VAL Chi-restraints excluded: chain LA residue 94 VAL Chi-restraints excluded: chain MA residue 94 VAL Chi-restraints excluded: chain NA residue 7 MET Chi-restraints excluded: chain NA residue 23 GLN Chi-restraints excluded: chain NA residue 58 ASP Chi-restraints excluded: chain OA residue 19 ILE Chi-restraints excluded: chain OA residue 25 LEU Chi-restraints excluded: chain PA residue 11 THR Chi-restraints excluded: chain PA residue 25 LEU Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 58 ASP Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain QA residue 94 VAL Chi-restraints excluded: chain QA residue 134 LEU Chi-restraints excluded: chain RA residue 94 VAL Chi-restraints excluded: chain SA residue 23 GLN Chi-restraints excluded: chain SA residue 25 LEU Chi-restraints excluded: chain TA residue 19 ILE Chi-restraints excluded: chain TA residue 25 LEU Chi-restraints excluded: chain UA residue 11 THR Chi-restraints excluded: chain UA residue 23 GLN Chi-restraints excluded: chain UA residue 25 LEU Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 94 VAL Chi-restraints excluded: chain UA residue 124 GLN Chi-restraints excluded: chain VA residue 58 ASP Chi-restraints excluded: chain VA residue 68 VAL Chi-restraints excluded: chain VA residue 94 VAL Chi-restraints excluded: chain VA residue 134 LEU Chi-restraints excluded: chain WA residue 94 VAL Chi-restraints excluded: chain XA residue 7 MET Chi-restraints excluded: chain XA residue 23 GLN Chi-restraints excluded: chain XA residue 58 ASP Chi-restraints excluded: chain YA residue 19 ILE Chi-restraints excluded: chain YA residue 25 LEU Chi-restraints excluded: chain ZA residue 11 THR Chi-restraints excluded: chain ZA residue 23 GLN Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain AB residue 23 GLN Chi-restraints excluded: chain AB residue 58 ASP Chi-restraints excluded: chain AB residue 68 VAL Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 134 LEU Chi-restraints excluded: chain BB residue 25 LEU Chi-restraints excluded: chain BB residue 94 VAL Chi-restraints excluded: chain CB residue 23 GLN Chi-restraints excluded: chain CB residue 25 LEU Chi-restraints excluded: chain CB residue 58 ASP Chi-restraints excluded: chain DB residue 19 ILE Chi-restraints excluded: chain DB residue 25 LEU Chi-restraints excluded: chain EB residue 11 THR Chi-restraints excluded: chain EB residue 23 GLN Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain FB residue 68 VAL Chi-restraints excluded: chain FB residue 94 VAL Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain FB residue 134 LEU Chi-restraints excluded: chain GB residue 94 VAL Chi-restraints excluded: chain HB residue 23 GLN Chi-restraints excluded: chain HB residue 25 LEU Chi-restraints excluded: chain HB residue 58 ASP Chi-restraints excluded: chain IB residue 19 ILE Chi-restraints excluded: chain IB residue 25 LEU Chi-restraints excluded: chain IB residue 68 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 453 optimal weight: 5.9990 chunk 608 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 526 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 572 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 587 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN B 23 GLN D 23 GLN F 23 GLN G 23 GLN I 23 GLN K 23 GLN ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN Q 23 GLN S 23 GLN V 23 GLN ** V 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 113 GLN Y 23 GLN AA 23 GLN ** BA 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 23 GLN FA 23 GLN GA 23 GLN IA 23 GLN KA 23 GLN LA 23 GLN NA 23 GLN QA 23 GLN SA 23 GLN UA 23 GLN VA 23 GLN VA 113 GLN XA 23 GLN ZA 23 GLN AB 23 GLN CB 23 GLN EB 23 GLN HB 23 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.176201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152478 restraints weight = 96453.648| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.40 r_work: 0.3902 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.204 63000 Z= 0.373 Angle : 1.320 59.196 84540 Z= 0.788 Chirality : 0.049 0.330 10080 Planarity : 0.006 0.155 10740 Dihedral : 3.461 24.331 8100 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.30 % Allowed : 16.12 % Favored : 81.58 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.10), residues: 7380 helix: 3.80 (0.08), residues: 3540 sheet: -0.17 (0.12), residues: 1800 loop : -1.02 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPYA 52 HIS 0.002 0.001 HISDB 85 PHE 0.007 0.002 PHEGB 32 TYR 0.013 0.002 TYR B 82 ARG 0.008 0.001 ARG V 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18212.86 seconds wall clock time: 314 minutes 32.78 seconds (18872.78 seconds total)