Starting phenix.real_space_refine on Fri Sep 27 09:45:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/09_2024/5wc3_8795.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/09_2024/5wc3_8795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/09_2024/5wc3_8795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/09_2024/5wc3_8795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/09_2024/5wc3_8795.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/09_2024/5wc3_8795.cif" } resolution = 3.5 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= 0.001 sd= 0.009 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: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 20130 2.51 5 N 5490 2.21 5 O 6840 1.98 5 H 33390 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 65880 Number of models: 1 Model: "" Number of chains: 1 Chain: "1" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Restraints were copied for chains: 0, 3, 2, A, C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z Time building chain proxies: 10.99, per 1000 atoms: 0.17 Number of scatterers: 65880 At special positions: 0 Unit cell: (230.85, 230.85, 82.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 6840 8.00 N 5490 7.00 C 20130 6.00 H 33390 1.00 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: 13.19 Conformation dependent library (CDL) restraints added in 3.9 seconds 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7980 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 91 sheets defined 28.8% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.21 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'C' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' Processing helix chain 'D' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR D 202 " --> pdb=" O GLN D 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'E' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR E 96 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'F' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS F 105 " --> pdb=" O GLU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR F 202 " --> pdb=" O GLN F 198 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'G' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR G 96 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR G 202 " --> pdb=" O GLN G 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 216 No H-bonds generated for 'chain 'G' and resid 214 through 216' Processing helix chain 'H' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR H 96 " --> pdb=" O SER H 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN H 103 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS H 105 " --> pdb=" O GLU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR H 202 " --> pdb=" O GLN H 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE H 203 " --> pdb=" O ILE H 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 216 No H-bonds generated for 'chain 'H' and resid 214 through 216' Processing helix chain 'I' and resid 90 through 109 removed outlier: 3.545A pdb=" N ASP I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN I 103 " --> pdb=" O GLU I 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR I 202 " --> pdb=" O GLN I 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 216 No H-bonds generated for 'chain 'I' and resid 214 through 216' Processing helix chain 'J' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP J 95 " --> pdb=" O ASP J 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR J 96 " --> pdb=" O SER J 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS J 105 " --> pdb=" O GLU J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR J 202 " --> pdb=" O GLN J 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE J 203 " --> pdb=" O ILE J 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL J 210 " --> pdb=" O ALA J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 216 No H-bonds generated for 'chain 'J' and resid 214 through 216' Processing helix chain 'K' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP K 95 " --> pdb=" O ASP K 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN K 103 " --> pdb=" O GLU K 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR K 202 " --> pdb=" O GLN K 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE K 203 " --> pdb=" O ILE K 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL K 210 " --> pdb=" O ALA K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 216 No H-bonds generated for 'chain 'K' and resid 214 through 216' Processing helix chain 'L' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN L 103 " --> pdb=" O GLU L 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS L 105 " --> pdb=" O GLU L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR L 202 " --> pdb=" O GLN L 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE L 203 " --> pdb=" O ILE L 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL L 210 " --> pdb=" O ALA L 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 216 No H-bonds generated for 'chain 'L' and resid 214 through 216' Processing helix chain 'M' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP M 95 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR M 96 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN M 103 " --> pdb=" O GLU M 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS M 105 " --> pdb=" O GLU M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR M 202 " --> pdb=" O GLN M 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE M 203 " --> pdb=" O ILE M 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG M 209 " --> pdb=" O GLU M 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL M 210 " --> pdb=" O ALA M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 216 No H-bonds generated for 'chain 'M' and resid 214 through 216' Processing helix chain 'N' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP N 95 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS N 105 " --> pdb=" O GLU N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR N 202 " --> pdb=" O GLN N 198 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG N 209 " --> pdb=" O GLU N 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL N 210 " --> pdb=" O ALA N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 216 No H-bonds generated for 'chain 'N' and resid 214 through 216' Processing helix chain 'O' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP O 95 " --> pdb=" O ASP O 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR O 96 " --> pdb=" O SER O 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN O 103 " --> pdb=" O GLU O 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS O 105 " --> pdb=" O GLU O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR O 202 " --> pdb=" O GLN O 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE O 203 " --> pdb=" O ILE O 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG O 209 " --> pdb=" O GLU O 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL O 210 " --> pdb=" O ALA O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 214 through 216 No H-bonds generated for 'chain 'O' and resid 214 through 216' Processing helix chain 'P' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP P 95 " --> pdb=" O ASP P 91 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN P 103 " --> pdb=" O GLU P 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS P 105 " --> pdb=" O GLU P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR P 202 " --> pdb=" O GLN P 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE P 203 " --> pdb=" O ILE P 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG P 209 " --> pdb=" O GLU P 