Starting phenix.real_space_refine on Sun Sep 29 00:32:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubg_42088/09_2024/8ubg_42088.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubg_42088/09_2024/8ubg_42088.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/8ubg_42088/09_2024/8ubg_42088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubg_42088/09_2024/8ubg_42088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubg_42088/09_2024/8ubg_42088.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubg_42088/09_2024/8ubg_42088.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= 0.000 sd= 0.389 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 40 5.16 5 C 21980 2.51 5 N 6220 2.21 5 O 6660 1.98 5 H 37600 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 72500 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "B" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "C" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "D" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "E" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "F" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "G" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "H" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "I" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "J" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "K" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "L" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "M" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "N" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "O" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "P" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "Q" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "R" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "S" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Chain: "T" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3625 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 3, 'TRANS': 222} Time building chain proxies: 23.84, per 1000 atoms: 0.33 Number of scatterers: 72500 At special positions: 0 Unit cell: (126.44, 126.44, 223.88, 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 40 16.00 O 6660 8.00 N 6220 7.00 C 21980 6.00 H 37600 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: 13.74 Conformation dependent library (CDL) restraints added in 4.0 seconds 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8960 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 0 sheets defined 92.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 2 through 33 removed outlier: 3.673A pdb=" N ARG A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 47 through 76 removed outlier: 3.586A pdb=" N ILE A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 109 removed outlier: 3.558A pdb=" N LYS A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 150 removed outlier: 4.019A pdb=" N VAL A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 188 removed outlier: 3.659A pdb=" N ALA A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 226 removed outlier: 3.594A pdb=" N GLU A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 33 removed outlier: 3.596A pdb=" N ARG B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 47 through 76 removed outlier: 3.524A pdb=" N ILE B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 109 removed outlier: 3.867A pdb=" N GLU B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 150 removed outlier: 3.857A pdb=" N VAL B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 188 removed outlier: 3.678A pdb=" N ALA B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 226 removed outlier: 3.658A pdb=" N GLU B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 33 removed outlier: 3.622A pdb=" N ARG C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 47 through 76 removed outlier: 3.515A pdb=" N ILE C 56 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 109 removed outlier: 3.508A pdb=" N VAL C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 150 removed outlier: 3.837A pdb=" N VAL C 119 " --> pdb=" O GLU C 115 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 188 removed outlier: 3.656A pdb=" N ALA C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 226 removed outlier: 3.654A pdb=" N GLU C 196 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 199 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 207 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 33 removed outlier: 3.632A pdb=" N ARG D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 47 through 76 removed outlier: 3.533A pdb=" N ALA D 74 " --> pdb=" O LEU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 109 removed outlier: 3.500A pdb=" N VAL D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 150 removed outlier: 3.876A pdb=" N VAL D 119 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D 134 " --> pdb=" O ALA D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 188 removed outlier: 3.650A pdb=" N ALA D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 226 removed outlier: 3.620A pdb=" N GLU D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 199 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE D 214 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 33 removed outlier: 3.632A pdb=" N ARG E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 47 through 76 Processing helix chain 'E' and resid 78 through 109 removed outlier: 3.794A pdb=" N GLU E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 150 removed outlier: 3.943A pdb=" N VAL E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU E 134 " --> pdb=" O ALA E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 188 removed outlier: 3.675A pdb=" N ALA E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 226 removed outlier: 3.593A pdb=" N GLU E 196 " --> pdb=" O ASP E 192 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG E 199 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE E 207 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE E 214 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 33 removed outlier: 3.649A pdb=" N ARG F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 47 through 76 removed outlier: 3.524A pdb=" N ILE F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 109 removed outlier: 3.527A pdb=" N LYS F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 150 removed outlier: 3.859A pdb=" N VAL F 119 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU F 134 " --> pdb=" O ALA F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 188 removed outlier: 3.630A pdb=" N ALA F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 226 removed outlier: 3.639A pdb=" N GLU F 196 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 199 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA F 200 " --> pdb=" O GLU F 196 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE F 207 " --> pdb=" O GLU F 203 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE F 214 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 33 removed outlier: 3.598A pdb=" N ARG G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS G 33 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 47 through 76 Processing helix chain 'G' and resid 78 through 109 removed outlier: 3.541A pdb=" N VAL G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU G 107 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 150 removed outlier: 3.852A pdb=" N VAL G 119 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU G 134 " --> pdb=" O ALA G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 188 removed outlier: 3.610A pdb=" N ALA G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 226 removed outlier: 3.604A pdb=" N GLU G 196 " --> pdb=" O ASP G 192 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG G 199 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA G 200 " --> pdb=" O GLU G 196 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE G 207 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 33 removed outlier: 3.640A pdb=" N ARG H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS H 33 " --> pdb=" O ASP H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 47 through 76 removed outlier: 3.516A pdb=" N ILE H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 109 removed outlier: 3.501A pdb=" N LYS H 96 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU H 107 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 150 removed outlier: 3.869A pdb=" N VAL H 119 " --> pdb=" O GLU H 115 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU H 134 " --> pdb=" O ALA H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 188 removed outlier: 3.638A pdb=" N ALA H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 226 removed outlier: 3.565A pdb=" N GLU H 196 " --> pdb=" O ASP H 192 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG H 199 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA H 200 " --> pdb=" O GLU H 196 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE H 207 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE H 214 " --> pdb=" O GLU H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 33 removed outlier: 3.677A pdb=" N ARG I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 47 through 76 removed outlier: 3.508A pdb=" N ALA I 74 " --> pdb=" O LEU I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 109 removed outlier: 3.582A pdb=" N LYS I 96 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU I 107 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 150 removed outlier: 3.855A pdb=" N VAL I 119 " --> pdb=" O GLU I 115 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU I 134 " --> pdb=" O ALA I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 188 removed outlier: 3.617A pdb=" N ALA I 166 " --> pdb=" O GLU I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 226 removed outlier: 3.614A pdb=" N GLU I 196 " --> pdb=" O ASP I 192 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG I 199 " --> pdb=" O VAL I 195 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE I 207 " --> pdb=" O GLU I 203 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE I 214 " --> pdb=" O GLU I 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 33 removed outlier: 3.697A pdb=" N ARG J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS J 33 " --> pdb=" O ASP J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 47 through 76 removed outlier: 3.520A pdb=" N ILE J 56 " --> pdb=" O GLU J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 109 removed outlier: 3.540A pdb=" N LYS J 96 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU J 107 " --> pdb=" O ARG J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 150 removed outlier: 3.901A pdb=" N VAL J 119 " --> pdb=" O GLU J 115 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU J 134 " --> pdb=" O ALA J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 188 removed outlier: 3.667A pdb=" N ALA J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 226 removed outlier: 3.630A pdb=" N GLU J 196 " --> pdb=" O ASP J 192 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG J 199 " --> pdb=" O VAL J 195 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA J 200 " --> pdb=" O GLU J 196 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE J 214 " --> pdb=" O GLU J 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 33 removed outlier: 3.665A pdb=" N ARG K 22 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS K 33 " --> pdb=" O ASP K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 47 through 76 removed outlier: 3.508A pdb=" N ILE K 56 " --> pdb=" O GLU K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 109 removed outlier: 3.522A pdb=" N LYS K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL K 97 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU K 107 " --> pdb=" O ARG K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 150 removed outlier: 4.022A pdb=" N VAL K 119 " --> pdb=" O GLU K 115 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU K 134 " --> pdb=" O ALA K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 188 removed outlier: 3.643A pdb=" N ALA K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 226 removed outlier: 3.619A pdb=" N GLU K 196 " --> pdb=" O ASP K 192 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG K 199 " --> pdb=" O VAL K 195 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE K 207 " --> pdb=" O GLU K 203 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE K 214 " --> pdb=" O GLU K 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 33 removed outlier: 3.672A pdb=" N ARG L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS L 33 " --> pdb=" O ASP L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 47 through 76 removed outlier: 3.530A pdb=" N ILE L 56 " --> pdb=" O GLU L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 109 removed outlier: 3.537A pdb=" N LYS L 96 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL L 97 " --> pdb=" O ALA L 93 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 150 removed outlier: 3.999A pdb=" N VAL L 119 " --> pdb=" O GLU L 115 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 188 removed outlier: 3.664A pdb=" N ALA L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 226 removed outlier: 3.599A pdb=" N GLU L 196 " --> pdb=" O ASP L 192 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG L 199 " --> pdb=" O VAL L 195 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA L 200 " --> pdb=" O GLU L 196 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE L 207 " --> pdb=" O GLU L 203 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE L 214 " --> pdb=" O GLU L 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 