Starting phenix.real_space_refine on Tue Feb 20 21:03:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/02_2024/8eky_28217.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/02_2024/8eky_28217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/02_2024/8eky_28217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/02_2024/8eky_28217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/02_2024/8eky_28217.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/02_2024/8eky_28217.pdb" } resolution = 3.47 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14407 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 9435 2.51 5 N 2451 2.21 5 O 2691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "I GLU 97": "OE1" <-> "OE2" Residue "I GLU 100": "OE1" <-> "OE2" Residue "J GLU 127": "OE1" <-> "OE2" Residue "J GLU 227": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14605 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "B" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1356 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "C" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1493 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 12, 'TRANS': 174} Chain: "D" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "E" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1356 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "F" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "G" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1346 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain: "H" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1346 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain: "I" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "J" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1356 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 8, 'TRANS': 159} Chain: "M" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 840 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 7.64, per 1000 atoms: 0.52 Number of scatterers: 14605 At special positions: 0 Unit cell: (85.32, 139.32, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 2691 8.00 N 2451 7.00 C 9435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 247 " - pdb=" SG CYS M 254 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.40 Conformation dependent library (CDL) restraints added in 2.4 seconds 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 13 sheets defined 36.9% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 104 through 107 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.594A pdb=" N GLN A 166 " --> pdb=" O PRO A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 224 through 241 removed outlier: 3.735A pdb=" N THR A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 107 removed outlier: 3.620A pdb=" N ARG B 107 " --> pdb=" O THR B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 107' Processing helix chain 'B' and resid 125 through 134 removed outlier: 3.582A pdb=" N ILE B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 4.202A pdb=" N PHE B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 162 Processing helix chain 'B' and resid 163 through 167 removed outlier: 3.557A pdb=" N GLN B 166 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 167 " --> pdb=" O ARG B 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 163 through 167' Processing helix chain 'B' and resid 182 through 189 removed outlier: 3.640A pdb=" N LYS B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 241 removed outlier: 3.622A pdb=" N THR B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 107 removed outlier: 3.647A pdb=" N ARG C 107 " --> pdb=" O THR C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 107' Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.785A pdb=" N ILE C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.837A pdb=" N PHE C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.728A pdb=" N GLN C 166 " --> pdb=" O PRO C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 225 through 242 Processing helix chain 'D' and resid 104 through 107 removed outlier: 3.736A pdb=" N ARG D 107 " --> pdb=" O THR D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 107' Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.850A pdb=" N PHE D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 162 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 182 through 189 Processing helix chain 'D' and resid 224 through 241 removed outlier: 3.749A pdb=" N THR D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 107 Processing helix chain 'E' and resid 125 through 134 removed outlier: 3.521A pdb=" N ILE E 129 " --> pdb=" O PRO E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 141 removed outlier: 3.879A pdb=" N PHE E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 162 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'E' and resid 224 through 241 removed outlier: 3.540A pdb=" N THR E 228 " --> pdb=" O SER E 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 107 Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.520A pdb=" N ARG F 134 " --> pdb=" O ALA F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 removed outlier: 3.767A pdb=" N PHE F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 162 Processing helix chain 'F' and resid 163 through 167 Processing helix chain 'F' and resid 182 through 188 Processing helix chain 'F' and resid 224 through 241 removed outlier: 3.720A pdb=" N THR F 228 " --> pdb=" O SER F 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 107 removed outlier: 3.589A pdb=" N ARG G 107 " --> pdb=" O THR G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 104 through 107' Processing helix chain 'G' and resid 125 through 134 removed outlier: 3.677A pdb=" N ILE G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 140 removed outlier: 3.978A pdb=" N PHE G 138 " --> pdb=" O ARG G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 162 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'G' and