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL P 210 " --> pdb=" O ALA P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 216 No H-bonds generated for 'chain 'P' and resid 214 through 216' Processing helix chain 'Q' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP Q 95 " --> pdb=" O ASP Q 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR Q 96 " --> pdb=" O SER Q 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN Q 103 " --> pdb=" O GLU Q 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR Q 202 " --> pdb=" O GLN Q 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE Q 203 " --> pdb=" O ILE Q 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG Q 209 " --> pdb=" O GLU Q 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Q 210 " --> pdb=" O ALA Q 206 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 216 No H-bonds generated for 'chain 'Q' and resid 214 through 216' Processing helix chain 'R' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP R 95 " --> pdb=" O ASP R 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR R 96 " --> pdb=" O SER R 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN R 103 " --> pdb=" O GLU R 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS R 105 " --> pdb=" O GLU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR R 202 " --> pdb=" O GLN R 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE R 203 " --> pdb=" O ILE R 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG R 209 " --> pdb=" O GLU R 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL R 210 " --> pdb=" O ALA R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 216 No H-bonds generated for 'chain 'R' and resid 214 through 216' Processing helix chain 'S' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP S 95 " --> pdb=" O ASP S 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR S 96 " --> pdb=" O SER S 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN S 103 " --> pdb=" O GLU S 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS S 105 " --> pdb=" O GLU S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR S 202 " --> pdb=" O GLN S 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE S 203 " --> pdb=" O ILE S 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG S 209 " --> pdb=" O GLU S 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL S 210 " --> pdb=" O ALA S 206 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 216 No H-bonds generated for 'chain 'S' and resid 214 through 216' Processing helix chain 'T' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP T 95 " --> pdb=" O ASP T 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR T 96 " --> pdb=" O SER T 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN T 103 " --> pdb=" O GLU T 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS T 105 " --> pdb=" O GLU T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR T 202 " --> pdb=" O GLN T 198 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE T 203 " --> pdb=" O ILE T 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG T 209 " --> pdb=" O GLU T 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL T 210 " --> pdb=" O ALA T 206 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 216 No H-bonds generated for 'chain 'T' and resid 214 through 216' Processing helix chain 'U' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP U 95 " --> pdb=" O ASP U 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR U 96 " --> pdb=" O SER U 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN U 103 " --> pdb=" O GLU U 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS U 105 " --> pdb=" O GLU U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR U 202 " --> pdb=" O GLN U 198 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE U 203 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG U 209 " --> pdb=" O GLU U 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL U 210 " --> pdb=" O ALA U 206 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 216 No H-bonds generated for 'chain 'U' and resid 214 through 216' Processing helix chain 'V' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP V 95 " --> pdb=" O ASP V 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR V 96 " --> pdb=" O SER V 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN V 103 " --> pdb=" O GLU V 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS V 105 " --> pdb=" O GLU V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR V 202 " --> pdb=" O GLN V 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE V 203 " --> pdb=" O ILE V 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG V 209 " --> pdb=" O GLU V 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL V 210 " --> pdb=" O ALA V 206 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 216 No H-bonds generated for 'chain 'V' and resid 214 through 216' Processing helix chain 'W' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP W 95 " --> pdb=" O ASP W 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR W 96 " --> pdb=" O SER W 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN W 103 " --> pdb=" O GLU W 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS W 105 " --> pdb=" O GLU W 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR W 202 " --> pdb=" O GLN W 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE W 203 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG W 209 " --> pdb=" O GLU W 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL W 210 " --> pdb=" O ALA W 206 " (cutoff:3.500A) Processing helix chain 'W' and resid 214 through 216 No H-bonds generated for 'chain 'W' and resid 214 through 216' Processing helix chain 'X' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP X 95 " --> pdb=" O ASP X 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR X 96 " --> pdb=" O SER X 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN X 103 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR X 202 " --> pdb=" O GLN X 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE X 203 " --> pdb=" O ILE X 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG X 209 " --> pdb=" O GLU X 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL X 210 " --> pdb=" O ALA X 206 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 216 No H-bonds generated for 'chain 'X' and resid 214 through 216' Processing helix chain 'Y' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP Y 95 " --> pdb=" O ASP Y 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR Y 96 " --> pdb=" O SER Y 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN Y 103 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS Y 105 " --> pdb=" O GLU Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR Y 202 " --> pdb=" O GLN Y 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE Y 203 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG Y 209 " --> pdb=" O GLU Y 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Y 210 " --> pdb=" O ALA Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 216 No H-bonds generated for 'chain 'Y' and resid 214 through 216' Processing helix chain 'Z' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP Z 95 " --> pdb=" O ASP Z 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR Z 96 " --> pdb=" O SER Z 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN Z 103 " --> pdb=" O GLU Z 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS Z 105 " --> pdb=" O GLU Z 101 " (cutoff:3.500A) Processing helix chain 'Z' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR Z 202 " --> pdb=" O GLN Z 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE Z 203 " --> pdb=" O ILE Z 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG Z 209 " --> pdb=" O GLU Z 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Z 210 " --> pdb=" O ALA Z 206 " (cutoff:3.500A) Processing helix chain 'Z' and resid 214 through 216 No H-bonds generated for 'chain 'Z' and resid 214 through 216' Processing helix chain '0' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP 0 95 " --> pdb=" O ASP 0 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR 0 96 " --> pdb=" O SER 0 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN 0 103 " --> pdb=" O GLU 0 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS 0 105 " --> pdb=" O GLU 0 101 " (cutoff:3.500A) Processing helix chain '0' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR 0 202 " --> pdb=" O GLN 0 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE 0 203 " --> pdb=" O ILE 0 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG 0 209 " --> pdb=" O GLU 0 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL 0 210 " --> pdb=" O ALA 0 206 " (cutoff:3.500A) Processing helix chain '0' and resid 214 through 216 No H-bonds generated for 'chain '0' and resid 214 through 216' Processing helix chain '1' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP 1 95 " --> pdb=" O ASP 1 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR 1 96 " --> pdb=" O SER 1 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN 1 103 " --> pdb=" O GLU 1 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS 1 105 " --> pdb=" O GLU 1 101 " (cutoff:3.500A) Processing helix chain '1' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR 1 202 " --> pdb=" O GLN 1 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE 1 203 " --> pdb=" O ILE 1 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG 1 209 " --> pdb=" O GLU 1 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL 1 210 " --> pdb=" O ALA 1 206 " (cutoff:3.500A) Processing helix chain '1' and resid 214 through 216 No H-bonds generated for 'chain '1' and resid 214 through 216' Processing helix chain '2' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP 2 95 " --> pdb=" O ASP 2 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR 2 96 " --> pdb=" O SER 2 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN 2 103 " --> pdb=" O GLU 2 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS 2 105 " --> pdb=" O GLU 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR 2 202 " --> pdb=" O GLN 2 198 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE 2 203 " --> pdb=" O ILE 2 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG 2 209 " --> pdb=" O GLU 2 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL 2 210 " --> pdb=" O ALA 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 214 through 216 No H-bonds generated for 'chain '2' and resid 214 through 216' Processing helix chain '3' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP 3 95 " --> pdb=" O ASP 3 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR 3 96 " --> pdb=" O SER 3 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN 3 103 " --> pdb=" O GLU 3 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS 3 105 " --> pdb=" O GLU 3 101 " (cutoff:3.500A) Processing helix chain '3' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR 3 202 " --> pdb=" O GLN 3 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE 3 203 " --> pdb=" O ILE 3 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG 3 209 " --> pdb=" O GLU 3 205 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL 3 210 " --> pdb=" O ALA 3 206 " (cutoff:3.500A) Processing helix chain '3' and resid 214 through 216 No H-bonds generated for 'chain '3' and resid 214 through 216' Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA A 219 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY A 186 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN A 178 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 144 removed outlier: 6.320A pdb=" N ILE A 163 " --> pdb=" O LYS 3 133 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N LYS 3 133 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE 3 163 " --> pdb=" O LYS 2 133 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N LYS 2 133 " --> pdb=" O ILE 3 163 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE 2 163 " --> pdb=" O LYS 1 133 " (cutoff:3.500A) removed outlier: 9.977A pdb=" N LYS 1 133 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE 1 163 " --> pdb=" O LYS 0 133 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N LYS 0 133 " --> pdb=" O ILE 1 163 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE 0 163 " --> pdb=" O LYS Z 133 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS Z 133 " --> pdb=" O ILE 0 163 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE Z 163 " --> pdb=" O LYS Y 133 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N LYS Y 133 " --> pdb=" O ILE Z 163 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE Y 163 " --> pdb=" O LYS X 133 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N LYS X 133 " --> pdb=" O ILE Y 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE X 163 " --> pdb=" O LYS W 133 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS W 133 " --> pdb=" O ILE X 163 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE W 163 " --> pdb=" O LYS V 133 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS V 133 " --> pdb=" O ILE W 163 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE V 163 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N LYS U 133 " --> pdb=" O ILE V 163 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE U 163 " --> pdb=" O LYS T 133 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N LYS T 133 " --> pdb=" O ILE U 163 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE T 163 " --> pdb=" O LYS S 133 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N LYS S 133 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE S 163 " --> pdb=" O LYS R 133 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N LYS R 133 " --> pdb=" O ILE S 163 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE R 163 " --> pdb=" O LYS Q 133 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N LYS Q 133 " --> pdb=" O ILE R 163 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE Q 163 " --> pdb=" O LYS P 133 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N LYS P 133 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE P 163 " --> pdb=" O LYS O 133 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LYS O 133 " --> pdb=" O ILE P 163 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE O 163 " --> pdb=" O LYS N 133 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N LYS N 133 " --> pdb=" O ILE O 163 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE N 163 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N LYS M 133 " --> pdb=" O ILE N 163 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE M 163 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N LYS L 133 " --> pdb=" O ILE M 163 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE L 163 " --> pdb=" O LYS K 133 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N LYS K 133 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE K 163 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS J 133 " --> pdb=" O ILE K 163 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE J 163 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS I 133 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE I 163 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N LYS H 133 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE H 163 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N LYS G 133 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE G 163 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS F 133 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE F 163 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N LYS E 133 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE E 163 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N LYS D 133 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE D 163 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N LYS C 133 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 163 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N LYS B 133 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 163 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS A 133 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA B 219 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY B 186 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN B 178 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AA8, first strand: chain 'C' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA C 219 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY C 186 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN C 178 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 165 through 168 Processing sheet with id=AB2, first strand: chain 'D' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA D 219 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY D 186 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN D 178 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AB5, first strand: chain 'E' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA E 219 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY E 186 " --> pdb=" O ALA E 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN E 178 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 165 through 168 Processing sheet with id=AB8, first strand: chain 'F' and resid 117 through 123 removed outlier: 9.655A pdb=" N ALA F 219 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY F 186 " --> pdb=" O ALA F 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN F 178 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 165 through 168 Processing sheet with id=AC2, first strand: chain 'G' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA G 219 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY G 186 " --> pdb=" O ALA G 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN G 178 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 165 through 168 Processing sheet with id=AC5, first strand: chain 'H' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA H 219 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY H 186 " --> pdb=" O ALA H 219 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN H 178 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 165 through 168 Processing sheet with id=AC8, first strand: chain 'I' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA I 219 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY I 186 " --> pdb=" O ALA I 219 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 128 through 131 removed outlier: 4.271A pdb=" N GLN I 178 " --> pdb=" O VAL I 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 165 through 168 Processing sheet with id=AD2, first strand: chain 'J' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA J 219 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY J 186 " --> pdb=" O ALA J 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN J 178 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 165 through 168 Processing sheet with id=AD5, first strand: chain 'K' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA K 219 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY K 186 " --> pdb=" O ALA K 219 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN K 178 " --> pdb=" O VAL K 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 165 through 168 Processing sheet with id=AD8, first strand: chain 'L' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA L 219 " --> pdb=" O ILE L 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY L 186 " --> pdb=" O ALA L 219 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN L 178 " --> pdb=" O VAL L 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 165 through 168 Processing sheet with id=AE2, first strand: chain 'M' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA M 219 " --> pdb=" O ILE M 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY M 186 " --> pdb=" O ALA M 219 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN M 178 " --> pdb=" O VAL M 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 165 through 168 Processing sheet with id=AE5, first strand: chain 'N' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA N 219 " --> pdb=" O ILE N 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY N 186 " --> pdb=" O ALA N 219 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN N 178 " --> pdb=" O VAL N 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 165 through 168 Processing sheet with id=AE8, first strand: chain 'O' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA O 219 " --> pdb=" O ILE O 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY O 186 " --> pdb=" O ALA O 219 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN O 178 " --> pdb=" O VAL O 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 165 through 168 Processing sheet with id=AF2, first strand: chain 'P' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA P 219 " --> pdb=" O ILE P 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY P 186 " --> pdb=" O ALA P 219 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN P 178 " --> pdb=" O VAL P 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 165 through 168 Processing sheet with id=AF5, first strand: chain 'Q' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA Q 219 " --> pdb=" O ILE Q 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY Q 186 " --> pdb=" O ALA Q 219 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN Q 178 " --> pdb=" O VAL Q 130 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 165 through 168 Processing sheet with id=AF8, first strand: chain 'R' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA R 219 " --> pdb=" O ILE R 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY R 186 " --> pdb=" O ALA R 219 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN R 178 " --> pdb=" O VAL R 130 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 165 through 168 Processing sheet with id=AG2, first strand: chain 'S' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA S 219 " --> pdb=" O ILE S 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY S 186 " --> pdb=" O ALA S 219 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN S 178 " --> pdb=" O VAL S 130 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 165 through 168 Processing sheet with id=AG5, first strand: chain 'T' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA T 219 " --> pdb=" O ILE T 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY T 186 " --> pdb=" O ALA T 219 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN T 178 " --> pdb=" O VAL T 130 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 165 through 168 Processing sheet with id=AG8, first strand: chain 'U' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA U 219 " --> pdb=" O ILE U 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY U 186 " --> pdb=" O ALA U 219 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN U 178 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 165 through 168 Processing sheet with id=AH2, first strand: chain 'V' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA V 219 " --> pdb=" O