33 removed outlier: 3.652A pdb=" N ARG M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS M 33 " --> pdb=" O ASP M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 45 Processing helix chain 'M' and resid 47 through 76 removed outlier: 3.569A pdb=" N ILE M 56 " --> pdb=" O GLU M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 109 removed outlier: 3.561A pdb=" N LYS M 96 " --> pdb=" O THR M 92 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL M 97 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU M 107 " --> pdb=" O ARG M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 150 removed outlier: 3.918A pdb=" N VAL M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU M 134 " --> pdb=" O ALA M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 188 removed outlier: 3.682A pdb=" N ALA M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 226 removed outlier: 3.637A pdb=" N GLU M 196 " --> pdb=" O ASP M 192 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG M 199 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA M 200 " --> pdb=" O GLU M 196 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE M 207 " --> pdb=" O GLU M 203 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE M 214 " --> pdb=" O GLU M 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 33 removed outlier: 3.651A pdb=" N ARG N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS N 33 " --> pdb=" O ASP N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 45 Processing helix chain 'N' and resid 47 through 76 removed outlier: 3.562A pdb=" N ILE N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 109 removed outlier: 3.531A pdb=" N LYS N 96 " --> pdb=" O THR N 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL N 97 " --> pdb=" O ALA N 93 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU N 107 " --> pdb=" O ARG N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 150 removed outlier: 3.978A pdb=" N VAL N 119 " --> pdb=" O GLU N 115 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU N 134 " --> pdb=" O ALA N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 188 removed outlier: 3.692A pdb=" N ALA N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 226 removed outlier: 3.635A pdb=" N GLU N 196 " --> pdb=" O ASP N 192 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG N 199 " --> pdb=" O VAL N 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA N 200 " --> pdb=" O GLU N 196 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE N 207 " --> pdb=" O GLU N 203 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE N 214 " --> pdb=" O GLU N 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 33 removed outlier: 3.646A pdb=" N ARG O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS O 33 " --> pdb=" O ASP O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 45 Processing helix chain 'O' and resid 47 through 76 removed outlier: 3.602A pdb=" N ILE O 56 " --> pdb=" O GLU O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 109 removed outlier: 3.864A pdb=" N GLU O 107 " --> pdb=" O ARG O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 150 removed outlier: 3.975A pdb=" N VAL O 119 " --> pdb=" O GLU O 115 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU O 134 " --> pdb=" O ALA O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 188 removed outlier: 3.701A pdb=" N ALA O 166 " --> pdb=" O GLU O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 226 removed outlier: 3.634A pdb=" N GLU O 196 " --> pdb=" O ASP O 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG O 199 " --> pdb=" O VAL O 195 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA O 200 " --> pdb=" O GLU O 196 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE O 207 " --> pdb=" O GLU O 203 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE O 214 " --> pdb=" O GLU O 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 33 removed outlier: 3.656A pdb=" N ARG P 22 " --> pdb=" O ALA P 18 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS P 33 " --> pdb=" O ASP P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 45 Processing helix chain 'P' and resid 47 through 76 removed outlier: 3.569A pdb=" N ILE P 56 " --> pdb=" O GLU P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 109 removed outlier: 3.873A pdb=" N GLU P 107 " --> pdb=" O ARG P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 150 removed outlier: 3.903A pdb=" N VAL P 119 " --> pdb=" O GLU P 115 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU P 134 " --> pdb=" O ALA P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 154 through 188 removed outlier: 3.673A pdb=" N ALA P 166 " --> pdb=" O GLU P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 190 through 226 removed outlier: 3.592A pdb=" N GLU P 196 " --> pdb=" O ASP P 192 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG P 199 " --> pdb=" O VAL P 195 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA P 200 " --> pdb=" O GLU P 196 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE P 207 " --> pdb=" O GLU P 203 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE P 214 " --> pdb=" O GLU P 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 33 removed outlier: 3.621A pdb=" N ARG Q 22 " --> pdb=" O ALA Q 18 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS Q 33 " --> pdb=" O ASP Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 45 Processing helix chain 'Q' and resid 47 through 76 removed outlier: 3.562A pdb=" N ILE Q 56 " --> pdb=" O GLU Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 109 removed outlier: 3.538A pdb=" N VAL Q 97 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 150 removed outlier: 3.894A pdb=" N VAL Q 119 " --> pdb=" O GLU Q 115 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU Q 134 " --> pdb=" O ALA Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 154 through 188 removed outlier: 3.709A pdb=" N ALA Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 226 removed outlier: 3.588A pdb=" N GLU Q 196 " --> pdb=" O ASP Q 192 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG Q 199 " --> pdb=" O VAL Q 195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA Q 200 " --> pdb=" O GLU Q 196 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE Q 207 " --> pdb=" O GLU Q 203 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE Q 214 " --> pdb=" O GLU Q 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 33 removed outlier: 3.658A pdb=" N ARG R 22 " --> pdb=" O ALA R 18 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS R 33 " --> pdb=" O ASP R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 47 through 76 removed outlier: 3.531A pdb=" N ILE R 56 " --> pdb=" O GLU R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 109 removed outlier: 3.882A pdb=" N GLU R 107 " --> pdb=" O ARG R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 150 removed outlier: 3.885A pdb=" N VAL R 119 " --> pdb=" O GLU R 115 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 188 removed outlier: 3.730A pdb=" N ALA R 166 " --> pdb=" O GLU R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 226 removed outlier: 3.675A pdb=" N GLU R 196 " --> pdb=" O ASP R 192 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG R 199 " --> pdb=" O VAL R 195 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE R 207 " --> pdb=" O GLU R 203 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE R 214 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 33 removed outlier: 3.608A pdb=" N ARG S 22 " --> pdb=" O ALA S 18 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS S 33 " --> pdb=" O ASP S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 45 Processing helix chain 'S' and resid 47 through 76 removed outlier: 3.560A pdb=" N ILE S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 109 removed outlier: 3.970A pdb=" N GLU S 107 " --> pdb=" O ARG S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 150 removed outlier: 3.890A pdb=" N VAL S 119 " --> pdb=" O GLU S 115 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU S 134 " --> pdb=" O ALA S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 154 through 188 removed outlier: 3.733A pdb=" N ALA S 166 " --> pdb=" O GLU S 162 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 226 removed outlier: 3.677A pdb=" N GLU S 196 " --> pdb=" O ASP S 192 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG S 199 " --> pdb=" O VAL S 195 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA S 200 " --> pdb=" O GLU S 196 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE S 207 " --> pdb=" O GLU S 203 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE S 214 " --> pdb=" O GLU S 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 33 removed outlier: 3.588A pdb=" N ARG T 22 " --> pdb=" O ALA T 18 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS T 33 " --> pdb=" O ASP T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 45 Processing helix chain 'T' and resid 47 through 76 removed outlier: 3.535A pdb=" N ILE T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 109 removed outlier: 3.944A pdb=" N GLU T 107 " --> pdb=" O ARG T 103 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 150 removed outlier: 3.874A pdb=" N VAL T 119 " --> pdb=" O GLU T 115 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU T 134 " --> pdb=" O ALA T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 154 through 188 removed outlier: 3.713A pdb=" N ALA T 166 " --> pdb=" O GLU T 162 " (cutoff:3.500A) Processing helix chain 'T' and resid 190 through 226 removed outlier: 3.677A pdb=" N GLU T 196 " --> pdb=" O ASP T 192 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG T 199 " --> pdb=" O VAL T 195 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE T 207 " --> pdb=" O GLU T 203 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE T 214 " --> pdb=" O GLU T 210 " (cutoff:3.500A) 3361 hydrogen bonds defined for protein. 10083 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: 23.65 Time building geometry restraints manager: 16.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 37600 1.03 - 1.22: 68 1.22 - 1.42: 12611 1.42 - 1.61: 22301 1.61 - 1.80: 80 Bond restraints: 72660 Sorted by residual: bond pdb=" N GLY J 1 " pdb=" CA GLY J 1 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.93e+00 bond pdb=" N GLY I 1 " pdb=" CA GLY I 1 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.91e+00 bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.81e+00 bond pdb=" N GLY K 1 " pdb=" CA GLY K 1 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.76e+00 bond pdb=" N GLY L 1 " pdb=" CA GLY L 1 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.67e+00 ... (remaining 72655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 115934 1.09 - 2.18: 16400 2.18 - 3.26: 676 3.26 - 4.35: 95 4.35 - 5.44: 35 Bond angle restraints: 133140 Sorted by residual: angle pdb=" N LEU L 20 " pdb=" CA LEU L 20 " pdb=" C LEU L 20 " ideal model delta sigma weight residual 111.82 115.12 -3.30 1.16e+00 7.43e-01 8.10e+00 angle pdb=" N LEU P 20 " pdb=" CA LEU P 20 " pdb=" C LEU P 20 " ideal model delta sigma weight residual 111.82 115.03 -3.21 1.16e+00 7.43e-01 7.67e+00 angle pdb=" N LEU K 20 " pdb=" CA LEU K 20 " pdb=" C LEU K 20 " ideal model delta sigma weight residual 111.82 115.02 -3.20 1.16e+00 7.43e-01 7.62e+00 angle pdb=" N LEU H 20 " pdb=" CA LEU H 20 " pdb=" C LEU H 20 " ideal model delta sigma weight residual 111.82 115.02 -3.20 1.16e+00 7.43e-01 7.61e+00 angle pdb=" N LEU A 20 " pdb=" CA LEU A 20 " pdb=" C LEU A 20 " ideal model delta sigma weight residual 111.82 114.98 -3.16 1.16e+00 7.43e-01 7.41e+00 ... (remaining 133135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 29312 14.80 - 29.61: 2213 29.61 - 44.41: 578 44.41 - 59.22: 388 59.22 - 74.02: 349 Dihedral angle restraints: 32840 sinusoidal: 19020 harmonic: 13820 Sorted by residual: dihedral pdb=" CA LYS I 33 " pdb=" C LYS I 33 " pdb=" N LEU I 34 " pdb=" CA LEU I 34 " ideal model delta harmonic sigma weight residual 180.00 158.13 21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LYS D 33 " pdb=" C LYS D 33 " pdb=" N LEU D 34 " pdb=" CA LEU D 34 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LYS B 33 " pdb=" C LYS B 33 " pdb=" N LEU B 34 " pdb=" CA LEU B 34 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 32837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 2800 0.022 - 0.044: 2100 0.044 - 0.066: 1010 0.066 - 0.088: 285 0.088 - 0.110: 45 Chirality restraints: 6240 Sorted by residual: chirality pdb=" CA LYS J 110 " pdb=" N LYS J 110 " pdb=" C LYS J 110 " pdb=" CB LYS J 110 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.05e-01 chirality pdb=" CA ILE F 226 " pdb=" N ILE F 226 " pdb=" C ILE F 226 " pdb=" CB ILE F 226 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.90e-01 chirality pdb=" CA ILE E 226 " pdb=" N ILE E 226 " pdb=" C ILE E 226 " pdb=" CB ILE E 226 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.88e-01 ... (remaining 6237 not shown) Planarity restraints: 10420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA M 49 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ALA M 49 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA M 49 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE M 50 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 49 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ALA L 49 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA L 49 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE L 50 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 49 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ALA N 49 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA N 49 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE N 50 " 0.020 