resid 225 through 241 Processing helix chain 'H' and resid 104 through 107 removed outlier: 3.680A pdb=" N ARG H 107 " --> pdb=" O THR H 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 125 through 134 Processing helix chain 'H' and resid 135 through 141 Processing helix chain 'H' and resid 152 through 161 Processing helix chain 'H' and resid 182 through 188 Processing helix chain 'H' and resid 224 through 241 Processing helix chain 'I' and resid 104 through 107 removed outlier: 3.811A pdb=" N ARG I 107 " --> pdb=" O THR I 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 104 through 107' Processing helix chain 'I' and resid 125 through 134 removed outlier: 3.525A pdb=" N ILE I 129 " --> pdb=" O PRO I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 141 removed outlier: 3.585A pdb=" N ILE I 141 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 162 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.567A pdb=" N GLN I 166 " --> pdb=" O PRO I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 189 Processing helix chain 'I' and resid 225 through 241 Processing helix chain 'J' and resid 104 through 107 Processing helix chain 'J' and resid 125 through 134 removed outlier: 3.791A pdb=" N ILE J 129 " --> pdb=" O PRO J 125 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG J 134 " --> pdb=" O ALA J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 141 Processing helix chain 'J' and resid 152 through 162 Processing helix chain 'J' and resid 163 through 167 Processing helix chain 'J' and resid 182 through 189 removed outlier: 3.692A pdb=" N LYS J 186 " --> pdb=" O HIS J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 241 Processing helix chain 'M' and resid 195 through 206 removed outlier: 4.674A pdb=" N GLU M 200 " --> pdb=" O ALA M 196 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU M 201 " --> pdb=" O SER M 197 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA M 204 " --> pdb=" O GLU M 200 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY M 206 " --> pdb=" O HIS M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 234 Proline residue: M 225 - end of helix Processing helix chain 'M' and resid 251 through 257 Processing helix chain 'M' and resid 282 through 295 Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 148 removed outlier: 6.660A pdb=" N TYR A 110 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 146 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 112 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N CYS A 148 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE A 114 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY A 201 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 202 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 214 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE A 204 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 214 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS B 83 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 148 removed outlier: 6.660A pdb=" N TYR A 110 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 146 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL A 112 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N CYS A 148 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE A 114 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY A 201 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 202 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 214 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE A 204 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 214 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 204 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE B 214 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 202 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 201 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B 110 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL B 146 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL B 112 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N CYS B 148 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE B 114 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU B 177 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 147 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 102 removed outlier: 5.065A pdb=" N THR C 91 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LEU C 177 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 147 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR C 110 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL C 146 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 112 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS C 148 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE C 114 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY C 201 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN C 213 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN D 213 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY D 201 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N LEU D 177 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA D 147 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR D 91 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 97 through 102 removed outlier: 5.195A pdb=" N THR E 91 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU E 177 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA E 147 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR E 110 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL E 146 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL E 112 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS E 148 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE E 114 " --> pdb=" O CYS E 148 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY E 201 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU E 202 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE E 214 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE E 204 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 214 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE J 214 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN J 213 " --> pdb=" O ILE J 204 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY J 201 " --> pdb=" O PHE J 115 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR J 110 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL J 146 " --> pdb=" O TYR J 110 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL J 112 " --> pdb=" O VAL J 146 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS J 148 " --> pdb=" O VAL J 112 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE J 114 " --> pdb=" O CYS J 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 97 through 102 removed outlier: 4.929A pdb=" N THR F 91 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU F 177 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA F 147 " --> pdb=" O LEU F 177 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR F 110 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL F 146 " --> pdb=" O TYR F 110 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL F 112 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N CYS F 148 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE F 114 " --> pdb=" O CYS F 148 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY F 201 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU F 202 " --> pdb=" O ILE F 214 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE F 214 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE F 204 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN G 213 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE G 204 " --> pdb=" O GLN G 213 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY G 201 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR G 110 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL G 146 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL G 112 " --> pdb=" O VAL G 146 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N CYS G 148 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE G 114 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LEU G 177 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA G 147 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU G 176 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL G 93 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR G 91 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 191 through 192 removed outlier: 3.602A pdb=" N HIS F 197 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 83 through 84 removed outlier: 4.163A pdb=" N LYS H 83 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN H 213 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY H 201 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR H 110 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL H 146 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL H 112 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS H 148 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE H 114 " --> pdb=" O CYS H 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 83 through 84 removed outlier: 4.163A pdb=" N LYS H 83 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE I 214 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN I 213 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG I 200 " --> pdb=" O ASN I 217 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY I 201 " --> pdb=" O PHE I 115 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR I 110 " --> pdb=" O GLU I 144 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL I 146 " --> pdb=" O TYR I 110 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL I 112 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS I 148 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE I 114 " --> pdb=" O CYS I 148 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LEU I 177 " --> pdb=" O VAL I 145 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA I 147 " --> pdb=" O LEU I 177 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 176 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL I 93 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER I 178 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N THR I 91 " --> pdb=" O SER I 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 97 through 102 Processing sheet with id=AB3, first strand: chain 'J' and resid 97 through 102 removed outlier: 3.532A pdb=" N VAL J 93 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 176 " --> pdb=" O VAL J 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 192 through 194 removed outlier: 5.771A pdb=" N TYR M 192 " --> pdb=" O LYS M 244 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP M 246 " --> pdb=" O TYR M 192 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU M 194 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE M 209 " --> pdb=" O GLY M 243 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL M 245 " --> pdb=" O PHE M 209 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS M 211 " --> pdb=" O VAL M 245 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU M 265 " --> pdb=" O GLN M 276 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN M 276 " --> pdb=" O LEU M 265 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TRP M 267 " --> pdb=" O VAL M 274 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1533 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: 4.04 Time building geometry restraints manager: 5.