ILE V 184 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY V 186 " --> pdb=" O ALA V 219 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN V 178 " --> pdb=" O VAL V 130 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'V' and resid 165 through 168 Processing sheet with id=AH5, first strand: chain 'W' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA W 219 " --> pdb=" O ILE W 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY W 186 " --> pdb=" O ALA W 219 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN W 178 " --> pdb=" O VAL W 130 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'W' and resid 165 through 168 Processing sheet with id=AH8, first strand: chain 'X' and resid 117 through 123 removed outlier: 9.655A pdb=" N ALA X 219 " --> pdb=" O ILE X 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY X 186 " --> pdb=" O ALA X 219 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 128 through 131 removed outlier: 4.271A pdb=" N GLN X 178 " --> pdb=" O VAL X 130 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 165 through 168 Processing sheet with id=AI2, first strand: chain 'Y' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA Y 219 " --> pdb=" O ILE Y 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY Y 186 " --> pdb=" O ALA Y 219 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN Y 178 " --> pdb=" O VAL Y 130 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Y' and resid 165 through 168 Processing sheet with id=AI5, first strand: chain 'Z' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA Z 219 " --> pdb=" O ILE Z 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY Z 186 " --> pdb=" O ALA Z 219 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Z' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN Z 178 " --> pdb=" O VAL Z 130 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Z' and resid 165 through 168 Processing sheet with id=AI8, first strand: chain '0' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA 0 219 " --> pdb=" O ILE 0 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY 0 186 " --> pdb=" O ALA 0 219 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '0' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN 0 178 " --> pdb=" O VAL 0 130 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain '0' and resid 165 through 168 Processing sheet with id=AJ2, first strand: chain '1' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA 1 219 " --> pdb=" O ILE 1 184 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY 1 186 " --> pdb=" O ALA 1 219 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain '1' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN 1 178 " --> pdb=" O VAL 1 130 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain '1' and resid 165 through 168 Processing sheet with id=AJ5, first strand: chain '2' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA 2 219 " --> pdb=" O ILE 2 184 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY 2 186 " --> pdb=" O ALA 2 219 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain '2' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN 2 178 " --> pdb=" O VAL 2 130 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain '2' and resid 165 through 168 Processing sheet with id=AJ8, first strand: chain '3' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA 3 219 " --> pdb=" O ILE 3 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY 3 186 " --> pdb=" O ALA 3 219 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain '3' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN 3 178 " --> pdb=" O VAL 3 130 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain '3' and resid 165 through 168 1680 hydrogen bonds defined for protein. 4770 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: 23.51 Time building geometry restraints manager: 16.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 33390 1.03 - 1.22: 0 1.22 - 1.41: 12076 1.41 - 1.61: 20594 1.61 - 1.80: 60 Bond restraints: 66120 Sorted by residual: bond pdb=" CB VAL U 210 " pdb=" CG2 VAL U 210 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.35e+00 bond pdb=" CB VAL K 210 " pdb=" CG2 VAL K 210 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.34e+00 bond pdb=" CB VAL G 210 " pdb=" CG2 VAL G 210 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.34e+00 bond pdb=" CB VAL S 210 " pdb=" CG2 VAL S 210 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.33e+00 bond pdb=" CB VAL L 210 " pdb=" CG2 VAL L 210 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.30e+00 ... (remaining 66115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 112537 1.63 - 3.26: 7204 3.26 - 4.90: 957 4.90 - 6.53: 172 6.53 - 8.16: 60 Bond angle restraints: 120930 Sorted by residual: angle pdb=" C PRO B 222 " pdb=" N LYS B 223 " pdb=" CA LYS B 223 " ideal model delta sigma weight residual 121.54 129.70 -8.16 1.91e+00 2.74e-01 1.83e+01 angle pdb=" C PRO 2 222 " pdb=" N LYS 2 223 " pdb=" CA LYS 2 223 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C PRO 3 222 " pdb=" N LYS 3 223 " pdb=" CA LYS 3 223 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C PRO K 222 " pdb=" N LYS K 223 " pdb=" CA LYS K 223 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C PRO U 222 " pdb=" N LYS U 223 " pdb=" CA LYS U 223 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 ... (remaining 120925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 27487 17.94 - 35.87: 1343 35.87 - 53.81: 510 53.81 - 71.75: 690 71.75 - 89.69: 390 Dihedral angle restraints: 30420 sinusoidal: 17760 harmonic: 12660 Sorted by residual: dihedral pdb=" CA ILE Y 111 " pdb=" C ILE Y 111 " pdb=" N ILE Y 112 " pdb=" CA ILE Y 112 " ideal model delta harmonic sigma weight residual 180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ILE D 111 " pdb=" C ILE D 111 " pdb=" N ILE D 112 " pdb=" CA ILE D 112 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ILE G 111 " pdb=" C ILE G 111 " pdb=" N ILE G 112 " pdb=" CA ILE G 112 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 30417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3053 0.046 - 0.092: 1648 0.092 - 0.139: 564 0.139 - 0.185: 165 0.185 - 0.231: 30 Chirality restraints: 5460 Sorted by residual: chirality pdb=" CB VAL G 187 " pdb=" CA VAL G 187 " pdb=" CG1 VAL G 187 " pdb=" CG2 VAL G 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB VAL W 187 " pdb=" CA VAL W 187 " pdb=" CG1 VAL W 187 " pdb=" CG2 VAL W 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL 0 187 " pdb=" CA VAL 0 187 " pdb=" CG1 VAL 0 187 " pdb=" CG2 VAL 0 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 5457 not shown) Planarity restraints: 9720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN S 103 " 0.214 2.00e-02 2.50e+03 2.55e-01 9.72e+02 pdb=" CD GLN S 103 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN S 103 " -0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN S 103 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN S 103 " -0.385 2.00e-02 2.50e+03 pdb="HE22 GLN S 103 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN Y 103 " -0.214 2.00e-02 2.50e+03 2.55e-01 9.72e+02 pdb=" CD GLN Y 103 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN Y 103 " 0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN Y 103 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN Y 103 " 0.385 2.00e-02 2.50e+03 pdb="HE22 GLN Y 103 " -0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 103 " -0.214 2.00e-02 2.50e+03 2.55e-01 9.72e+02 pdb=" CD GLN H 103 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN H 103 " 0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN H 103 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN H 103 " 0.385 2.00e-02 2.50e+03 pdb="HE22 GLN H 103 " -0.391 2.00e-02 2.50e+03 ... (remaining 9717 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 3093 2.15 - 2.76: 141585 2.76 - 3.38: 166837 3.38 - 3.99: 218445 3.99 - 4.60: 348110 Nonbonded interactions: 878070 Sorted by model distance: nonbonded pdb=" O LYS 1 90 " pdb=" H ILE 1 93 " model vdw 1.541 2.450 nonbonded pdb=" O LYS Z 90 " pdb=" H ILE Z 93 " model vdw 1.541 2.450 nonbonded pdb=" O LYS Q 90 " pdb=" H ILE Q 93 " model vdw 1.541 2.450 nonbonded pdb=" O LYS N 90 " pdb=" H ILE N 93 " model vdw 1.541 2.450 nonbonded pdb=" O LYS I 90 " pdb=" H ILE I 93 " model vdw 1.541 2.450 ... (remaining 878065 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.920 Extract box with map and model: 1.780 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 94.340 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.350 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:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.015 0.083 32730 Z= 0.980 Angle : 1.179 8.162 44220 Z= 0.686 Chirality : 0.063 0.231 5460 Planarity : 0.006 0.062 5700 Dihedral : 9.370 59.727 12870 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 1.46 % Allowed : 8.03 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % 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: -5.20 (0.09), residues: 4110 helix: -4.93 (0.06), residues: 960 sheet: -1.37 (0.12), residues: 960 loop : -3.86 (0.09), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS X 216 TYR 0.011 0.003 TYR Y 100 ARG 0.013 0.003 ARG V 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 4.127 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: I 124 ASP cc_start: 0.7919 (t70) cc_final: 0.7624 (t0) REVERT: X 124 ASP cc_start: 0.7912 (t70) cc_final: 0.7625 (t0) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.7197 time to fit residues: 478.8374 Evaluate side-chains 135 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 305 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 354 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 196 ASN W 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32730 Z= 0.244 Angle : 0.792 5.694 44220 Z= 0.444 Chirality : 0.051 0.164 5460 Planarity : 0.005 0.048 5700 Dihedral : 7.809 36.087 4350 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 1.02 % Allowed : 7.83 % Favored : 91.14 % Rotamer: Outliers : 0.91 % Allowed : 1.25 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -3.52 (0.11), residues: 4110 helix: -2.56 (0.14), residues: 960 sheet: -0.43 (0.14), residues: 960 loop : -3.24 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS 2 216 TYR 0.005 0.001 TYR F 96 ARG 0.005 0.001 ARG N 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 235 time to evaluate : 4.714 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: G 109 GLU cc_start: 0.6505 (tm-30) cc_final: 0.6295 (tm-30) REVERT: G 212 ASP cc_start: 0.7906 (t0) cc_final: 0.7493 (t0) REVERT: H 91 ASP cc_start: 0.3264 (m-30) cc_final: 0.2977 (p0) REVERT: I 124 ASP cc_start: 0.7830 (t70) cc_final: 0.7443 (t0) REVERT: N 212 ASP cc_start: 0.7733 (t0) cc_final: 0.7448 (t0) REVERT: V 109 GLU cc_start: 0.6506 (tm-30) cc_final: 0.6299 (tm-30) REVERT: V 212 ASP cc_start: 0.7904 (t0) cc_final: 0.7494 (t0) REVERT: W 91 ASP cc_start: 0.3272 (m-30) cc_final: 0.2980 (p0) REVERT: X 124 ASP cc_start: 0.7830 (t70) cc_final: 0.7454 (t0) REVERT: 2 212 ASP cc_start: 0.7735 (t0) cc_final: 0.7447 (t0) outliers start: 35 outliers final: 30 residues processed: 241 average time/residue: 0.8726 time to fit residues: 336.4884 Evaluate side-chains 169 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 4.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain V residue 188 LEU Chi-restraints excluded: chain W residue 188 LEU Chi-restraints excluded: chain X residue 188 LEU Chi-restraints excluded: chain Y residue 188 LEU Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 1 residue 188 LEU Chi-restraints excluded: chain 2 residue 188 LEU Chi-restraints excluded: chain 3 residue 188 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 354 optimal weight: 0.6980 chunk 383 optimal weight: 20.0000 chunk 315 optimal weight: 0.9990 chunk 351 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.7430 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32730 Z= 0.205 Angle : 0.689 5.766 44220 Z= 0.384 Chirality : 0.049 0.158 5460 Planarity : 0.004 0.038 5700 Dihedral : 6.902 31.320 4350 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 1.09 % Allowed : 8.88 % Favored : 90.02 % Rotamer: Outliers : 1.20 % Allowed : 2.06 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -2.78 (0.12), residues: 4110 helix: -0.81 (0.17), residues: 1050 sheet: -0.38 (0.15), residues: 780 loop : -3.05 (0.11), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 216 TYR 0.005 0.001 TYR 1 100 ARG 0.003 0.001 ARG K 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 224 time to evaluate : 4.133 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: A 188 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6872 (tp) REVERT: B 188 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6764 (tp) REVERT: G 212 ASP cc_start: 0.7821 (t0) cc_final: 0.7373 (t0) REVERT: H 91 ASP cc_start: 0.3175 (m-30) cc_final: 0.2902 (p0) REVERT: I 124 ASP cc_start: 0.8095 (t70) cc_final: 0.7775 (t0) REVERT: N 212 ASP cc_start: 0.7559 (t0) cc_final: 0.7249 (t0) REVERT: P 188 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6950 (tp) REVERT: Q 188 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6764 (tp) REVERT: V 212 ASP cc_start: 0.7817 (t0) cc_final: 0.7372 (t0) REVERT: W 91 ASP cc_start: 0.3234 (m-30) cc_final: 0.2949 (p0) REVERT: X 124 ASP cc_start: 0.8104 (t70) cc_final: 0.7790 (t0) REVERT: 2 212 ASP cc_start: 0.7558 (t0) cc_final: 0.7248 (t0) outliers start: 46 outliers final: 35 residues processed: 239 average time/residue: 0.7598 time to fit residues: 306.0399 Evaluate side-chains 168 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 188 LEU Chi-restraints excluded: chain W residue 188 LEU Chi-restraints excluded: chain Y residue 188 LEU Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 1 residue 188 LEU Chi-restraints excluded: chain 2 residue 188 LEU Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 188 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 184 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 356 optimal weight: 2.9990 chunk 376 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 337 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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: 0.7530 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32730 Z= 0.303 Angle : 0.728 5.889 44220 Z= 0.411 Chirality : 0.049 0.178 5460 Planarity : 0.005 0.058 5700 Dihedral : 6.614 27.338 4350 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.09 % Allowed : 9.00 % Favored : 89.90 % Rotamer: Outliers : 1.41 % Allowed : 2.63 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % 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: -2.74 (0.12), residues: 4110 helix: -0.49 (0.17), residues: 1050 sheet: -1.28 (0.13), residues: 1290 loop : -3.07 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 216 TYR 0.009 0.002 TYR C 100 ARG 0.008 0.001 ARG N 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 194 time to evaluate : 4.153 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: D 188 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6395 (tp) REVERT: F 188 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6852 (tp) REVERT: G 212 ASP cc_start: 0.7908 (t0) cc_final: 0.7675 (t0) REVERT: L 188 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7087 (tp) REVERT: U 188 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6846 (tp) REVERT: V 212 ASP cc_start: 0.7906 (t0) cc_final: 0.7675 (t0) REVERT: 0 188 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7095 (tp) outliers start: 54 outliers final: 43 residues processed: 216 average time/residue: 0.6915 time to fit residues: 260.7072 Evaluate side-chains 177 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 129 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 188 LEU Chi-restraints excluded: chain W residue 188 LEU Chi-restraints excluded: chain X residue 188 LEU Chi-restraints excluded: chain Y residue 91 ASP Chi-restraints excluded: chain Y residue 188 LEU Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain 0 residue 91 ASP Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 1 residue 188 LEU Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain 2 residue 188 LEU Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 188 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 321 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 338 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.7539 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32730 Z= 0.252 Angle : 0.671 5.551 44220 Z= 0.377 Chirality : 0.048 0.169 5460 Planarity : 0.004 0.029 5700 Dihedral : 6.362 25.374 4350 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 1.09 % Allowed : 9.08 % Favored : 89.83 % Rotamer: Outliers : 1.43 % Allowed : 3.91 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % 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: -2.35 (0.12), residues: 4110 helix: -0.32 (0.18), residues: 1050 sheet: -0.44 (0.15), residues: 780 loop : -2.71 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS U 216 TYR 0.007 0.001 TYR J 100 ARG 0.003 0.001 ARG Z 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 167 time to evaluate : 4.165 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: M 188 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6817 (tp) REVERT: 1 188 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6824 (tp) outliers start: 55 outliers final: 44 residues processed: 190 average time/residue: 0.7286 time to fit residues: 236.0777 Evaluate side-chains 183 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 188 LEU Chi-restraints excluded: chain W residue 188 LEU Chi-restraints excluded: chain Y residue 188 LEU Chi-restraints excluded: chain Z residue 102 ASN Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain 0 residue 91 ASP Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 1 residue 188 LEU Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain 2 residue 188 LEU Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 188 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 5.9990 chunk 339 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 377 optimal weight: 0.7980 chunk 313 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 192 GLN X 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32730 Z= 0.162 Angle : 0.604 5.501 44220 Z= 0.334 Chirality : 0.047 0.177 5460 Planarity : 0.003 0.027 5700 Dihedral : 5.867 25.627 4350 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 1.02 % Allowed : 7.81 % Favored : 91.17 % Rotamer: Outliers : 1.25 % Allowed : 5.55 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % 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: -2.23 (0.13), residues: 4110 helix: -0.03 (0.18), residues: 1050 sheet: -1.11 (0.13), residues: 1290 loop : -2.66 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 216 TYR 0.003 0.001 TYR A 100 ARG 0.005 0.000 ARG I 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 173 time to evaluate : 4.099 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: F 91 ASP cc_start: 0.3582 (m-30) cc_final: 0.3302 (p0) REVERT: F 212 ASP cc_start: 0.7911 (t0) cc_final: 0.7627 (t0) REVERT: G 212 ASP cc_start: 0.7798 (t0) cc_final: 0.7457 (t0) REVERT: H 91 ASP cc_start: 0.4092 (m-30) cc_final: 0.3440 (p0) REVERT: U 91 ASP cc_start: 0.3578 (m-30) cc_final: 0.3301 (p0) REVERT: U 212 ASP cc_start: 0.7908 (t0) cc_final: 0.7624 (t0) REVERT: V 212 ASP cc_start: 0.7797 (t0) cc_final: 0.7454 (t0) REVERT: W 91 ASP cc_start: 0.4098 (m-30) cc_final: 0.3441 (p0) outliers start: 48 outliers final: 40 residues processed: 191 average time/residue: 0.6752 time to fit residues: 226.6993 Evaluate side-chains 174 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 5.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 188 LEU Chi-restraints excluded: chain W residue 188 LEU Chi-restraints excluded: chain Y residue 188 LEU Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain 0 residue 91 ASP Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 1 residue 188 LEU Chi-restraints excluded: chain 2 residue 188 LEU Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 188 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 214 optimal weight: 8.9990 chunk 275 optimal weight: 0.5980 chunk 213 optimal weight: 0.9990 chunk 317 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 375 optimal weight: 0.0980 chunk 235 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 192 GLN W 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32730 Z= 0.148 Angle : 0.575 5.384 44220 Z= 0.317 Chirality : 0.046 0.183 5460 Planarity : 0.003 0.025 5700 Dihedral : 5.519 23.818 4350 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.95 % Allowed : 7.54 % Favored : 91.51 % Rotamer: Outliers : 1.20 % Allowed : 5.78 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % 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: -1.88 (0.13), residues: 4110 helix: 0.62 (0.19), residues: 960 sheet: -1.23 (0.12), residues: 1500 loop : -2.32 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS U 216 TYR 0.004 0.001 TYR P 100 ARG 0.004 0.000 ARG X 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 4.137 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: F 212 ASP cc_start: 0.7825 (t0) cc_final: 0.7514 (t0) REVERT: G 212 ASP cc_start: 0.7824 (t0) cc_final: 0.7545 (t0) REVERT: H 91 ASP cc_start: 0.4110 (m-30) cc_final: 0.3461 (p0) REVERT: K 212 ASP cc_start: 0.7697 (t0) cc_final: 0.7261 (t0) REVERT: Q 109 GLU cc_start: 0.6481 (tm-30) cc_final: 0.6016 (tm-30) REVERT: U 212 ASP cc_start: 0.7830 (t0) cc_final: 0.7518 (t0) REVERT: V 212 ASP cc_start: 0.7779 (t0) cc_final: 0.7464 (t0) REVERT: W 91 ASP cc_start: 0.4120 (m-30) cc_final: 0.3464 (p0) REVERT: Z 212 ASP cc_start: 0.7688 (t0) cc_final: 0.7263 (t0) outliers start: 46 outliers final: 42 residues processed: 189 average time/residue: 0.7439 time to fit residues: 245.6015 Evaluate side-chains 177 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 135 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain U residue 188 LEU Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 188 LEU Chi-restraints excluded: chain W residue 188 LEU Chi-restraints excluded: chain Y residue 188 LEU Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 1 residue 188 LEU Chi-restraints excluded: chain 2 residue 188 LEU Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 188 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32730 Z= 0.153 Angle : 0.571 5.402 44220 Z= 0.314 Chirality : 0.046 0.193 5460 Planarity : 0.003 0.031 5700 Dihedral : 5.411 23.708 4350 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.05 % Favored : 91.02 % Rotamer: Outliers : 1.51 % Allowed : 6.22 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % 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: -1.70 (0.13), residues: 4110 helix: 0.64 (0.19), residues: 900 sheet: -1.19 (0.12), residues: 1500 loop : -1.95 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS U 216 TYR 