2.00e-02 2.50e+03 ... (remaining 10417 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 5811 2.24 - 2.83: 172993 2.83 - 3.42: 187580 3.42 - 4.01: 243557 4.01 - 4.60: 398067 Nonbonded interactions: 1008008 Sorted by model distance: nonbonded pdb="HH11 ARG N 158 " pdb=" OE2 GLU N 162 " model vdw 1.650 2.450 nonbonded pdb=" OE2 GLU Q 184 " pdb="HD21 ASN Q 188 " model vdw 1.661 2.450 nonbonded pdb=" HG SER H 2 " pdb=" OE1 GLU H 4 " model vdw 1.662 2.450 nonbonded pdb="HH11 ARG Q 158 " pdb=" OE2 GLU Q 162 " model vdw 1.674 2.450 nonbonded pdb=" HG SER K 2 " pdb=" OE1 GLU K 4 " model vdw 1.675 2.450 ... (remaining 1008003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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' } 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: 1.930 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: 1.900 Check model and map are aligned: 0.400 Set scattering table: 0.490 Process input model: 107.970 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.005 0.050 35060 Z= 0.350 Angle : 0.736 5.439 47440 Z= 0.472 Chirality : 0.035 0.110 6240 Planarity : 0.010 0.072 5980 Dihedral : 13.097 74.024 13480 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.10), residues: 4480 helix: -1.34 (0.06), residues: 4100 sheet: None (None), residues: 0 loop : -3.06 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS S 121 ARG 0.014 0.002 ARG L 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 925 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8218 (mttt) cc_final: 0.7702 (mtmt) REVERT: A 103 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7448 (ttm-80) REVERT: A 108 GLU cc_start: 0.7850 (tp30) cc_final: 0.7516 (tp30) REVERT: A 144 GLU cc_start: 0.7154 (tt0) cc_final: 0.6792 (tt0) REVERT: A 151 ASN cc_start: 0.8156 (t0) cc_final: 0.7726 (t0) REVERT: A 172 LYS cc_start: 0.8120 (tttt) cc_final: 0.7839 (ttmm) REVERT: B 19 GLU cc_start: 0.7336 (tp30) cc_final: 0.7086 (tp30) REVERT: B 69 GLU cc_start: 0.7730 (tt0) cc_final: 0.7215 (mm-30) REVERT: B 87 LYS cc_start: 0.7429 (mttt) cc_final: 0.7078 (mttp) REVERT: B 89 LYS cc_start: 0.8259 (mttt) cc_final: 0.7749 (mtpp) REVERT: B 134 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7146 (mm-30) REVERT: C 19 GLU cc_start: 0.7293 (tp30) cc_final: 0.6789 (tt0) REVERT: C 59 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7156 (mm-30) REVERT: C 69 GLU cc_start: 0.7685 (tt0) cc_final: 0.6731 (tp30) REVERT: C 89 LYS cc_start: 0.8482 (mttt) cc_final: 0.8032 (mtpp) REVERT: C 172 LYS cc_start: 0.7120 (tttt) cc_final: 0.6852 (tttt) REVERT: D 69 GLU cc_start: 0.7620 (tt0) cc_final: 0.6679 (tp30) REVERT: D 89 LYS cc_start: 0.8528 (mttt) cc_final: 0.8121 (mtpp) REVERT: D 94 ARG cc_start: 0.7995 (ttt-90) cc_final: 0.7655 (ttm-80) REVERT: D 103 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6699 (mtt-85) REVERT: D 106 THR cc_start: 0.8631 (m) cc_final: 0.8091 (p) REVERT: D 170 GLU cc_start: 0.8016 (tp30) cc_final: 0.7551 (tp30) REVERT: E 77 MET cc_start: 0.7663 (mtt) cc_final: 0.7331 (mtm) REVERT: E 87 LYS cc_start: 0.7779 (mttt) cc_final: 0.7439 (mttm) REVERT: E 89 LYS cc_start: 0.8323 (mttt) cc_final: 0.7754 (mtpp) REVERT: E 111 LYS cc_start: 0.7169 (ttpt) cc_final: 0.6925 (tptp) REVERT: E 144 GLU cc_start: 0.7419 (tt0) cc_final: 0.7080 (tt0) REVERT: F 11 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6498 (mt-10) REVERT: F 103 ARG cc_start: 0.7757 (mtt180) cc_final: 0.7395 (tpp-160) REVERT: F 144 GLU cc_start: 0.7410 (tt0) cc_final: 0.6442 (mt-10) REVERT: F 170 GLU cc_start: 0.8320 (tp30) cc_final: 0.7793 (tp30) REVERT: F 172 LYS cc_start: 0.7606 (tttt) cc_final: 0.7316 (ttmm) REVERT: F 196 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6158 (mm-30) REVERT: G 47 ASN cc_start: 0.8284 (m-40) cc_final: 0.8020 (m110) REVERT: G 69 GLU cc_start: 0.7305 (tt0) cc_final: 0.6923 (mt-10) REVERT: G 89 LYS cc_start: 0.8251 (mttt) cc_final: 0.8009 (mtpp) REVERT: G 103 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7062 (mtt-85) REVERT: G 108 GLU cc_start: 0.8096 (tp30) cc_final: 0.7874 (tp30) REVERT: G 144 GLU cc_start: 0.7469 (tt0) cc_final: 0.7245 (tt0) REVERT: G 172 LYS cc_start: 0.7299 (tttt) cc_final: 0.7093 (tttm) REVERT: H 87 LYS cc_start: 0.7960 (mttt) cc_final: 0.7704 (mttm) REVERT: H 89 LYS cc_start: 0.8278 (mttt) cc_final: 0.7859 (mtmt) REVERT: H 108 GLU cc_start: 0.8227 (tp30) cc_final: 0.7664 (tp30) REVERT: H 111 LYS cc_start: 0.7645 (ttpt) cc_final: 0.7073 (tptp) REVERT: H 144 GLU cc_start: 0.7214 (tt0) cc_final: 0.6959 (mt-10) REVERT: H 177 SER cc_start: 0.8770 (t) cc_final: 0.8415 (p) REVERT: I 21 LYS cc_start: 0.7490 (mtpt) cc_final: 0.7277 (tppt) REVERT: I 52 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7132 (mt-10) REVERT: I 89 LYS cc_start: 0.8061 (mttt) cc_final: 0.7745 (mtpt) REVERT: I 172 LYS cc_start: 0.7633 (tttt) cc_final: 0.7427 (tttm) REVERT: J 11 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6676 (mm-30) REVERT: J 89 LYS cc_start: 0.7997 (mttt) cc_final: 0.7747 (mtmt) REVERT: J 151 ASN cc_start: 0.8131 (t0) cc_final: 0.7710 (t0) REVERT: J 172 LYS cc_start: 0.7321 (tttt) cc_final: 0.7094 (tttm) REVERT: K 80 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6878 (mt-10) REVERT: K 144 GLU cc_start: 0.7277 (tt0) cc_final: 0.6970 (mt-10) REVERT: K 151 ASN cc_start: 0.8334 (t0) cc_final: 0.8112 (t0) REVERT: K 172 LYS cc_start: 0.7931 (tttt) cc_final: 0.7585 (tttm) REVERT: L 89 LYS cc_start: 0.8082 (mttt) cc_final: 0.7705 (mtpt) REVERT: L 103 ARG cc_start: 0.7520 (mtt180) cc_final: 0.6917 (tpp-160) REVERT: L 116 ASP cc_start: 0.7505 (m-30) cc_final: 0.7304 (m-30) REVERT: L 144 GLU cc_start: 0.6979 (tt0) cc_final: 0.6521 (mt-10) REVERT: L 170 GLU cc_start: 0.7861 (tp30) cc_final: 0.7631 (tp30) REVERT: L 172 LYS cc_start: 0.8203 (tttt) cc_final: 0.7917 (ttmm) REVERT: M 26 LYS cc_start: 0.7133 (tptt) cc_final: 0.6752 (tttp) REVERT: M 52 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6802 (mt-10) REVERT: M 59 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7201 (tt0) REVERT: M 77 MET cc_start: 0.6879 (mtt) cc_final: 0.6658 (mtt) REVERT: M 89 LYS cc_start: 0.7800 (mttt) cc_final: 0.7501 (mtmt) REVERT: M 103 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7065 (mtt-85) REVERT: M 107 GLU cc_start: 0.8034 (tt0) cc_final: 0.7770 (mt-10) REVERT: M 151 ASN cc_start: 0.8193 (t0) cc_final: 0.7804 (t0) REVERT: N 103 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7285 (mtt-85) REVERT: N 144 GLU cc_start: 0.7634 (tt0) cc_final: 0.7427 (tt0) REVERT: N 170 GLU cc_start: 0.8033 (tp30) cc_final: 0.7451 (tp30) REVERT: N 172 LYS cc_start: 0.7814 (tttt) cc_final: 0.7606 (ttmm) REVERT: O 8 LYS cc_start: 0.7716 (tttm) cc_final: 0.7514 (ttpp) REVERT: O 26 LYS cc_start: 0.6962 (tptt) cc_final: 0.6706 (tptp) REVERT: O 69 GLU cc_start: 0.6829 (tt0) cc_final: 0.6287 (tp30) REVERT: O 89 LYS cc_start: 0.8201 (mttt) cc_final: 0.7610 (mtpt) REVERT: O 96 LYS cc_start: 0.8224 (mttt) cc_final: 0.7913 (mtpp) REVERT: O 139 ILE cc_start: 0.8767 (mt) cc_final: 0.8506 (mt) REVERT: O 144 GLU cc_start: 0.7656 (tt0) cc_final: 0.7148 (tt0) REVERT: O 153 THR cc_start: 0.8493 (p) cc_final: 0.8254 (m) REVERT: P 11 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7158 (mm-30) REVERT: P 89 LYS cc_start: 0.8533 (mttt) cc_final: 0.8107 (mttm) REVERT: P 103 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7461 (ttm-80) REVERT: P 144 GLU cc_start: 0.7176 (tt0) cc_final: 0.6811 (tt0) REVERT: P 172 LYS cc_start: 0.7970 (tttt) cc_final: 0.7759 (ttpp) REVERT: P 203 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7482 (tt0) REVERT: Q 69 GLU cc_start: 0.6908 (tt0) cc_final: 0.6497 (tp30) REVERT: Q 87 LYS cc_start: 0.7777 (mttt) cc_final: 0.7505 (mtmt) REVERT: Q 89 LYS cc_start: 0.8231 (mttt) cc_final: 0.7759 (mtpp) REVERT: Q 110 LYS cc_start: 0.7554 (mttt) cc_final: 0.7128 (mttp) REVERT: Q 111 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6942 (tptp) REVERT: Q 144 GLU cc_start: 0.7464 (tt0) cc_final: 0.7226 (tt0) REVERT: Q 151 ASN cc_start: 0.7722 (t0) cc_final: 0.7436 (t0) REVERT: Q 153 THR cc_start: 0.8196 (p) cc_final: 0.7903 (m) REVERT: R 26 LYS cc_start: 0.7381 (tptt) cc_final: 0.6985 (tttp) REVERT: R 47 ASN cc_start: 0.8842 (m-40) cc_final: 0.8549 (m110) REVERT: R 87 LYS cc_start: 0.7580 (mttt) cc_final: 0.7120 (mtpt) REVERT: R 89 LYS cc_start: 0.8264 (mttt) cc_final: 0.7830 (mtpt) REVERT: R 107 GLU cc_start: 0.8298 (tt0) cc_final: 0.7963 (tt0) REVERT: R 109 LEU cc_start: 0.7771 (tp) cc_final: 0.7503 (tt) REVERT: R 144 GLU cc_start: 0.7231 (tt0) cc_final: 0.6769 (tt0) REVERT: R 153 THR cc_start: 0.7928 (p) cc_final: 0.7724 (m) REVERT: R 173 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6684 (mtp-110) REVERT: R 177 SER cc_start: 0.8282 (t) cc_final: 0.8021 (p) REVERT: R 196 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7631 (mm-30) REVERT: S 52 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6833 (mt-10) REVERT: S 87 LYS cc_start: 0.7594 (mttt) cc_final: 0.7081 (mtpp) REVERT: S 123 ARG cc_start: 0.8074 (mtp-110) cc_final: 0.7667 (mtp85) REVERT: S 127 ASN cc_start: 0.8270 (m-40) cc_final: 0.7851 (m110) REVERT: S 144 GLU cc_start: 0.7503 (tt0) cc_final: 0.7133 (tt0) REVERT: S 172 LYS cc_start: 0.7812 (tttt) cc_final: 0.7520 (ttmm) REVERT: S 181 ILE cc_start: 0.7247 (tt) cc_final: 0.7046 (mp) REVERT: S 203 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7282 (mm-30) REVERT: T 60 ASN cc_start: 0.8262 (t0) cc_final: 0.7974 (t0) REVERT: T 87 LYS cc_start: 0.7830 (mttt) cc_final: 0.7270 (mtmt) REVERT: T 96 LYS cc_start: 0.8304 (mttt) cc_final: 0.8097 (mtpp) REVERT: T 123 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7904 (mtp85) REVERT: T 144 GLU cc_start: 0.7212 (tt0) cc_final: 0.6775 (tt0) REVERT: T 171 LEU cc_start: 0.8552 (tp) cc_final: 0.8332 (tp) REVERT: T 203 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7731 (mt-10) outliers start: 0 outliers final: 0 residues processed: 925 average time/residue: 1.1927 time to fit residues: 1635.8591 Evaluate side-chains 711 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 711 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 0.9990 chunk 333 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 224 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 399 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN B 197 HIS C 151 ASN C 197 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN H 47 ASN H 197 HIS H 198 ASN ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 197 HIS K 205 ASN ** L 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 197 HIS ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 ASN N 61 ASN N 135 ASN N 197 HIS ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 HIS Q 61 ASN ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 197 HIS S 61 ASN S 122 ASN S 151 ASN S 205 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35060 Z= 0.235 Angle : 0.510 4.758 47440 Z= 0.288 Chirality : 0.028 0.102 6240 Planarity : 0.003 0.051 5980 Dihedral : 3.943 16.950 4760 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.05 % Allowed : 6.65 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.12), residues: 4480 helix: 1.91 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -3.60 (0.21), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS T 197 ARG 0.006 0.000 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 692 time to evaluate : 4.074 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: A 73 ARG cc_start: 0.7190 (tpp-160) cc_final: 0.6653 (mmm-85) REVERT: A 86 LEU cc_start: 0.7787 (mt) cc_final: 0.7188 (mp) REVERT: A 108 GLU cc_start: 0.7717 (tp30) cc_final: 0.7301 (tp30) REVERT: A 151 ASN cc_start: 0.8175 (t0) cc_final: 0.7831 (t0) REVERT: B 69 GLU cc_start: 0.7654 (tt0) cc_final: 0.7237 (mm-30) REVERT: B 77 MET cc_start: 0.6747 (mtm) cc_final: 0.6450 (mtm) REVERT: B 87 LYS cc_start: 0.7271 (mttt) cc_final: 0.6891 (mttt) REVERT: B 106 THR cc_start: 0.8738 (m) cc_final: 0.8233 (p) REVERT: B 107 GLU cc_start: 0.7237 (tt0) cc_final: 0.7027 (mt-10) REVERT: B 134 GLU cc_start: 0.7245 (mm-30) cc_final: 0.7030 (mm-30) REVERT: C 19 GLU cc_start: 0.7226 (tp30) cc_final: 0.6842 (tt0) REVERT: C 69 GLU cc_start: 0.7555 (tt0) cc_final: 0.6676 (tp30) REVERT: C 89 LYS cc_start: 0.8464 (mttt) cc_final: 0.8118 (mtpp) REVERT: C 94 ARG cc_start: 0.8100 (ttt-90) cc_final: 0.7696 (mtp85) REVERT: C 106 THR cc_start: 0.8736 (m) cc_final: 0.8258 (p) REVERT: C 148 ARG cc_start: 0.6939 (ttp-110) cc_final: 0.6720 (ttm110) REVERT: D 69 GLU cc_start: 0.7527 (tt0) cc_final: 0.6672 (tp30) REVERT: D 89 LYS cc_start: 0.8464 (mttt) cc_final: 0.8081 (mtpp) REVERT: D 103 ARG cc_start: 0.7042 (mtt180) cc_final: 0.6833 (mtt-85) REVERT: D 106 THR cc_start: 0.8592 (m) cc_final: 0.7975 (p) REVERT: D 170 GLU cc_start: 0.7983 (tp30) cc_final: 0.7574 (tp30) REVERT: E 77 MET cc_start: 0.7978 (mtt) cc_final: 0.7630 (mtm) REVERT: E 87 LYS cc_start: 0.7778 (mttt) cc_final: 0.7438 (mttm) REVERT: E 89 LYS cc_start: 0.8272 (mttt) cc_final: 0.7710 (mtpp) REVERT: F 107 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7499 (mt-10) REVERT: F 170 GLU cc_start: 0.8407 (tp30) cc_final: 0.8149 (tp30) REVERT: F 172 LYS cc_start: 0.7582 (tttt) cc_final: 0.7222 (ttmt) REVERT: G 89 LYS cc_start: 0.8207 (mttt) cc_final: 0.7978 (mtpp) REVERT: G 96 LYS cc_start: 0.8550 (mttt) cc_final: 0.8328 (mttm) REVERT: G 144 GLU cc_start: 0.7475 (tt0) cc_final: 0.7235 (tt0) REVERT: G 156 GLU cc_start: 0.6664 (mp0) cc_final: 0.6425 (mt-10) REVERT: G 172 LYS cc_start: 0.7309 (tttt) cc_final: 0.7092 (tttm) REVERT: H 8 LYS cc_start: 0.7836 (tttm) cc_final: 0.7365 (ttpp) REVERT: H 11 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6216 (mt-10) REVERT: H 87 LYS cc_start: 0.7884 (mttt) cc_final: 0.7606 (mttm) REVERT: H 89 LYS cc_start: 0.8188 (mttt) cc_final: 0.7809 (mtmt) REVERT: H 108 GLU cc_start: 0.8260 (tp30) cc_final: 0.7949 (tm-30) REVERT: H 111 LYS cc_start: 0.7605 (ttpt) cc_final: 0.7212 (tptp) REVERT: H 144 GLU cc_start: 0.7209 (tt0) cc_final: 0.6885 (mt-10) REVERT: H 198 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.8003 (m-40) REVERT: I 26 LYS cc_start: 0.6702 (tptt) cc_final: 0.6486 (tppt) REVERT: I 187 LYS cc_start: 0.7916 (tppt) cc_final: 0.7388 (tppt) REVERT: J 89 LYS cc_start: 0.7871 (mttt) cc_final: 0.7639 (mtmt) REVERT: J 151 ASN cc_start: 0.8361 (t0) cc_final: 0.7909 (t0) REVERT: J 172 LYS cc_start: 0.7389 (tttt) cc_final: 0.7144 (tttm) REVERT: J 187 LYS cc_start: 0.7631 (tptp) cc_final: 0.7427 (tppt) REVERT: K 5 GLU cc_start: 0.7656 (tt0) cc_final: 0.7450 (mt-10) REVERT: K 144 GLU cc_start: 0.7228 (tt0) cc_final: 0.6844 (mt-10) REVERT: K 151 ASN cc_start: 0.8561 (t0) cc_final: 0.8234 (t0) REVERT: K 172 LYS cc_start: 0.7920 (tttt) cc_final: 0.7578 (tttm) REVERT: L 80 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6706 (tt0) REVERT: L 89 LYS cc_start: 0.7884 (mttt) cc_final: 0.7657 (mtpt) REVERT: L 148 ARG cc_start: 0.7125 (ttp80) cc_final: 0.6868 (ttp80) REVERT: L 170 GLU cc_start: 0.7795 (tp30) cc_final: 0.7296 (tt0) REVERT: L 172 LYS cc_start: 0.8287 (tttt) cc_final: 0.8031 (ttmm) REVERT: M 26 LYS cc_start: 0.7145 (tptt) cc_final: 0.6679 (mttt) REVERT: M 52 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6569 (mt-10) REVERT: M 77 MET cc_start: 0.7239 (mtt) cc_final: 0.6999 (mtt) REVERT: M 80 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6710 (tt0) REVERT: M 89 LYS cc_start: 0.7883 (mttt) cc_final: 0.7579 (mtmt) REVERT: M 148 ARG cc_start: 0.7179 (mpt180) cc_final: 0.6783 (tpp-160) REVERT: M 151 ASN cc_start: 0.8300 (t0) cc_final: 0.7943 (t0) REVERT: N 107 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7441 (mt-10) REVERT: N 151 ASN cc_start: 0.7811 (t0) cc_final: 0.7227 (t0) REVERT: N 172 LYS cc_start: 0.7698 (tttt) cc_final: 0.7493 (ttmm) REVERT: O 8 LYS cc_start: 0.7750 (tttm) cc_final: 0.7539 (ttpp) REVERT: O 26 LYS cc_start: 0.6775 (tptt) cc_final: 0.6551 (tptp) REVERT: O 69 GLU cc_start: 0.6541 (tt0) cc_final: 0.6200 (tp30) REVERT: O 87 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7701 (mtmt) REVERT: O 89 LYS cc_start: 0.8111 (mttt) cc_final: 0.7580 (mtpt) REVERT: O 94 ARG cc_start: 0.8332 (ttt-90) cc_final: 0.7929 (ttt90) REVERT: O 153 THR cc_start: 0.8571 (p) cc_final: 0.8328 (m) REVERT: O 165 LYS cc_start: 0.7648 (mtpp) cc_final: 0.7412 (mtpp) REVERT: P 11 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7178 (mm-30) REVERT: P 89 LYS cc_start: 0.8154 (mttt) cc_final: 0.7826 (mttm) REVERT: P 111 LYS cc_start: 0.7618 (tptm) cc_final: 0.7380 (ttmt) REVERT: P 165 LYS cc_start: 0.7389 (mtpp) cc_final: 0.7166 (mtpp) REVERT: P 172 LYS cc_start: 0.8017 (tttt) cc_final: 0.7802 (ttpp) REVERT: Q 52 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6618 (mt-10) REVERT: Q 69 GLU cc_start: 0.6600 (tt0) cc_final: 0.6305 (tp30) REVERT: Q 87 LYS cc_start: 0.7546 (mttt) cc_final: 0.7328 (mtmt) REVERT: Q 89 LYS cc_start: 0.8140 (mttt) cc_final: 0.7837 (mtpp) REVERT: Q 110 LYS cc_start: 0.7603 (mttt) cc_final: 0.7126 (mttp) REVERT: Q 151 ASN cc_start: 0.7735 (t0) cc_final: 0.7339 (t0) REVERT: Q 153 THR cc_start: 0.8180 (p) cc_final: 0.7870 (m) REVERT: Q 163 GLU cc_start: 0.8429 (tp30) cc_final: 0.7901 (tp30) REVERT: Q 196 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6655 (mm-30) REVERT: R 4 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6268 (tt0) REVERT: R 26 LYS cc_start: 0.7294 (tptt) cc_final: 0.6920 (tttp) REVERT: R 47 ASN cc_start: 0.8465 (m-40) cc_final: 0.8079 (m-40) REVERT: R 87 LYS cc_start: 0.7589 (mttt) cc_final: 0.7080 (mtmt) REVERT: R 89 LYS cc_start: 0.8068 (mttt) cc_final: 0.7805 (mtpt) REVERT: R 107 GLU cc_start: 0.8393 (tt0) cc_final: 0.8165 (tt0) REVERT: R 144 GLU cc_start: 0.7133 (tt0) cc_final: 0.6828 (tt0) REVERT: R 173 ARG cc_start: 0.6975 (mtm-85) cc_final: 0.6579 (mtp-110) REVERT: S 5 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7195 (tt0) REVERT: S 111 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7667 (ttmt) REVERT: S 127 ASN cc_start: 0.8268 (m-40) cc_final: 0.7951 (m110) REVERT: S 144 GLU cc_start: 0.7546 (tt0) cc_final: 0.7254 (tt0) REVERT: S 151 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7100 (t0) REVERT: S 172 LYS cc_start: 0.7796 (tttt) cc_final: 0.7474 (ttmm) REVERT: T 87 LYS cc_start: 0.7802 (mttt) cc_final: 0.7320 (mtmt) REVERT: T 96 LYS cc_start: 0.8295 (mttt) cc_final: 0.8073 (tttp) REVERT: T 123 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7605 (mtp85) REVERT: T 144 GLU cc_start: 0.7077 (tt0) cc_final: 0.6750 (tt0) REVERT: T 172 LYS cc_start: 0.7509 (tttm) cc_final: 0.6612 (ptmm) REVERT: T 203 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7506 (mt-10) outliers start: 40 outliers final: 32 residues processed: 706 average time/residue: 1.1868 time to fit residues: 1269.9925 Evaluate side-chains 630 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 595 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 183 GLU Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 111 LYS Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 151 ASN Chi-restraints excluded: chain T residue 208 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 400 optimal weight: 4.9990 chunk 432 optimal weight: 2.9990 chunk 356 optimal weight: 4.9990 chunk 396 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 321 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN A 136 ASN A 197 HIS A 211 ASN A 212 ASN B 47 ASN D 47 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 HIS G 135 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN K 61 ASN K 136 ASN K 211 ASN K 212 ASN L 47 ASN L 60 ASN L 61 ASN L 136 ASN L 211 ASN L 212 ASN ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 ASN ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 60 ASN T 205 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35060 Z= 0.254 Angle : 0.483 4.565 47440 Z= 0.271 Chirality : 0.028 0.112 6240 Planarity : 0.003 0.038 5980 Dihedral : 3.666 16.072 4760 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.15 % Allowed : 7.51 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.12), residues: 4480 helix: 2.58 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -3.12 (0.23), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS H 197 ARG 0.006 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 626 time to evaluate : 4.089 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: A 73 ARG cc_start: 0.7185 (tpp-160) cc_final: 0.6587 (mpt-90) REVERT: A 86 LEU cc_start: 0.7835 (mt) cc_final: 0.7181 (mp) REVERT: A 144 GLU cc_start: 0.6899 (tt0) cc_final: 0.6509 (tt0) REVERT: A 151 ASN cc_start: 0.8222 (t0) cc_final: 0.7837 (t0) REVERT: B 69 GLU cc_start: 0.7569 (tt0) cc_final: 0.7232 (mm-30) REVERT: B 77 MET cc_start: 0.6759 (mtm) cc_final: 0.6509 (mtm) REVERT: B 87 LYS cc_start: 0.7199 (mttt) cc_final: 0.6816 (mttt) REVERT: B 106 THR cc_start: 0.8818 (m) cc_final: 0.8276 (p) REVERT: B 107 GLU cc_start: 0.7168 (tt0) cc_final: 0.6951 (mt-10) REVERT: B 134 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6810 (mm-30) REVERT: B 137 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7103 (ttm-80) REVERT: C 19 GLU cc_start: 0.7274 (tp30) cc_final: 0.6882 (tt0) REVERT: C 26 LYS cc_start: 0.7887 (ttmm) cc_final: 0.7640 (tptp) REVERT: C 69 GLU cc_start: 0.7580 (tt0) cc_final: 0.6686 (tp30) REVERT: C 89 LYS cc_start: 0.8480 (mttt) cc_final: 0.8150 (mtpp) REVERT: C 170 GLU cc_start: 0.7962 (tp30) cc_final: 0.7674 (tp30) REVERT: D 69 GLU cc_start: 0.7334 (tt0) cc_final: 0.6591 (tp30) REVERT: D 89 LYS cc_start: 0.8368 (mttt) cc_final: 0.8039 (mtpp) REVERT: D 103 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6736 (mtt-85) REVERT: D 106 THR cc_start: 0.8616 (m) cc_final: 0.8025 (p) REVERT: D 170 GLU cc_start: 0.7977 (tp30) cc_final: 0.7564 (tp30) REVERT: E 77 MET cc_start: 0.7947 (mtt) cc_final: 0.7653 (mtt) REVERT: E 89 LYS cc_start: 0.8203 (mttt) cc_final: 0.7736 (mtpp) REVERT: E 107 GLU cc_start: 0.7577 (tt0) cc_final: 0.7037 (tt0) REVERT: E 210 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7375 (tm-30) REVERT: F 11 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6574 (mt-10) REVERT: F 172 LYS cc_start: 0.7572 (tttt) cc_final: 0.7226 (ttmt) REVERT: G 89 LYS cc_start: 0.8239 (mttt) cc_final: 0.8005 (mtpp) REVERT: H 8 LYS cc_start: 0.7853 (tttm) cc_final: 0.7358 (ttpp) REVERT: H 87 LYS cc_start: 0.7642 (mttt) cc_final: 0.7377 (mttm) REVERT: H 89 LYS cc_start: 0.8197 (mttt) cc_final: 0.7828 (mtmt) REVERT: H 108 GLU cc_start: 0.8225 (tp30) cc_final: 0.7991 (tm-30) REVERT: H 111 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7179 (tptp) REVERT: H 144 GLU cc_start: 0.7260 (tt0) cc_final: 0.6893 (mt-10) REVERT: H 210 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7908 (tm-30) REVERT: I 26 LYS cc_start: 0.6711 (tptt) cc_final: 0.6249 (mmmt) REVERT: I 73 ARG cc_start: 0.7785 (tpp-160) cc_final: 0.7356 (mmt-90) REVERT: I 173 ARG cc_start: 0.7136 (ttp80) cc_final: 0.6916 (ttp80) REVERT: J 11 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6497 (mm-30) REVERT: J 89 LYS cc_start: 0.7873 (mttt) cc_final: 0.7630 (mtmt) REVERT: J 151 ASN cc_start: 0.8384 (t0) cc_final: 0.7889 (t0) REVERT: J 172 LYS cc_start: 0.7420 (tttt) cc_final: 0.7102 (tttm) REVERT: J 187 LYS cc_start: 0.7502 (tptp) cc_final: 0.7249 (tppt) REVERT: K 144 GLU cc_start: 0.7242 (tt0) cc_final: 0.6862 (mt-10) REVERT: K 151 ASN cc_start: 0.8578 (t0) cc_final: 0.8179 (t0) REVERT: L 26 LYS cc_start: 0.6594 (tptp) cc_final: 0.6079 (mtpt) REVERT: L 80 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6769 (tt0) REVERT: L 170 GLU cc_start: 0.7784 (tp30) cc_final: 0.7273 (tt0) REVERT: L 172 LYS cc_start: 0.8250 (tttt) cc_final: 0.7979 (ttmm) REVERT: M 26 LYS cc_start: 0.7053 (tptt) cc_final: 0.6605 (mtpt) REVERT: M 52 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6580 (mt-10) REVERT: M 77 MET cc_start: 0.7283 (mtt) cc_final: 0.6996 (mtt) REVERT: M 80 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6692 (tt0) REVERT: M 89 LYS cc_start: 0.7849 (mttt) cc_final: 0.7510 (mtmt) REVERT: M 148 ARG cc_start: 0.7110 (mpt180) cc_final: 0.6758 (tpp-160) REVERT: M 165 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7794 (mtpp) REVERT: N 107 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: N 172 LYS cc_start: 0.7707 (tttt) cc_final: 0.7506 (ttmm) REVERT: O 4 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6235 (mm-30) REVERT: O 8 LYS cc_start: 0.7769 (tttm) cc_final: 0.7548 (ttpp) REVERT: O 26 LYS cc_start: 0.6827 (tptt) cc_final: 0.6490 (mmmt) REVERT: O 69 GLU cc_start: 0.6527 (tt0) cc_final: 0.6204 (tp30) REVERT: O 87 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7743 (mtmt) REVERT: O 89 LYS cc_start: 0.8134 (mttt) cc_final: 0.7575 (mtpt) REVERT: O 94 ARG cc_start: 0.8353 (ttt-90) cc_final: 0.7965 (ttm-80) REVERT: O 153 THR cc_start: 0.8611 (p) cc_final: 0.8407 (m) REVERT: O 165 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7454 (mtpp) REVERT: P 11 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7227 (mm-30) REVERT: P 89 LYS cc_start: 0.8209 (mttt) cc_final: 0.7895 (mttm) REVERT: P 111 LYS cc_start: 0.7588 (tptm) cc_final: 0.7346 (ttmt) REVERT: P 165 LYS cc_start: 0.7423 (mtpp) cc_final: 0.7175 (mtpp) REVERT: P 172 LYS cc_start: 0.8020 (tttt) cc_final: 0.7788 (ttpp) REVERT: Q 52 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6575 (mt-10) REVERT: Q 69 GLU cc_start: 0.6691 (tt0) cc_final: 0.6438 (tp30) REVERT: Q 87 LYS cc_start: 0.7647 (mttt) cc_final: 0.7409 (mtmt) REVERT: Q 89 LYS cc_start: 0.8076 (mttt) cc_final: 0.7822 (mtpp) REVERT: Q 110 LYS cc_start: 0.7688 (mttt) cc_final: 0.7174 (mttp) REVERT: Q 153 THR cc_start: 0.8278 (p) cc_final: 0.8031 (m) REVERT: Q 163 GLU cc_start: 0.8406 (tp30) cc_final: 0.8118 (tp30) REVERT: Q 170 GLU cc_start: 0.8225 (tp30) cc_final: 0.7696 (tp30) REVERT: Q 196 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6848 (mm-30) REVERT: R 26 LYS cc_start: 0.7285 (tptt) cc_final: 0.6927 (tttp) REVERT: R 77 MET cc_start: 0.5042 (ptp) cc_final: 0.4593 (ptp) REVERT: R 87 LYS cc_start: 0.7560 (mttt) cc_final: 0.7012 (mtmt) REVERT: R 89 LYS cc_start: 0.8096 (mttt) cc_final: 0.7803 (mtpt) REVERT: R 107 GLU cc_start: 0.8324 (tt0) cc_final: 0.8098 (tt0) REVERT: R 151 ASN cc_start: 0.8368 (t0) cc_final: 0.8159 (t0) REVERT: R 173 ARG cc_start: 0.6972 (mtm-85) cc_final: 0.6572 (mtp-110) REVERT: R 203 GLU cc_start: 0.7786 (tt0) cc_final: 0.7060 (mm-30) REVERT: S 5 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7278 (tt0) REVERT: S 8 LYS cc_start: 0.7983 (tttp) cc_final: 0.7490 (ttpp) REVERT: S 111 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7877 (ttmt) REVERT: S 123 ARG cc_start: 0.7912 (mtp-110) cc_final: 0.7646 (mtp85) REVERT: S 127 ASN cc_start: 0.8359 (m-40) cc_final: 0.8015 (m110) REVERT: S 172 LYS cc_start: 0.7802 (tttt) cc_final: 0.7453 (ttmm) REVERT: T 69 GLU cc_start: 0.6766 (tt0) cc_final: 0.6180 (mm-30) REVERT: T 87 LYS cc_start: 0.7838 (mttt) cc_final: 0.7313 (mtmt) REVERT: T 123 ARG cc_start: 0.8134 (mtp-110) cc_final: 0.7754 (mtp85) REVERT: T 170 GLU cc_start: 0.7556 (tp30) cc_final: 0.7328 (tp30) REVERT: T 203 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7748 (mt-10) outliers start: 44 outliers final: 33 residues processed: 637 average time/residue: 1.2037 time to fit residues: 1153.5739 Evaluate side-chains 622 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 586 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 183 GLU Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 111 LYS Chi-restraints excluded: chain S residue 131 ILE Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 