0.005 0.001 TYR A 100 ARG 0.004 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 157 time to evaluate : 4.486 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: F 212 ASP cc_start: 0.7804 (t0) cc_final: 0.7503 (t0) REVERT: G 212 ASP cc_start: 0.7860 (t0) cc_final: 0.7579 (t0) REVERT: H 91 ASP cc_start: 0.4092 (m-30) cc_final: 0.3327 (p0) REVERT: K 212 ASP cc_start: 0.7693 (t0) cc_final: 0.7235 (t0) REVERT: T 151 LYS cc_start: 0.5272 (tptt) cc_final: 0.4951 (mmmt) REVERT: U 212 ASP cc_start: 0.7803 (t0) cc_final: 0.7495 (t0) REVERT: V 212 ASP cc_start: 0.7860 (t0) cc_final: 0.7580 (t0) REVERT: W 91 ASP cc_start: 0.4103 (m-30) cc_final: 0.3332 (p0) REVERT: Z 212 ASP cc_start: 0.7687 (t0) cc_final: 0.7236 (t0) outliers start: 58 outliers final: 49 residues processed: 184 average time/residue: 0.7485 time to fit residues: 244.8694 Evaluate side-chains 183 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 134 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 188 LEU Chi-restraints excluded: chain W residue 188 LEU Chi-restraints excluded: chain Y residue 188 LEU Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain 0 residue 91 ASP Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 1 residue 91 ASP Chi-restraints excluded: chain 1 residue 188 LEU Chi-restraints excluded: chain 2 residue 188 LEU Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 188 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 4.9990 chunk 360 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 350 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 316 optimal weight: 0.1980 chunk 331 optimal weight: 8.9990 chunk 349 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 192 GLN L 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32730 Z= 0.170 Angle : 0.576 5.451 44220 Z= 0.319 Chirality : 0.046 0.164 5460 Planarity : 0.003 0.050 5700 Dihedral : 5.392 22.590 4350 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.27 % Favored : 90.80 % Rotamer: Outliers : 1.43 % Allowed : 6.56 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % 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: -2.04 (0.13), residues: 4110 helix: -0.00 (0.18), residues: 1020 sheet: -1.20 (0.12), residues: 1500 loop : -2.30 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 216 TYR 0.007 0.001 TYR P 100 ARG 0.002 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 147 time to evaluate : 3.939 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: F 212 ASP cc_start: 0.7726 (t0) cc_final: 0.7376 (t0) REVERT: G 212 ASP cc_start: 0.7896 (t0) cc_final: 0.7589 (t0) REVERT: H 91 ASP cc_start: 0.4078 (m-30) cc_final: 0.3713 (p0) REVERT: K 212 ASP cc_start: 0.7684 (t0) cc_final: 0.7289 (t0) REVERT: U 212 ASP cc_start: 0.7723 (t0) cc_final: 0.7375 (t0) REVERT: V 212 ASP cc_start: 0.7891 (t0) cc_final: 0.7588 (t0) REVERT: W 91 ASP cc_start: 0.4088 (m-30) cc_final: 0.3717 (p0) REVERT: Z 212 ASP cc_start: 0.7675 (t0) cc_final: 0.7288 (t0) outliers start: 55 outliers final: 52 residues processed: 174 average time/residue: 0.7269 time to fit residues: 216.8280 Evaluate side-chains 187 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 135 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 188 LEU Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 188 LEU Chi-restraints excluded: chain Y residue 188 LEU Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain 0 residue 91 ASP Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 1 residue 91 ASP Chi-restraints excluded: chain 1 residue 188 LEU Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain 2 residue 188 LEU Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 0.9990 chunk 370 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 257 optimal weight: 0.7980 chunk 388 optimal weight: 0.7980 chunk 357 optimal weight: 0.8980 chunk 309 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 238 optimal weight: 0.4980 chunk 189 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7448 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32730 Z= 0.143 Angle : 0.557 5.426 44220 Z= 0.305 Chirality : 0.046 0.161 5460 Planarity : 0.003 0.056 5700 Dihedral : 5.272 23.265 4350 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.57 % Favored : 91.56 % Rotamer: Outliers : 1.33 % Allowed : 7.08 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % 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: -1.92 (0.13), residues: 4110 helix: 0.07 (0.18), residues: 1020 sheet: -1.13 (0.12), residues: 1500 loop : -2.21 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS U 216 TYR 0.004 0.001 TYR P 100 ARG 0.006 0.000 ARG X 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 135 time to evaluate : 4.202 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: F 212 ASP cc_start: 0.7641 (t0) cc_final: 0.7309 (t0) REVERT: G 212 ASP cc_start: 0.7815 (t0) cc_final: 0.7509 (t0) REVERT: H 91 ASP cc_start: 0.4166 (m-30) cc_final: 0.3495 (p0) REVERT: K 212 ASP cc_start: 0.7641 (t0) cc_final: 0.7278 (t0) REVERT: U 212 ASP cc_start: 0.7642 (t0) cc_final: 0.7315 (t0) REVERT: V 212 ASP cc_start: 0.7809 (t0) cc_final: 0.7503 (t0) REVERT: W 91 ASP cc_start: 0.4174 (m-30) cc_final: 0.3497 (p0) REVERT: X 151 LYS cc_start: 0.5042 (tptt) cc_final: 0.4545 (mmtt) REVERT: Z 212 ASP cc_start: 0.7628 (t0) cc_final: 0.7276 (t0) outliers start: 51 outliers final: 50 residues processed: 158 average time/residue: 0.7163 time to fit residues: 198.2091 Evaluate side-chains 177 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 127 time to evaluate : 4.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 188 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain N residue 115 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain V residue 188 LEU Chi-restraints excluded: chain W residue 188 LEU Chi-restraints excluded: chain Y residue 188 LEU Chi-restraints excluded: chain Z residue 188 LEU Chi-restraints excluded: chain 0 residue 91 ASP Chi-restraints excluded: chain 0 residue 188 LEU Chi-restraints excluded: chain 1 residue 91 ASP Chi-restraints excluded: chain 1 residue 188 LEU Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain 2 residue 188 LEU Chi-restraints excluded: chain 3 residue 115 ASP Chi-restraints excluded: chain 3 residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 3.9990 chunk 329 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 285 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 GLN D 192 GLN F 192 GLN G 192 GLN J 192 GLN K 192 GLN N 192 GLN O 192 GLN P 192 GLN R 192 GLN S 192 GLN U 192 GLN V 192 GLN Y 192 GLN Z 192 GLN 0 192 GLN 2 192 GLN 3 192 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.131121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.115755 restraints weight = 227798.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.118693 restraints weight = 95906.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.120478 restraints weight = 55103.170| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32730 Z= 0.195 Angle : 0.588 5.300 44220 Z= 0.327 Chirality : 0.047 0.162 5460 Planarity : 0.003 0.056 5700 Dihedral : 5.369 22.177 4350 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.00 % Favored : 90.12 % Rotamer: Outliers : 1.28 % Allowed : 7.32 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % 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 (0.13), residues: 4110 helix: 0.04 (0.18), residues: 1020 sheet: -1.18 (0.12), residues: 1500 loop : -2.27 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 216 TYR 0.007 0.001 TYR A 100 ARG 0.008 0.000 ARG X 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7547.73 seconds wall clock time: 136 minutes 32.46 seconds (8192.46 seconds total)