63 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 401 optimal weight: 1.9990 chunk 425 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 380 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 136 ASN B 211 ASN D 61 ASN E 47 ASN G 61 ASN G 136 ASN G 211 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN J 136 ASN J 211 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 136 ASN K 211 ASN K 212 ASN L 60 ASN L 61 ASN L 136 ASN L 211 ASN L 212 ASN M 47 ASN M 197 HIS M 205 ASN N 205 ASN ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN S 61 ASN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35060 Z= 0.273 Angle : 0.482 5.882 47440 Z= 0.272 Chirality : 0.028 0.107 6240 Planarity : 0.003 0.041 5980 Dihedral : 3.487 17.577 4760 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.39 % Allowed : 8.25 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.62 (0.12), residues: 4480 helix: 2.77 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -3.04 (0.24), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 197 ARG 0.007 0.000 ARG C 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 642 time to evaluate : 4.031 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: A 73 ARG cc_start: 0.7264 (tpp-160) cc_final: 0.6620 (mpt-90) REVERT: A 86 LEU cc_start: 0.7755 (mt) cc_final: 0.7096 (mp) REVERT: A 89 LYS cc_start: 0.8015 (mttt) cc_final: 0.7784 (mttm) REVERT: A 108 GLU cc_start: 0.7678 (tp30) cc_final: 0.7252 (tp30) REVERT: A 144 GLU cc_start: 0.6915 (tt0) cc_final: 0.6503 (tt0) REVERT: A 151 ASN cc_start: 0.8191 (t0) cc_final: 0.7893 (t0) REVERT: B 69 GLU cc_start: 0.7539 (tt0) cc_final: 0.7215 (mm-30) REVERT: B 87 LYS cc_start: 0.7203 (mttt) cc_final: 0.6850 (mttt) REVERT: B 134 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6815 (mm-30) REVERT: B 137 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7142 (ttm-80) REVERT: B 203 GLU cc_start: 0.7728 (tt0) cc_final: 0.7259 (mt-10) REVERT: B 210 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6774 (tt0) REVERT: C 19 GLU cc_start: 0.7318 (tp30) cc_final: 0.6951 (tt0) REVERT: C 22 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8144 (tpp80) REVERT: C 26 LYS cc_start: 0.7880 (ttmm) cc_final: 0.7630 (tptp) REVERT: C 69 GLU cc_start: 0.7557 (tt0) cc_final: 0.6614 (tp30) REVERT: C 89 LYS cc_start: 0.8458 (mttt) cc_final: 0.8100 (mtpp) REVERT: C 94 ARG cc_start: 0.8064 (ttt-90) cc_final: 0.7675 (ttt-90) REVERT: C 170 GLU cc_start: 0.7975 (tp30) cc_final: 0.7681 (tp30) REVERT: D 69 GLU cc_start: 0.7350 (tt0) cc_final: 0.6568 (tp30) REVERT: D 89 LYS cc_start: 0.8412 (mttt) cc_final: 0.8118 (mtpp) REVERT: D 103 ARG cc_start: 0.7161 (mtt180) cc_final: 0.6892 (mtt-85) REVERT: D 170 GLU cc_start: 0.7921 (tp30) cc_final: 0.7497 (tp30) REVERT: E 77 MET cc_start: 0.8091 (mtt) cc_final: 0.7783 (mtt) REVERT: E 89 LYS cc_start: 0.8164 (mttt) cc_final: 0.7784 (mtpp) REVERT: E 107 GLU cc_start: 0.7307 (tt0) cc_final: 0.6777 (tt0) REVERT: E 210 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7459 (tm-30) REVERT: F 11 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6467 (mt-10) REVERT: F 17 LEU cc_start: 0.7980 (mp) cc_final: 0.7778 (tt) REVERT: F 172 LYS cc_start: 0.7577 (tttt) cc_final: 0.7222 (ttmt) REVERT: G 89 LYS cc_start: 0.8260 (mttt) cc_final: 0.8015 (mtpp) REVERT: G 151 ASN cc_start: 0.8800 (t0) cc_final: 0.8527 (t0) REVERT: H 8 LYS cc_start: 0.7878 (tttm) cc_final: 0.7414 (ttpp) REVERT: H 26 LYS cc_start: 0.6565 (tptt) cc_final: 0.6273 (mmmt) REVERT: H 89 LYS cc_start: 0.8206 (mttt) cc_final: 0.7840 (mtmt) REVERT: H 111 LYS cc_start: 0.7639 (ttpt) cc_final: 0.7134 (tptp) REVERT: H 144 GLU cc_start: 0.7346 (tt0) cc_final: 0.6936 (mt-10) REVERT: I 21 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7334 (tppt) REVERT: I 26 LYS cc_start: 0.6535 (tptt) cc_final: 0.6082 (mmmt) REVERT: I 73 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7283 (mmt-90) REVERT: I 156 GLU cc_start: 0.7325 (mp0) cc_final: 0.7118 (mt-10) REVERT: I 172 LYS cc_start: 0.7752 (tttt) cc_final: 0.7432 (tttm) REVERT: I 173 ARG cc_start: 0.7164 (ttp80) cc_final: 0.6940 (ttp80) REVERT: I 187 LYS cc_start: 0.7526 (tptp) cc_final: 0.7195 (tppt) REVERT: J 11 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6520 (mm-30) REVERT: J 172 LYS cc_start: 0.7449 (tttt) cc_final: 0.7116 (tttm) REVERT: J 187 LYS cc_start: 0.7468 (tptp) cc_final: 0.7248 (tppt) REVERT: K 111 LYS cc_start: 0.7500 (ttpt) cc_final: 0.7090 (mmmt) REVERT: K 144 GLU cc_start: 0.7241 (tt0) cc_final: 0.6822 (mt-10) REVERT: K 151 ASN cc_start: 0.8594 (t0) cc_final: 0.8213 (t0) REVERT: L 26 LYS cc_start: 0.6625 (tptp) cc_final: 0.6067 (mtpt) REVERT: L 80 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6865 (tt0) REVERT: L 89 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7552 (ttpp) REVERT: L 170 GLU cc_start: 0.7794 (tp30) cc_final: 0.7224 (tt0) REVERT: L 172 LYS cc_start: 0.8240 (tttt) cc_final: 0.7984 (ttmm) REVERT: L 183 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: M 26 LYS cc_start: 0.6960 (tptt) cc_final: 0.6515 (mtpt) REVERT: M 52 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6463 (mt-10) REVERT: M 59 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7112 (tt0) REVERT: M 77 MET cc_start: 0.7561 (mtt) cc_final: 0.7238 (mtt) REVERT: M 80 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6635 (tt0) REVERT: M 89 LYS cc_start: 0.7807 (mttt) cc_final: 0.7395 (mtmt) REVERT: M 148 ARG cc_start: 0.7126 (mpt180) cc_final: 0.6810 (tpp-160) REVERT: O 4 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6333 (mm-30) REVERT: O 8 LYS cc_start: 0.7942 (tttm) cc_final: 0.7570 (ttpp) REVERT: O 26 LYS cc_start: 0.6888 (tptt) cc_final: 0.6509 (mmmt) REVERT: O 69 GLU cc_start: 0.6427 (tt0) cc_final: 0.6087 (tp30) REVERT: O 87 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7727 (mtmt) REVERT: O 89 LYS cc_start: 0.8189 (mttt) cc_final: 0.7585 (mtpt) REVERT: O 127 ASN cc_start: 0.8198 (m-40) cc_final: 0.7939 (m110) REVERT: O 165 LYS cc_start: 0.7775 (mtpp) cc_final: 0.7473 (mtpp) REVERT: P 11 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7172 (mm-30) REVERT: P 26 LYS cc_start: 0.7587 (tttp) cc_final: 0.7380 (tptm) REVERT: P 89 LYS cc_start: 0.8204 (mttt) cc_final: 0.7879 (mttm) REVERT: P 111 LYS cc_start: 0.7589 (tptm) cc_final: 0.7367 (tppp) REVERT: P 165 LYS cc_start: 0.7456 (mtpp) cc_final: 0.7165 (mtpp) REVERT: P 172 LYS cc_start: 0.7950 (tttt) cc_final: 0.7733 (ttpp) REVERT: Q 69 GLU cc_start: 0.6699 (tt0) cc_final: 0.6401 (tp30) REVERT: Q 87 LYS cc_start: 0.7701 (mttt) cc_final: 0.7425 (mtmt) REVERT: Q 110 LYS cc_start: 0.7843 (mttt) cc_final: 0.7413 (mttp) REVERT: Q 163 GLU cc_start: 0.8406 (tp30) cc_final: 0.8106 (tp30) REVERT: Q 170 GLU cc_start: 0.8291 (tp30) cc_final: 0.7788 (tp30) REVERT: Q 196 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6850 (mm-30) REVERT: R 26 LYS cc_start: 0.7234 (tptt) cc_final: 0.6899 (tttp) REVERT: R 77 MET cc_start: 0.5146 (ptp) cc_final: 0.4672 (ptp) REVERT: R 87 LYS cc_start: 0.7602 (mttt) cc_final: 0.7049 (mtmt) REVERT: R 89 LYS cc_start: 0.8085 (mttt) cc_final: 0.7837 (mtpt) REVERT: R 104 MET cc_start: 0.7440 (mtp) cc_final: 0.7171 (mtt) REVERT: R 107 GLU cc_start: 0.8265 (tt0) cc_final: 0.8023 (tt0) REVERT: R 109 LEU cc_start: 0.7624 (tp) cc_final: 0.7409 (tt) REVERT: R 173 ARG cc_start: 0.7003 (mtm-85) cc_final: 0.6583 (mtp-110) REVERT: S 5 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7299 (tt0) REVERT: S 8 LYS cc_start: 0.7967 (tttp) cc_final: 0.7536 (ttpp) REVERT: S 87 LYS cc_start: 0.7582 (mttt) cc_final: 0.7110 (mtpp) REVERT: S 111 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7960 (ttmt) REVERT: S 151 ASN cc_start: 0.7376 (t0) cc_final: 0.7072 (t0) REVERT: S 172 LYS cc_start: 0.7751 (tttt) cc_final: 0.7383 (ttmm) REVERT: S 181 ILE cc_start: 0.6758 (mt) cc_final: 0.6500 (mt) REVERT: T 69 GLU cc_start: 0.6775 (tt0) cc_final: 0.6189 (mm-30) REVERT: T 87 LYS cc_start: 0.7849 (mttt) cc_final: 0.7307 (mtmt) REVERT: T 123 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7759 (mtp85) REVERT: T 170 GLU cc_start: 0.7446 (tp30) cc_final: 0.7240 (tp30) REVERT: T 203 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7811 (mt-10) outliers start: 53 outliers final: 41 residues processed: 661 average time/residue: 1.1434 time to fit residues: 1138.7353 Evaluate side-chains 639 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 594 time to evaluate : 4.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 183 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 111 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 381 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 136 ASN G 211 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN J 136 ASN J 211 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 136 ASN K 211 ASN K 212 ASN L 60 ASN L 61 ASN L 136 ASN L 211 ASN L 212 ASN ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 HIS ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35060 Z= 0.219 Angle : 0.448 6.555 47440 Z= 0.252 Chirality : 0.028 0.122 6240 Planarity : 0.002 0.045 5980 Dihedral : 3.353 16.400 4760 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.54 % Allowed : 9.16 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.12), residues: 4480 helix: 3.03 (0.07), residues: 4180 sheet: None (None), residues: 0 loop : -3.32 (0.28), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS M 197 ARG 0.005 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 590 time to evaluate : 4.072 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: A 73 ARG cc_start: 0.7243 (tpp-160) cc_final: 0.6616 (mpt-90) REVERT: A 86 LEU cc_start: 0.7766 (mt) cc_final: 0.7091 (mp) REVERT: A 108 GLU cc_start: 0.7635 (tp30) cc_final: 0.7232 (tp30) REVERT: A 144 GLU cc_start: 0.6948 (tt0) cc_final: 0.6598 (tp30) REVERT: A 151 ASN cc_start: 0.8184 (t0) cc_final: 0.7882 (t0) REVERT: B 69 GLU cc_start: 0.7456 (tt0) cc_final: 0.7098 (mm-30) REVERT: B 107 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: B 134 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6614 (mm-30) REVERT: B 137 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7230 (ttm-80) REVERT: B 203 GLU cc_start: 0.7655 (tt0) cc_final: 0.7169 (mt-10) REVERT: C 19 GLU cc_start: 0.7327 (tp30) cc_final: 0.6913 (tt0) REVERT: C 26 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7620 (tptp) REVERT: C 89 LYS cc_start: 0.8457 (mttt) cc_final: 0.8160 (mtpp) REVERT: D 89 LYS cc_start: 0.8410 (mttt) cc_final: 0.8199 (mtpp) REVERT: D 103 ARG cc_start: 0.7199 (mtt180) cc_final: 0.6925 (mtt-85) REVERT: D 170 GLU cc_start: 0.7940 (tp30) cc_final: 0.7509 (tp30) REVERT: E 77 MET cc_start: 0.8074 (mtt) cc_final: 0.7625 (mtm) REVERT: E 80 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6348 (tt0) REVERT: E 89 LYS cc_start: 0.8148 (mttt) cc_final: 0.7770 (mtpp) REVERT: E 107 GLU cc_start: 0.7269 (tt0) cc_final: 0.6765 (tt0) REVERT: E 210 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7445 (tm-30) REVERT: F 11 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6670 (mt-10) REVERT: G 89 LYS cc_start: 0.8255 (mttt) cc_final: 0.8005 (mtpp) REVERT: G 203 GLU cc_start: 0.7287 (tt0) cc_final: 0.7026 (mt-10) REVERT: H 8 LYS cc_start: 0.7853 (tttm) cc_final: 0.7390 (ttpp) REVERT: H 26 LYS cc_start: 0.6526 (tptt) cc_final: 0.6241 (mmmt) REVERT: H 89 LYS cc_start: 0.8194 (mttt) cc_final: 0.7830 (mtmt) REVERT: H 111 LYS cc_start: 0.7609 (ttpt) cc_final: 0.7203 (tptp) REVERT: H 144 GLU cc_start: 0.7360 (tt0) cc_final: 0.6919 (mt-10) REVERT: I 26 LYS cc_start: 0.6460 (tptt) cc_final: 0.6061 (mmmt) REVERT: I 73 ARG cc_start: 0.7756 (tpp-160) cc_final: 0.7282 (mmt-90) REVERT: I 89 LYS cc_start: 0.8086 (mttt) cc_final: 0.7708 (mtpp) REVERT: I 156 GLU cc_start: 0.7323 (mp0) cc_final: 0.7092 (mt-10) REVERT: I 187 LYS cc_start: 0.7593 (tptp) cc_final: 0.7255 (tppt) REVERT: J 11 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6550 (mm-30) REVERT: J 172 LYS cc_start: 0.7392 (tttt) cc_final: 0.7075 (tttm) REVERT: K 111 LYS cc_start: 0.7411 (ttpt) cc_final: 0.7076 (mmmt) REVERT: K 144 GLU cc_start: 0.7304 (tt0) cc_final: 0.6818 (mt-10) REVERT: L 26 LYS cc_start: 0.6594 (tptp) cc_final: 0.6031 (mtpt) REVERT: L 80 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6840 (tt0) REVERT: L 89 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7556 (ttpp) REVERT: L 170 GLU cc_start: 0.7755 (tp30) cc_final: 0.7190 (tt0) REVERT: L 172 LYS cc_start: 0.8216 (tttt) cc_final: 0.7974 (ttmm) REVERT: L 183 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: M 26 LYS cc_start: 0.6946 (tptt) cc_final: 0.6485 (mtpt) REVERT: M 52 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6448 (mt-10) REVERT: M 59 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7312 (mm-30) REVERT: M 77 MET cc_start: 0.7432 (mtt) cc_final: 0.7123 (mtt) REVERT: M 80 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6635 (tt0) REVERT: M 89 LYS cc_start: 0.7763 (mttt) cc_final: 0.7376 (mtmt) REVERT: M 148 ARG cc_start: 0.7023 (mpt180) cc_final: 0.6750 (tpp-160) REVERT: O 4 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6272 (mm-30) REVERT: O 8 LYS cc_start: 0.7926 (tttm) cc_final: 0.7556 (ttpp) REVERT: O 26 LYS cc_start: 0.6818 (tptt) cc_final: 0.6505 (mmmt) REVERT: O 69 GLU cc_start: 0.6495 (tt0) cc_final: 0.6102 (tp30) REVERT: O 87 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7715 (mtmt) REVERT: O 89 LYS cc_start: 0.8167 (mttt) cc_final: 0.7546 (mtpt) REVERT: O 94 ARG cc_start: 0.8340 (ttt-90) cc_final: 0.7949 (ttm-80) REVERT: O 165 LYS cc_start: 0.7771 (mtpp) cc_final: 0.7456 (mtpp) REVERT: P 11 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7274 (mm-30) REVERT: P 26 LYS cc_start: 0.7547 (tttp) cc_final: 0.7332 (tptm) REVERT: P 89 LYS cc_start: 0.8129 (mttt) cc_final: 0.7896 (mttm) REVERT: P 108 GLU cc_start: 0.7967 (tp30) cc_final: 0.7641 (tm-30) REVERT: Q 69 GLU cc_start: 0.6635 (tt0) cc_final: 0.6400 (tp30) REVERT: Q 87 LYS cc_start: 0.7647 (mttt) cc_final: 0.7409 (mtmt) REVERT: Q 110 LYS cc_start: 0.7786 (mttt) cc_final: 0.7360 (mttp) REVERT: Q 163 GLU cc_start: 0.8338 (tp30) cc_final: 0.8040 (tp30) REVERT: Q 170 GLU cc_start: 0.8261 (tp30) cc_final: 0.7778 (tp30) REVERT: Q 196 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6870 (mm-30) REVERT: R 26 LYS cc_start: 0.7192 (tptt) cc_final: 0.6847 (tttp) REVERT: R 77 MET cc_start: 0.5183 (ptp) cc_final: 0.4725 (ptp) REVERT: R 87 LYS cc_start: 0.7585 (mttt) cc_final: 0.7034 (mtmt) REVERT: R 89 LYS cc_start: 0.8084 (mttt) cc_final: 0.7813 (mtpt) REVERT: R 104 MET cc_start: 0.7354 (mtp) cc_final: 0.7060 (mtt) REVERT: R 107 GLU cc_start: 0.8251 (tt0) cc_final: 0.7649 (tp30) REVERT: R 109 LEU cc_start: 0.7574 (tp) cc_final: 0.7373 (tt) REVERT: R 173 ARG cc_start: 0.7000 (mtm-85) cc_final: 0.6626 (mtp85) REVERT: S 5 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7280 (tt0) REVERT: S 8 LYS cc_start: 0.7963 (tttp) cc_final: 0.7523 (ttpp) REVERT: S 87 LYS cc_start: 0.7589 (mttt) cc_final: 0.7109 (mtpp) REVERT: S 111 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7916 (ttmt) REVERT: S 151 ASN cc_start: 0.7368 (t0) cc_final: 0.7099 (t0) REVERT: S 172 LYS cc_start: 0.7728 (tttt) cc_final: 0.7369 (ttmm) REVERT: S 181 ILE cc_start: 0.6738 (mt) cc_final: 0.6462 (mt) REVERT: T 69 GLU cc_start: 0.6760 (tt0) cc_final: 0.6199 (mm-30) REVERT: T 87 LYS cc_start: 0.7852 (mttt) cc_final: 0.7300 (mtmt) REVERT: T 181 ILE cc_start: 0.6587 (mt) cc_final: 0.6352 (mt) REVERT: T 203 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7568 (mt-10) outliers start: 59 outliers final: 45 residues processed: 613 average time/residue: 1.1666 time to fit residues: 1089.8054 Evaluate side-chains 627 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 578 time to evaluate : 4.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 183 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain S residue 111 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 1.9990 chunk 383 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 425 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN C 136 ASN C 211 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 136 ASN G 211 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN J 61 ASN J 136 ASN J 211 ASN J 212 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN K 61 ASN K 136 ASN K 211 ASN K 212 ASN L 60 ASN L 61 ASN L 136 ASN L 211 ASN L 212 ASN ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN R 135 ASN T 136 ASN ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 211 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35060 Z= 0.222 Angle : 0.447 7.224 47440 Z= 0.251 Chirality : 0.028 0.091 6240 Planarity : 0.003 0.054 5980 Dihedral : 3.257 15.884 4760 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.49 % Allowed : 9.97 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.12), residues: 4480 helix: 3.23 (0.07), residues: 4180 sheet: None (None), residues: 0 loop : -3.08 (0.30), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS M 197 ARG 0.009 0.000 ARG I 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 592 time to evaluate : 4.139 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: A 73 ARG cc_start: 0.7268 (tpp-160) cc_final: 0.6701 (mpt-90) REVERT: A 86 LEU cc_start: 0.7806 (mt) cc_final: 0.7118 (mp) REVERT: A 108 GLU cc_start: 0.7663 (tp30) cc_final: 0.7273 (tp30) REVERT: A 144 GLU cc_start: 0.6830 (tt0) cc_final: 0.6446 (tp30) REVERT: A 151 ASN cc_start: 0.8186 (t0) cc_final: 0.7890 (t0) REVERT: B 69 GLU cc_start: 0.7485 (tt0) cc_final: 0.7032 (mm-30) REVERT: B 77 MET cc_start: 0.6593 (mtm) cc_final: 0.6223 (mtm) REVERT: B 87 LYS cc_start: 0.7133 (mttp) cc_final: 0.6910 (mttp) REVERT: B 89 LYS cc_start: 0.8132 (mttt) cc_final: 0.7632 (mtpp) REVERT: B 107 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: B 134 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6684 (mm-30) REVERT: B 137 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.7271 (ttm-80) REVERT: B 203 GLU cc_start: 0.7608 (tt0) cc_final: 0.7008 (mt-10) REVERT: B 210 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6467 (tp30) REVERT: C 19 GLU cc_start: 0.7392 (tp30) cc_final: 0.6993 (tt0) REVERT: C 22 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.8077 (tpp80) REVERT: C 26 LYS cc_start: 0.7851 (ttmm) cc_final: 0.7626 (tptp) REVERT: C 89 LYS cc_start: 0.8474 (mttt) cc_final: 0.8163 (mtpp) REVERT: C 148 ARG cc_start: 0.6916 (ttp-110) cc_final: 0.6622 (ttm110) REVERT: D 89 LYS cc_start: 0.8419 (mttt) cc_final: 0.8202 (mtpp) REVERT: D 103 ARG cc_start: 0.7206 (mtt180) cc_final: 0.6926 (mtt-85) REVERT: D 163 GLU cc_start: 0.7743 (tp30) cc_final: 0.7407 (tp30) REVERT: D 170 GLU cc_start: 0.7985 (tp30) cc_final: 0.7560 (tp30) REVERT: E 77 MET cc_start: 0.7911 (mtt) cc_final: 0.7464 (mtm) REVERT: E 80 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6248 (tt0) REVERT: E 89 LYS cc_start: 0.8150 (mttt) cc_final: 0.7784 (mtpp) REVERT: E 107 GLU cc_start: 0.7268 (tt0) cc_final: 0.6758 (tt0) REVERT: E 145 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7406 (tp) REVERT: G 89 LYS cc_start: 0.8267 (mttt) cc_final: 0.8013 (mtpp) REVERT: G 151 ASN cc_start: 0.8780 (t0) cc_final: 0.8507 (t0) REVERT: G 203 GLU cc_start: 0.7250 (tt0) cc_final: 0.7014 (mt-10) REVERT: H 8 LYS cc_start: 0.7856 (tttm) cc_final: 0.7391 (ttpp) REVERT: H 26 LYS cc_start: 0.6506 (tptt) cc_final: 0.6246 (mmmt) REVERT: H 89 LYS cc_start: 0.8163 (mttt) cc_final: 0.7796 (mtmt) REVERT: H 111 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7192 (tptp) REVERT: H 144 GLU cc_start: 0.7418 (tt0) cc_final: 0.6890 (mt-10) REVERT: I 26 LYS cc_start: 0.6440 (tptt) cc_final: 0.6059 (mmmt) REVERT: I 73 ARG cc_start: 0.7759 (tpp-160) cc_final: 0.7294 (mmt-90) REVERT: I 89 LYS cc_start: 0.7996 (mttt) cc_final: 0.7609 (mtpp) REVERT: I 107 GLU cc_start: 0.8372 (tt0) cc_final: 0.8097 (tt0) REVERT: I 156 GLU cc_start: 0.7388 (mp0) cc_final: 0.7130 (mt-10) REVERT: J 11 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6592 (mm-30) REVERT: J 172 LYS cc_start: 0.7392 (tttt) cc_final: 0.7105 (tttm) REVERT: K 144 GLU cc_start: 0.7320 (tt0) cc_final: 0.6837 (mt-10) REVERT: K 172 LYS cc_start: 0.7883 (tttm) cc_final: 0.7599 (tttm) REVERT: L 26 LYS cc_start: 0.6596 (tptp) cc_final: 0.6036 (mtpt) REVERT: L 80 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6828 (tt0) REVERT: L 89 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7545 (ttpp) REVERT: L 108 GLU cc_start: 0.7939 (tp30) cc_final: 0.7716 (tp30) REVERT: L 170 GLU cc_start: 0.7716 (tp30) cc_final: 0.7167 (tt0) REVERT: L 172 LYS cc_start: 0.8214 (tttt) cc_final: 0.7963 (ttmm) REVERT: L 183 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6687 (mt-10) REVERT: M 26 LYS cc_start: 0.6939 (tptt) cc_final: 0.6486 (mtpt) REVERT: M 52 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6474 (mt-10) REVERT: M 77 MET cc_start: 0.7425 (mtt) cc_final: 0.7118 (mtt) REVERT: M 80 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6642 (tt0) REVERT: M 89 LYS cc_start: 0.7665 (mttt) cc_final: 0.7376 (mtmt) REVERT: O 4 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6353 (mm-30) REVERT: O 8 LYS cc_start: 0.7944 (tttm) cc_final: 0.7557 (ttpp) REVERT: O 26 LYS cc_start: 0.6784 (tptt) cc_final: 0.6485 (mmmt) REVERT: O 69 GLU cc_start: 0.6540 (tt0) cc_final: 0.6108 (tp30) REVERT: O 87 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7716 (mtmt) REVERT: O 89 LYS cc_start: 0.8169 (mttt) cc_final: 0.7533 (mtpt) REVERT: O 94 ARG cc_start: 0.8349 (ttt-90) cc_final: 0.7954 (ttm-80) REVERT: O 127 ASN cc_start: 0.8175 (m-40) cc_final: 0.7878 (m110) REVERT: O 165 LYS cc_start: 0.7779 (mtpp) cc_final: 0.7450 (mtpp) REVERT: P 11 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7353 (mm-30) REVERT: P 26 LYS cc_start: 0.7540 (tttp) cc_final: 0.7331 (tptm) REVERT: P 89 LYS cc_start: 0.8153 (mttt) cc_final: 0.7918 (mttm) REVERT: P 108 GLU cc_start: 0.7920 (tp30) cc_final: 0.7652 (tm-30) REVERT: P 144 GLU cc_start: 0.6854 (tt0) cc_final: 0.6133 (tt0) REVERT: P 165 LYS cc_start: 0.7504 (mtpp) cc_final: 0.7104 (mtpp) REVERT: Q 69 GLU cc_start: 0.6609 (tt0) cc_final: 0.6389 (tp30) REVERT: Q 87 LYS cc_start: 0.7642 (mttt) cc_final: 0.7396 (mtmt) REVERT: Q 110 LYS cc_start: 0.7760 (mttt) cc_final: 0.7336 (mttp) REVERT: Q 163 GLU cc_start: 0.8314 (tp30) cc_final: 0.8013 (tp30) REVERT: Q 170 GLU cc_start: 0.8319 (tp30) cc_final: 0.7863 (tp30) REVERT: Q 196 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6879 (mm-30) REVERT: R 26 LYS cc_start: 0.7271 (tptt) cc_final: 0.6920 (tttp) REVERT: R 87 LYS cc_start: 0.7568 (mttt) cc_final: 0.7027 (mtmt) REVERT: R 89 LYS cc_start: 0.8095 (mttt) cc_final: 0.7797 (mtpt) REVERT: R 107 GLU cc_start: 0.8128 (tt0) cc_final: 0.7570 (tp30) REVERT: R 173 ARG cc_start: 0.6978 (mtm-85) cc_final: 0.6596 (mtp85) REVERT: S 5 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7273 (tt0) REVERT: S 8 LYS cc_start: 0.7951 (tttp) cc_final: 0.7500 (ttpp) REVERT: S 111 LYS cc_start: 0.8175 (tttp) cc_final: 0.7853 (ttmt) REVERT: S 151 ASN cc_start: 0.7315 (t0) cc_final: 0.7063 (t0) REVERT: S 163 GLU cc_start: 0.8207 (tp30) cc_final: 0.7650 (tp30) REVERT: S 172 LYS cc_start: 0.7722 (tttt) cc_final: 0.7359 (ttmm) REVERT: T 87 LYS cc_start: 0.7858 (mttt) cc_final: 0.7304 (mtmt) REVERT: T 181 ILE cc_start: 0.6574 (mt) cc_final: 0.6339 (mt) REVERT: T 203 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7624 (mt-10) outliers start: 57 outliers final: 46 residues processed: 613 average time/residue: 1.1798 time to fit residues: 1099.2156 Evaluate side-chains 627 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 576 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 181 ILE Chi-restraints excluded: chain O residue 183 GLU Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain S residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 358 optimal weight: 2.9990 chunk 237 optimal weight: 0.8980 chunk 424 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 136 ASN G 211 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN J 61 ASN J 136 ASN J 197 HIS J 211 ASN J 212 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 136 ASN K 211 ASN L 60 ASN L 61 ASN L 136 ASN L 211 ASN L 212 ASN ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN R 135 ASN T 61 ASN T 136 ASN T 211 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35060 Z= 0.246 Angle : 0.457 7.464 47440 Z= 0.257 Chirality : 0.028 0.086 6240 Planarity : 0.003 0.048 5980 Dihedral : 3.246 16.027 4760 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.62 % Allowed : 9.92 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.45 (0.12), residues: 4480 helix: 3.26 (0.07), residues: 4180 sheet: None (None), residues: 0 loop : -2.89 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 197 ARG 0.007 0.000 ARG I 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 595 time to evaluate : 4.031 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: A 26 LYS cc_start: 0.5942 (tptt) cc_final: 0.5347 (mmmt) REVERT: A 73 ARG cc_start: 0.7298 (tpp-160) cc_final: 0.6717 (mpt-90) REVERT: A 86 LEU cc_start: 0.7798 (mt) cc_final: 0.7106 (mp) REVERT: A 108 GLU cc_start: 0.7671 (tp30) cc_final: 0.7268 (tp30) REVERT: A 144 GLU cc_start: 0.6835 (tt0) cc_final: 0.6451 (tp30) REVERT: A 151 ASN cc_start: 0.8185 (t0) cc_final: 0.7885 (t0) REVERT: B 69 GLU cc_start: 0.7520 (tt0) cc_final: 0.7024 (mm-30) REVERT: B 77 MET cc_start: 0.6550 (mtm) cc_final: 0.6183 (mtm) REVERT: B 87 LYS cc_start: 0.7161 (mttp) cc_final: 0.6928 (mttp) REVERT: B 89 LYS cc_start: 0.8177 (mttt) cc_final: 0.7676 (mtpp) REVERT: B 134 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6815 (mm-30) REVERT: B 137 ARG cc_start: 0.7523 (ttm-80) cc_final: 0.7287 (ttm-80) REVERT: B 203 GLU cc_start: 0.7602 (tt0) cc_final: 0.6977 (mt-10) REVERT: B 210 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6627 (tt0) REVERT: C 19 GLU cc_start: 0.7411 (tp30) cc_final: 0.7000 (tt0) REVERT: C 22 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8081 (tpp80) REVERT: C 26 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7638 (tptp) REVERT: C 89 LYS cc_start: 0.8488 (mttt) cc_final: 0.8162 (mtpp) REVERT: C 148 ARG cc_start: 0.6930 (ttp-110) cc_final: 0.6627 (ttm110) REVERT: D 103 ARG cc_start: 0.7217 (mtt180) cc_final: 0.6939 (mtt-85) REVERT: D 163 GLU cc_start: 0.7586 (tp30) cc_final: 0.7168 (tp30) REVERT: D 170 GLU cc_start: 0.7979 (tp30) cc_final: 0.7562 (tp30) REVERT: E 77 MET cc_start: 0.8037 (mtt) cc_final: 0.7589 (mtm) REVERT: E 80 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6328 (tt0) REVERT: E 89 LYS cc_start: 0.8138 (mttt) cc_final: 0.7778 (mtpp) REVERT: E 107 GLU cc_start: 0.7269 (tt0) cc_final: 0.6759 (tt0) REVERT: G 203 GLU cc_start: 0.7281 (tt0) cc_final: 0.7038 (mt-10) REVERT: H 8 LYS cc_start: 0.7875 (tttm) cc_final: 0.7417 (ttpp) REVERT: H 26 LYS cc_start: 0.6526 (tptt) cc_final: 0.6255 (mmmt) REVERT: H 87 LYS cc_start: 0.7626 (mttt) cc_final: 0.7190 (mttm) REVERT: H 89 LYS cc_start: 0.8186 (mttt) cc_final: 0.7793 (mtmt) REVERT: H 111 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7243 (tptp) REVERT: I 26 LYS cc_start: 0.6446 (tptt) cc_final: 0.6078 (mmmt) REVERT: I 73 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7313 (mmt-90) REVERT: I 89 LYS cc_start: 0.8108 (mttt) cc_final: 0.7725 (mtpp) REVERT: I 107 GLU cc_start: 0.8282 (tt0) cc_final: 0.8028 (tt0) REVERT: I 156 GLU cc_start: 0.7392 (mp0) cc_final: 0.7135 (mt-10) REVERT: I 187 LYS cc_start: 0.7618 (tptp) cc_final: 0.7218 (tppt) REVERT: J 11 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6622 (mm-30) REVERT: J 109 LEU cc_start: 0.7698 (tp) cc_final: 0.7393 (tt) REVERT: J 172 LYS cc_start: 0.7413 (tttt) cc_final: 0.7129 (tttm) REVERT: K 144 GLU cc_start: 0.7334 (tt0) cc_final: 0.6867 (mt-10) REVERT: K 172 LYS cc_start: 0.7899 (tttm) cc_final: 0.7620 (tttm) REVERT: L 26 LYS cc_start: 0.6621 (tptp) cc_final: 0.6062 (mtpt) REVERT: L 80 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6838 (tt0) REVERT: L 89 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7561 (ttpp) REVERT: L 170 GLU cc_start: 0.7744 (tp30) cc_final: 0.7179 (tt0) REVERT: L 172 LYS cc_start: 0.8217 (tttt) cc_final: 0.7976 (ttmm) REVERT: L 183 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6710 (mt-10) REVERT: M 26 LYS cc_start: 0.6937 (tptt) cc_final: 0.6467 (mtpt) REVERT: M 52 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6483 (mt-10) REVERT: M 77 MET cc_start: 0.7481 (mtt) cc_final: 0.7138 (mtt) REVERT: M 80 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6612 (tt0) REVERT: M 89 LYS cc_start: 0.7701 (mttt) cc_final: 0.7420 (mtmt) REVERT: N 170 GLU cc_start: 0.7796 (tp30) cc_final: 0.7331 (tt0) REVERT: O 4 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6425 (mm-30) REVERT: O 8 LYS cc_start: 0.7947 (tttm) cc_final: 0.7554 (ttpp) REVERT: O 26 LYS cc_start: 0.6800 (tptt) cc_final: 0.6496 (mmmt) REVERT: O 69 GLU cc_start: 0.6440 (tt0) cc_final: 0.6095 (tp30) REVERT: O 77 MET cc_start: 0.6159 (mtt) cc_final: 0.5903 (mtm) REVERT: O 87 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7720 (mtmt) REVERT: O 89 LYS cc_start: 0.8105 (mttt) cc_final: 0.7481 (mtpt) REVERT: O 94 ARG cc_start: 0.8359 (ttt-90) cc_final: 0.7966 (ttm-80) REVERT: O 127 ASN cc_start: 0.8178 (m-40) cc_final: 0.7891 (m110) REVERT: O 165 LYS cc_start: 0.7795 (mtpp) cc_final: 0.7457 (mtpp) REVERT: P 11 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7332 (mm-30) REVERT: P 26 LYS cc_start: 0.7553 (tttp) cc_final: 0.7338 (tptm) REVERT: P 89 LYS cc_start: 0.8187 (mttt) cc_final: 0.7938 (mttm) REVERT: P 144 GLU cc_start: 0.6865 (tt0) cc_final: 0.6351 (tt0) REVERT: P 165 LYS cc_start: 0.7544 (mtpp) cc_final: 0.7124 (mtpp) REVERT: Q 69 GLU cc_start: 0.6636 (tt0) cc_final: 0.6399 (tp30) REVERT: Q 87 LYS cc_start: 0.7663 (mttt) cc_final: 0.7408 (mtmt) REVERT: Q 110 LYS cc_start: 0.7737 (mttt) cc_final: 0.7191 (mttp) REVERT: Q 163 GLU cc_start: 0.8296 (tp30) cc_final: 0.8001 (tp30) REVERT: Q 170 GLU cc_start: 0.8342 (tp30) cc_final: 0.7893 (tp30) REVERT: Q 196 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6905 (mm-30) REVERT: R 26 LYS cc_start: 0.7222 (tptt) cc_final: 0.6896 (tttp) REVERT: R 87 LYS cc_start: 0.7576 (mttt) cc_final: 0.7017 (mtmt) REVERT: R 89 LYS cc_start: 0.8124 (mttt) cc_final: 0.7840 (mtpt) REVERT: R 107 GLU cc_start: 0.8121 (tt0) cc_final: 0.7581 (tp30) REVERT: R 111 LYS cc_start: 0.8510 (tppp) cc_final: 0.7956 (tptp) REVERT: R 173 ARG cc_start: 0.6928 (mtm-85) cc_final: 0.6586 (mtp85) REVERT: S 5 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7276 (tt0) REVERT: S 8 LYS cc_start: 0.7939 (tttp) cc_final: 0.7494 (ttpp) REVERT: S 87 LYS cc_start: 0.7609 (mttt) cc_final: 0.7141 (mtpp) REVERT: S 111 LYS cc_start: 0.8223 (tttp) cc_final: 0.7898 (ttmt) REVERT: S 148 ARG cc_start: 0.7094 (tpp80) cc_final: 0.6885 (tpp80) REVERT: S 151 ASN cc_start: 0.7278 (t0) cc_final: 0.7057 (t0) REVERT: S 163 GLU cc_start: 0.8253 (tp30) cc_final: 0.7744 (tp30) REVERT: S 172 LYS cc_start: 0.7723 (tttt) cc_final: 0.7361 (ttmm) REVERT: T 69 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6320 (mm-30) REVERT: T 87 LYS cc_start: 0.7912 (mttt) cc_final: 0.7321 (mtmt) REVERT: T 181 ILE cc_start: 0.6572 (mt) cc_final: 0.6341 (mt) REVERT: T 203 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7631 (mt-10) outliers start: 62 outliers final: 51 residues processed: 617 average time/residue: 1.1115 time to fit residues: 1039.3230 Evaluate side-chains 629 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 574 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain J residue 214 ILE Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 183 GLU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain N residue 183 GLU Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 183 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain S residue 170 GLU Chi-restraints excluded: chain T residue 69 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 269 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 333 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN A 136 ASN A 211 ASN A 212 ASN C 136 ASN C 211 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 136 ASN G 211 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN J 61 ASN J 136 ASN J 211 ASN J 212 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 136 ASN K 211 ASN L 60 ASN L 61 ASN L 136 ASN L 211 ASN L 212 ASN P 46 HIS P 47 ASN ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN R 135 ASN T 61 ASN T 135 ASN T 136 ASN ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 211 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 35060 Z= 0.154 Angle : 0.409 7.578 47440 Z= 0.229 Chirality : 0.028 0.088 6240 Planarity : 0.002 0.056 5980 Dihedral : 3.103 16.281 4760 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.10 % Allowed : 10.65 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.18 (0.12), residues: 4480 helix: 3.73 (0.07), residues: 4180 sheet: None (None), residues: 0 loop : -2.68 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 197 ARG 0.008 0.000 ARG I 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 590 time to evaluate : 4.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.5867 (tptt) cc_final: 0.5269 (mmmt) REVERT: A 73 ARG cc_start: 0.7297 (tpp-160) cc_final: 0.6725 (mpt-90) REVERT: A 86 LEU cc_start: 0.7791 (mt) cc_final: 0.7125 (mp) REVERT: A 108 GLU cc_start: 0.7617 (tp30) cc_final: 0.7338 (tp30) REVERT: A 144 GLU cc_start: 0.6833 (tt0) cc_final: 0.6431 (tp30) REVERT: A 151 ASN cc_start: 0.8194 (t0) cc_final: 0.7892 (t0) REVERT: B 69 GLU cc_start: 0.7513 (tt0) cc_final: 0.6749 (mm-30) REVERT: B 77 MET cc_start: 0.6521 (mtm) cc_final: 0.6132 (mtm) REVERT: B 89 LYS cc_start: 0.8141 (mttt) cc_final: 0.7621 (mtpp) REVERT: B 107 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6983 (mt-10) REVERT: B 134 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6803 (mm-30) REVERT: B 137 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.7286 (ttm-80) REVERT: B 203 GLU cc_start: 0.7429 (tt0) cc_final: 0.6890 (mt-10) REVERT: B 210 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6409 (tp30) REVERT: C 19 GLU cc_start: 0.7392 (tp30) cc_final: 0.6982 (tt0) REVERT: C 22 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8060 (tpp80) REVERT: C 26 LYS cc_start: 0.7825 (ttmm) cc_final: 0.7616 (tptp) REVERT: C 89 LYS cc_start: 0.8447 (mttt) cc_final: 0.8144 (mtpp) REVERT: C 203 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7523 (mt-10) REVERT: D 103 ARG cc_start: 0.7191 (mtt180) cc_final: 0.6917 (mtt-85) REVERT: D 163 GLU cc_start: 0.7564 (tp30) cc_final: 0.7158 (tp30) REVERT: D 170 GLU cc_start: 0.7948 (tp30) cc_final: 0.7527 (tp30) REVERT: E 77 MET cc_start: 0.7866 (mtt) cc_final: 0.7428 (mtm) REVERT: E 80 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6154 (tt0) REVERT: E 89 LYS cc_start: 0.8129 (mttt) cc_final: 0.7765 (mtpp) REVERT: E 107 GLU cc_start: 0.7153 (tt0) cc_final: 0.6646 (tt0) REVERT: E 145 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7217 (tp) REVERT: G 89 LYS cc_start: 0.8257 (mttt) cc_final: 0.7978 (mtpp) REVERT: G 203 GLU cc_start: 0.7340 (tt0) cc_final: 0.7022 (mt-10) REVERT: H 8 LYS cc_start: 0.8015 (tttm) cc_final: 0.7539 (ttpp) REVERT: H 26 LYS cc_start: 0.6493 (tptt) cc_final: 0.6223 (mmmt) REVERT: H 87 LYS cc_start: 0.7605 (mttt) cc_final: 0.7168 (mttm) REVERT: H 89 LYS cc_start: 0.8160 (mttt) cc_final: 0.7819 (mtmt) REVERT: H 111 LYS cc_start: 0.7718 (ttpt) cc_final: 0.7314 (tptp) REVERT: I 26 LYS cc_start: 0.6475 (tptt) cc_final: 0.6124 (mmmt) REVERT: I 73 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.7312 (mmt-90) REVERT: I 89 LYS cc_start: 0.7965 (mttt) cc_final: 0.7596 (mtpp) REVERT: I 156 GLU cc_start: 0.7427 (mp0) cc_final: 0.7113 (mt-10) REVERT: J 11 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6583 (mm-30) REVERT: J 109 LEU cc_start: 0.7736 (tp) cc_final: 0.7460 (tt) REVERT: J 172 LYS cc_start: 0.7330 (tttt) cc_final: 0.7053 (tttm) REVERT: L 26 LYS cc_start: 0.6512 (tptp) cc_final: 0.5968 (mtpt) REVERT: L 80 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6773 (tt0) REVERT: L 89 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7518 (ttpp) REVERT: L 170 GLU cc_start: 0.7683 (tp30) cc_final: 0.7136 (tt0) REVERT: L 172 LYS cc_start: 0.8176 (tttt) cc_final: 0.7937 (ttmm) REVERT: M 26 LYS cc_start: 0.6840 (tptt) cc_final: 0.6343 (mtpt) REVERT: M 52 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6395 (mt-10) REVERT: M 77 MET cc_start: 0.7391 (mtt) cc_final: 0.7103 (mtt) REVERT: M 80 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6550 (tt0) REVERT: M 89 LYS cc_start: 0.7713 (mttt) cc_final: 0.7457 (mtmt) REVERT: O 8 LYS cc_start: 0.7923 (tttm) cc_final: 0.7555 (ttpp) REVERT: O 26 LYS cc_start: 0.6759 (tptt) cc_final: 0.6466 (mmmt) REVERT: O 69 GLU cc_start: 0.6549 (tt0) cc_final: 0.6094 (tp30) REVERT: O 77 MET cc_start: 0.6026 (mtt) cc_final: 0.5777 (mtm) REVERT: O 87 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7690 (mtmt) REVERT: O 89 LYS cc_start: 0.8060 (mttt) cc_final: 0.7438 (mtpt) REVERT: O 94 ARG cc_start: 0.8298 (ttt-90) cc_final: 0.7901 (ttm-80) REVERT: P 11 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7287 (mm-30) REVERT: P 26 LYS cc_start: 0.7493 (tttp) cc_final: 0.7265 (tptm) REVERT: P 89 LYS cc_start: 0.8100 (mttt) cc_final: 0.7888 (mttm) REVERT: P 108 GLU cc_start: 0.7937 (tp30) cc_final: 0.7730 (tm-30) REVERT: Q 69 GLU cc_start: 0.6623 (tt0) cc_final: 0.6390 (tp30) REVERT: Q 87 LYS cc_start: 0.7712 (mttt) cc_final: 0.7422 (mtmt) REVERT: Q 110 LYS cc_start: 0.7728 (mttt) cc_final: 0.7317 (mttp) REVERT: Q 163 GLU cc_start: 0.8259 (tp30) cc_final: 0.7957 (tp30) REVERT: Q 170 GLU cc_start: 0.8282 (tp30) cc_final: 0.7867 (tp30) REVERT: R 26 LYS cc_start: 0.7249 (tptt) cc_final: 0.6912 (tttp) REVERT: R 87 LYS cc_start: 0.7555 (mttt) cc_final: 0.7051 (mtmt) REVERT: R 89 LYS cc_start: 0.7991 (mttt) cc_final: 0.7666 (mtpt) REVERT: R 107 GLU cc_start: 0.8035 (tt0) cc_final: 0.7580 (tp30) REVERT: R 173 ARG cc_start: 0.6915 (mtm-85) cc_final: 0.6580 (mtp85) REVERT: S 5 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7237 (tt0) REVERT: S 8 LYS cc_start: 0.7959 (tttp) cc_final: 0.7539 (ttpp) REVERT: S 111 LYS cc_start: 0.8214 (tttp) cc_final: 0.7906 (ttmt) REVERT: S 127 ASN cc_start: 0.8300 (m-40) cc_final: 0.7975 (m110) REVERT: S 148 ARG cc_start: 0.7073 (tpp80) cc_final: 0.6853 (tpp80) REVERT: S 151 ASN cc_start: 0.7302 (t0) cc_final: 0.7093 (t0) REVERT: S 172 LYS cc_start: 0.7678 (tttt) cc_final: 0.7325 (ttmm) REVERT: T 69 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6312 (mm-30) REVERT: T 87 LYS cc_start: 0.7932 (mttt) cc_final: 0.7326 (mtmt) REVERT: T 181 ILE cc_start: 0.6588 (mt) cc_final: 0.6366 (mt) REVERT: T 203 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7519 (mt-10) outliers start: 42 outliers final: 31 residues processed: 605 average time/residue: 1.0852 time to fit residues: 998.5905 Evaluate side-chains 598 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 564 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain T residue 69 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 5.9990 chunk 406 optimal weight: 0.8980 chunk 370 optimal weight: 0.9990 chunk 395 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 357 optimal weight: 1.9990 chunk 373 optimal weight: 1.9990 chunk 393 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 211 ASN C 61 ASN C 136 ASN C 211 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 136 ASN G 211 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN J 61 ASN J 136 ASN J 211 ASN J 212 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 136 ASN K 211 ASN L 60 ASN L 61 ASN L 136 ASN L 211 ASN L 212 ASN P 46 HIS P 47 ASN ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 ASN T 135 ASN T 136 ASN ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 211 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35060 Z= 0.151 Angle : 0.411 7.247 47440 Z= 0.229 Chirality : 0.028 0.131 6240 Planarity : 0.002 0.056 5980 Dihedral : 3.040 15.512 4760 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.02 % Allowed : 11.07 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.53 (0.11), residues: 4480 helix: 3.95 (0.07), residues: 4180 sheet: None (None), residues: 0 loop : -2.51 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 197 ARG 0.008 0.000 ARG I 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 600 time to evaluate : 4.092 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: A 26 LYS cc_start: 0.5844 (tptt) cc_final: 0.5247 (mmmt) REVERT: A 73 ARG cc_start: 0.7268 (tpp-160) cc_final: 0.6722 (mpt-90) REVERT: A 86 LEU cc_start: 0.7865 (mt) cc_final: 0.7208 (mp) REVERT: A 144 GLU cc_start: 0.6795 (tt0) cc_final: 0.6380 (tp30) REVERT: A 151 ASN cc_start: 0.8185 (t0) cc_final: 0.7882 (t0) REVERT: B 69 GLU cc_start: 0.7612 (tt0) cc_final: 0.6934 (mm-30) REVERT: B 77 MET cc_start: 0.6507 (mtm) cc_final: 0.6142 (mtm) REVERT: B 107 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7007 (mt-10) REVERT: B 134 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6809 (mm-30) REVERT: B 137 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.7259 (ttm-80) REVERT: B 210 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6398 (tp30) REVERT: C 19 GLU cc_start: 0.7396 (tp30) cc_final: 0.6981 (tt0) REVERT: C 22 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8059 (tpp80) REVERT: C 26 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7600 (tptp) REVERT: C 89 LYS cc_start: 0.8463 (mttt) cc_final: 0.8158 (mtpp) REVERT: C 189 PRO cc_start: 0.7937 (Cg_endo) cc_final: 0.7609 (Cg_exo) REVERT: D 103 ARG cc_start: 0.7059 (mtt180) cc_final: 0.6832 (mtt-85) REVERT: D 163 GLU cc_start: 0.7532 (tp30) cc_final: 0.7117 (tp30) REVERT: D 170 GLU cc_start: 0.7901 (tp30) cc_final: 0.7465 (tp30) REVERT: D 203 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7081 (mm-30) REVERT: E 77 MET cc_start: 0.7894 (mtt) cc_final: 0.7454 (mtm) REVERT: E 80 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6123 (tt0) REVERT: E 89 LYS cc_start: 0.8115 (mttt) cc_final: 0.7746 (mtpp) REVERT: E 107 GLU cc_start: 0.7124 (tt0) cc_final: 0.6624 (tt0) REVERT: E 145 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7215 (tp) REVERT: G 203 GLU cc_start: 0.7214 (tt0) cc_final: 0.6924 (mt-10) REVERT: H 8 LYS cc_start: 0.8008 (tttm) cc_final: 0.7533 (ttpp) REVERT: H 26 LYS cc_start: 0.6496 (tptt) cc_final: 0.6222 (mmmt) REVERT: H 87 LYS cc_start: 0.7628 (mttt) cc_final: 0.7200 (mttm) REVERT: H 89 LYS cc_start: 0.8103 (mttt) cc_final: 0.7787 (mtmt) REVERT: H 111 LYS cc_start: 0.7714 (ttpt) cc_final: 0.7285 (tptp) REVERT: I 26 LYS cc_start: 0.6460 (tptt) cc_final: 0.6124 (mmmt) REVERT: I 89 LYS cc_start: 0.7960 (mttt) cc_final: 0.7587 (mtpp) REVERT: J 11 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6626 (mm-30) REVERT: J 109 LEU cc_start: 0.7757 (tp) cc_final: 0.7445 (tt) REVERT: J 172 LYS cc_start: 0.7316 (tttt) cc_final: 0.7041 (tttm) REVERT: K 111 LYS cc_start: 0.7432 (mttt) cc_final: 0.7187 (mmmt) REVERT: K 144 GLU cc_start: 0.7759 (tt0) cc_final: 0.6974 (mt-10) REVERT: L 26 LYS cc_start: 0.6492 (tptp) cc_final: 0.5897 (mtpt) REVERT: L 80 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6646 (tt0) REVERT: L 89 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7507 (ttpp) REVERT: L 170 GLU cc_start: 0.7635 (tp30) cc_final: 0.7107 (tt0) REVERT: L 172 LYS cc_start: 0.8171 (tttt) cc_final: 0.7932 (ttmm) REVERT: M 26 LYS cc_start: 0.6748 (tptt) cc_final: 0.6234 (mtpt) REVERT: M 52 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6318 (mt-10) REVERT: M 77 MET cc_start: 0.7422 (mtt) cc_final: 0.7052 (mtt) REVERT: M 80 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6487 (tt0) REVERT: M 89 LYS cc_start: 0.7740 (mttt) cc_final: 0.7414 (mtmt) REVERT: N 69 GLU cc_start: 0.6982 (tt0) cc_final: 0.6564 (mm-30) REVERT: N 170 GLU cc_start: 0.7617 (tp30) cc_final: 0.7190 (tt0) REVERT: O 4 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6303 (mm-30) REVERT: O 8 LYS cc_start: 0.7962 (tttm) cc_final: 0.7543 (ttpp) REVERT: O 26 LYS cc_start: 0.6682 (tptt) cc_final: 0.6394 (mmmt) REVERT: O 69 GLU cc_start: 0.6548 (tt0) cc_final: 0.6071 (tp30) REVERT: O 87 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7688 (mtmt) REVERT: O 89 LYS cc_start: 0.8059 (mttt) cc_final: 0.7424 (mtpt) REVERT: O 94 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.7897 (ttm-80) REVERT: P 11 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7313 (mm-30) REVERT: P 89 LYS cc_start: 0.8107 (mttt) cc_final: 0.7882 (mttm) REVERT: P 144 GLU cc_start: 0.6858 (tt0) cc_final: 0.6527 (tt0) REVERT: Q 69 GLU cc_start: 0.6645 (tt0) cc_final: 0.6376 (tp30) REVERT: Q 87 LYS cc_start: 0.7668 (mttt) cc_final: 0.7418 (mtmt) REVERT: Q 107 GLU cc_start: 0.8151 (tt0) cc_final: 0.7573 (tp30) REVERT: Q 163 GLU cc_start: 0.8238 (tp30) cc_final: 0.7932 (tp30) REVERT: Q 170 GLU cc_start: 0.8291 (tp30) cc_final: 0.7871 (tp30) REVERT: R 26 LYS cc_start: 0.7248 (tptt) cc_final: 0.6923 (tttp) REVERT: R 87 LYS cc_start: 0.7565 (mttt) cc_final: 0.7081 (mtpt) REVERT: R 89 LYS cc_start: 0.7992 (mttt) cc_final: 0.7662 (mtpt) REVERT: R 107 GLU cc_start: 0.8026 (tt0) cc_final: 0.7576 (tp30) REVERT: R 123 ARG cc_start: 0.7862 (mtp-110) cc_final: 0.7427 (mtp-110) REVERT: R 173 ARG cc_start: 0.6887 (mtm-85) cc_final: 0.6565 (mtp85) REVERT: S 8 LYS cc_start: 0.7928 (tttp) cc_final: 0.7522 (ttpp) REVERT: S 111 LYS cc_start: 0.8216 (tttp) cc_final: 0.7938 (ttmt) REVERT: S 172 LYS cc_start: 0.7672 (tttt) cc_final: 0.7307 (ttmm) REVERT: T 87 LYS cc_start: 0.7935 (mttt) cc_final: 0.7332 (mtmt) REVERT: T 181 ILE cc_start: 0.6462 (mt) cc_final: 0.6245 (mt) REVERT: T 203 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7408 (mt-10) outliers start: 39 outliers final: 34 residues processed: 615 average time/residue: 1.1225 time to fit residues: 1053.5326 Evaluate side-chains 609 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 572 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 181 ILE Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain S residue 91 SER Chi-restraints excluded: chain T residue 4 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 1.9990 chunk 417 optimal weight: 0.9990 chunk 255 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 438 optimal weight: 1.9990 chunk 403 optimal weight: 0.4980 chunk 349 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 136 ASN A 211 ASN C 61 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN J 61 ASN J 136 ASN J 211 ASN J 212 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 136 ASN K 211 ASN L 60 ASN L 61 ASN L 136 ASN L 211 ASN L 212 ASN ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN T 61 ASN T 135 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35060 Z= 0.182 Angle : 0.426 7.080 47440 Z= 0.237 Chirality : 0.028 0.092 6240 Planarity : 0.002 0.058 5980 Dihedral : 3.030 15.322 4760 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.97 % Allowed : 11.31 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.50 (0.11), residues: 4480 helix: 3.92 (0.07), residues: 4180 sheet: None (None), residues: 0 loop : -2.41 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 197 ARG 0.017 0.000 ARG C 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8960 Ramachandran restraints generated. 4480 Oldfield, 0 Emsley, 4480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 577 time to evaluate : 4.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.5861 (tptt) cc_final: 0.5431 (mmmt) REVERT: A 73 ARG cc_start: 0.7272 (tpp-160) cc_final: 0.6715 (mpt-90) REVERT: A 86 LEU cc_start: 0.7869 (mt) cc_final: 0.7230 (mp) REVERT: A 108 GLU cc_start: 0.7617 (tp30) cc_final: 0.7337 (tp30) REVERT: A 144 GLU cc_start: 0.6842 (tt0) cc_final: 0.6435 (tp30) REVERT: A 151 ASN cc_start: 0.8182 (t0) cc_final: 0.7932 (t0) REVERT: B 69 GLU cc_start: 0.7622 (tt0) cc_final: 0.6931 (mm-30) REVERT: B 77 MET cc_start: 0.6547 (mtm) cc_final: 0.6199 (mtm) REVERT: B 107 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6994 (mt-10) REVERT: B 134 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6824 (mm-30) REVERT: B 137 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.7284 (ttm-80) REVERT: B 203 GLU cc_start: 0.7412 (tt0) cc_final: 0.6965 (mt-10) REVERT: B 210 GLU cc_start: 0.6674 (tt0) cc_final: 0.6417 (tp30) REVERT: C 19 GLU cc_start: 0.7406 (tp30) cc_final: 0.6988 (tt0) REVERT: C 22 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8063 (tpp80) REVERT: C 26 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7610 (tptp) REVERT: C 89 LYS cc_start: 0.8476 (mttt) cc_final: 0.8165 (mtpp) REVERT: C 189 PRO cc_start: 0.8037 (Cg_endo) cc_final: 0.7690 (Cg_exo) REVERT: C 203 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7600 (mt-10) REVERT: D 163 GLU cc_start: 0.7547 (tp30) cc_final: 0.7115 (tp30) REVERT: D 170 GLU cc_start: 0.7914 (tp30) cc_final: 0.7474 (tp30) REVERT: D 203 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7129 (mm-30) REVERT: E 77 MET cc_start: 0.7979 (mtt) cc_final: 0.7533 (mtm) REVERT: E 80 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6247 (tt0) REVERT: E 89 LYS cc_start: 0.8126 (mttt) cc_final: 0.7756 (mtpp) REVERT: E 107 GLU cc_start: 0.7139 (tt0) cc_final: 0.6638 (tt0) REVERT: G 203 GLU cc_start: 0.7225 (tt0) cc_final: 0.6931 (mt-10) REVERT: H 8 LYS cc_start: 0.8020 (tttm) cc_final: 0.7544 (ttpp) REVERT: H 26 LYS cc_start: 0.6509 (tptt) cc_final: 0.6236 (mmmt) REVERT: H 87 LYS cc_start: 0.7642 (mttt) cc_final: 0.7214 (mttm) REVERT: H 89 LYS cc_start: 0.8118 (mttt) cc_final: 0.7795 (mtmt) REVERT: H 111 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7303 (tptp) REVERT: I 26 LYS cc_start: 0.6479 (tptt) cc_final: 0.6140 (mmmt) REVERT: I 73 ARG cc_start: 0.7739 (tpp-160) cc_final: 0.7318 (mmt-90) REVERT: I 89 LYS cc_start: 0.7981 (mttt) cc_final: 0.7610 (mtpp) REVERT: I 156 GLU cc_start: 0.7438 (mp0) cc_final: 0.7114 (mt-10) REVERT: J 11 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6629 (mm-30) REVERT: J 109 LEU cc_start: 0.7748 (tp) cc_final: 0.7467 (tt) REVERT: J 172 LYS cc_start: 0.7341 (tttt) cc_final: 0.7073 (tttm) REVERT: K 111 LYS cc_start: 0.7453 (mttt) cc_final: 0.7205 (mmmt) REVERT: L 26 LYS cc_start: 0.6523 (tptp) cc_final: 0.5971 (mtpt) REVERT: L 80 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6631 (tt0) REVERT: L 89 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7517 (ttpp) REVERT: L 108 GLU cc_start: 0.8024 (tp30) cc_final: 0.7791 (tp30) REVERT: L 170 GLU cc_start: 0.7656 (tp30) cc_final: 0.7121 (tt0) REVERT: L 172 LYS cc_start: 0.8191 (tttt) cc_final: 0.7945 (ttmm) REVERT: M 26 LYS cc_start: 0.6736 (tptt) cc_final: 0.6240 (mtpt) REVERT: M 52 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6349 (mt-10) REVERT: M 77 MET cc_start: 0.7425 (mtt) cc_final: 0.7055 (mtt) REVERT: M 80 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6513 (tt0) REVERT: M 89 LYS cc_start: 0.7713 (mttt) cc_final: 0.7376 (mtmt) REVERT: N 69 GLU cc_start: 0.7024 (tt0) cc_final: 0.6679 (mm-30) REVERT: O 4 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6329 (mm-30) REVERT: O 8 LYS cc_start: 0.7997 (tttm) cc_final: 0.7574 (ttpp) REVERT: O 26 LYS cc_start: 0.6820 (tptt) cc_final: 0.6548 (mmmt) REVERT: O 69 GLU cc_start: 0.6457 (tt0) cc_final: 0.6097 (tp30) REVERT: O 87 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7695 (mtmt) REVERT: O 89 LYS cc_start: 0.8083 (mttt) cc_final: 0.7438 (mtpt) REVERT: O 94 ARG cc_start: 0.8308 (ttt-90) cc_final: 0.7904 (ttm-80) REVERT: O 165 LYS cc_start: 0.7720 (mtpp) cc_final: 0.7406 (mtpp) REVERT: P 11 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7286 (mm-30) REVERT: P 89 LYS cc_start: 0.8116 (mttt) cc_final: 0.7883 (mttm) REVERT: Q 69 GLU cc_start: 0.6696 (tt0) cc_final: 0.6400 (tp30) REVERT: Q 87 LYS cc_start: 0.7684 (mttt) cc_final: 0.7422 (mtmt) REVERT: Q 107 GLU cc_start: 0.8125 (tt0) cc_final: 0.7582 (tp30) REVERT: Q 110 LYS cc_start: 0.7500 (mttt) cc_final: 0.7194 (mttp) REVERT: Q 163 GLU cc_start: 0.8252 (tp30) cc_final: 0.7938 (tp30) REVERT: Q 170 GLU cc_start: 0.8307 (tp30) cc_final: 0.7880 (tp30) REVERT: R 26 LYS cc_start: 0.7189 (tptt) cc_final: 0.6894 (tttp) REVERT: R 87 LYS cc_start: 0.7571 (mttt) cc_final: 0.7088 (mtpt) REVERT: R 89 LYS cc_start: 0.8011 (mttt) cc_final: 0.7757 (mtpt) REVERT: R 107 GLU cc_start: 0.8060 (tt0) cc_final: 0.7582 (tp30) REVERT: R 123 ARG cc_start: 0.7857 (mtp-110) cc_final: 0.7448 (mtp-110) REVERT: R 173 ARG cc_start: 0.6905 (mtm-85) cc_final: 0.6574 (mtp85) REVERT: S 8 LYS cc_start: 0.7937 (tttp) cc_final: 0.7528 (ttpp) REVERT: S 111 LYS cc_start: 0.8256 (tttp) cc_final: 0.7974 (ttmt) REVERT: S 127 ASN cc_start: 0.8301 (m-40) cc_final: 0.7979 (m110) REVERT: S 172 LYS cc_start: 0.7685 (tttt) cc_final: 0.7322 (ttmm) REVERT: T 87 LYS cc_start: 0.7931 (mttt) cc_final: 0.7331 (mtmt) REVERT: T 181 ILE cc_start: 0.6473 (mt) cc_final: 0.6253 (mt) REVERT: T 203 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7421 (mt-10) outliers start: 37 outliers final: 33 residues processed: 591 average time/residue: 1.1380 time to fit residues: 1019.7053 Evaluate side-chains 606 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 572 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 2 SER Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 4 GLU Chi-restraints excluded: chain O residue 134 GLU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 181 ILE Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 0.9980 chunk 371 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 321 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 349 optimal weight: 0.0980 chunk 146 optimal weight: 1.9990 chunk 359 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 211 ASN C 61 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN J 61 ASN J 136 ASN J 211 ASN J 212 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 136 ASN K 211 ASN L 60 ASN L 61 ASN L 136 ASN L 211 ASN L 212 ASN O 47 ASN ** P 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN ** T 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.151465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.113219 restraints weight = 118851.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.119127 restraints weight = 62720.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.123138 restraints weight = 42377.782| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35060 Z= 0.145 Angle : 0.403 6.906 47440 Z= 0.224 Chirality : 0.028 0.088 6240 Planarity : 0.002 0.060 5980 Dihedral : 2.971 15.480 4760 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.92 % Allowed : 11.52 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.86 (0.11), residues: 4480 helix: 4.15 (0.07), residues: 4180 sheet: None (None), residues: 0 loop : -2.24 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 197 ARG 0.009 0.000 ARG D 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16764.56 seconds wall clock time: 286 minutes 12.47 seconds (17172.47 seconds total)