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4687 1.34 - 1.46: 3067 1.46 - 1.58: 7188 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 14970 Sorted by residual: bond pdb=" N THR C 255 " pdb=" CA THR C 255 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.35e+00 bond pdb=" C ALA J 85 " pdb=" N PRO J 86 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.32e-02 5.74e+03 5.23e+00 bond pdb=" CA ALA J 85 " pdb=" C ALA J 85 " ideal model delta sigma weight residual 1.527 1.547 -0.020 1.02e-02 9.61e+03 3.89e+00 bond pdb=" CA ILE C 257 " pdb=" CB ILE C 257 " ideal model delta sigma weight residual 1.534 1.547 -0.013 6.80e-03 2.16e+04 3.42e+00 bond pdb=" CA ILE C 256 " pdb=" C ILE C 256 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.27e-02 6.20e+03 2.87e+00 ... (remaining 14965 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.25: 502 107.25 - 114.01: 8306 114.01 - 120.77: 6459 120.77 - 127.52: 4879 127.52 - 134.28: 156 Bond angle restraints: 20302 Sorted by residual: angle pdb=" N GLU C 254 " pdb=" CA GLU C 254 " pdb=" C GLU C 254 " ideal model delta sigma weight residual 108.14 115.61 -7.47 1.52e+00 4.33e-01 2.41e+01 angle pdb=" C ILE C 257 " pdb=" N PRO C 258 " pdb=" CA PRO C 258 " ideal model delta sigma weight residual 119.90 115.00 4.90 1.05e+00 9.07e-01 2.18e+01 angle pdb=" N THR C 255 " pdb=" CA THR C 255 " pdb=" C THR C 255 " ideal model delta sigma weight residual 110.80 120.55 -9.75 2.13e+00 2.20e-01 2.10e+01 angle pdb=" N ILE J 141 " pdb=" CA ILE J 141 " pdb=" C ILE J 141 " ideal model delta sigma weight residual 111.91 108.37 3.54 8.90e-01 1.26e+00 1.58e+01 angle pdb=" CA GLU E 227 " pdb=" CB GLU E 227 " pdb=" CG GLU E 227 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 ... (remaining 20297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 7809 16.76 - 33.52: 772 33.52 - 50.27: 180 50.27 - 67.03: 31 67.03 - 83.79: 26 Dihedral angle restraints: 8818 sinusoidal: 3591 harmonic: 5227 Sorted by residual: dihedral pdb=" CB CYS M 247 " pdb=" SG CYS M 247 " pdb=" SG CYS M 254 " pdb=" CB CYS M 254 " ideal model delta sinusoidal sigma weight residual 93.00 171.42 -78.42 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" N THR C 255 " pdb=" C THR C 255 " pdb=" CA THR C 255 " pdb=" CB THR C 255 " ideal model delta harmonic sigma weight residual 123.40 135.65 -12.25 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C THR C 255 " pdb=" N THR C 255 " pdb=" CA THR C 255 " pdb=" CB THR C 255 " ideal model delta harmonic sigma weight residual -122.00 -133.99 11.99 0 2.50e+00 1.60e-01 2.30e+01 ... (remaining 8815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2145 0.105 - 0.210: 98 0.210 - 0.315: 3 0.315 - 0.420: 0 0.420 - 0.525: 1 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA THR C 255 " pdb=" N THR C 255 " pdb=" C THR C 255 " pdb=" CB THR C 255 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA LYS C 250 " pdb=" N LYS C 250 " pdb=" C LYS C 250 " pdb=" CB LYS C 250 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE E 141 " pdb=" CA ILE E 141 " pdb=" CG1 ILE E 141 " pdb=" CG2 ILE E 141 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2244 not shown) Planarity restraints: 2599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 257 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.81e+00 pdb=" N PRO C 258 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 258 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 258 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 170 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO G 171 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO G 171 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 171 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 83 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO H 84 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 84 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 84 " -0.027 5.00e-02 4.00e+02 ... (remaining 2596 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1820 2.75 - 3.29: 14282 3.29 - 3.82: 23301 3.82 - 4.36: 27433 4.36 - 4.90: 48620 Nonbonded interactions: 115456 Sorted by model distance: nonbonded pdb=" OE2 GLU D 127 " pdb=" NH1 ARG D 200 " model vdw 2.211 2.520 nonbonded pdb=" NE2 GLN F 213 " pdb=" OD1 ASN G 217 " model vdw 2.228 2.520 nonbonded pdb=" OD2 ASP M 246 " pdb=" OG1 THR M 248 " model vdw 2.246 2.440 nonbonded pdb=" NE2 GLN A 213 " pdb=" OD1 ASN B 217 " model vdw 2.269 2.520 nonbonded pdb=" NE2 GLN C 213 " pdb=" OD1 ASN D 217 " model vdw 2.276 2.520 ... (remaining 115451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 76 through 242) selection = (chain 'B' and resid 76 through 242) selection = (chain 'C' and resid 76 through 242) selection = (chain 'D' and resid 76 through 242) selection = (chain 'E' and resid 76 through 242) selection = (chain 'F' and resid 76 through 242) selection = chain 'G' selection = chain 'H' selection = (chain 'I' and resid 76 through 242) selection = (chain 'J' and resid 76 through 242) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 6.430 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 38.810 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.004 0.037 14970 Z= 0.265 Angle : 0.681 10.209 20302 Z= 0.366 Chirality : 0.048 0.525 2247 Planarity : 0.005 0.065 2599 Dihedral : 14.659 83.790 5467 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1793 helix: 0.68 (0.22), residues: 534 sheet: -0.89 (0.22), residues: 468 loop : -0.23 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 88 HIS 0.010 0.001 HIS F 241 PHE 0.015 0.001 PHE I 114 TYR 0.026 0.001 TYR J 116 ARG 0.010 0.001 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.778 Fit side-chains REVERT: A 183 GLN cc_start: 0.8151 (tp40) cc_final: 0.7886 (tp-100) REVERT: A 237 TYR cc_start: 0.8472 (t80) cc_final: 0.8225 (t80) REVERT: B 179 ASP cc_start: 0.7489 (t70) cc_final: 0.6801 (t0) REVERT: C 179 ASP cc_start: 0.7972 (t0) cc_final: 0.7514 (t0) REVERT: D 109 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7743 (mmtt) REVERT: D 116 TYR cc_start: 0.9124 (p90) cc_final: 0.8886 (p90) REVERT: D 213 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8328 (tm-30) REVERT: E 227 GLU cc_start: 0.8123 (tp30) cc_final: 0.7669 (tp30) REVERT: E 231 LEU cc_start: 0.9174 (mp) cc_final: 0.8879 (mp) REVERT: H 142 ASN cc_start: 0.8825 (t0) cc_final: 0.8616 (t0) REVERT: H 195 SER cc_start: 0.8885 (t) cc_final: 0.8565 (t) REVERT: J 179 ASP cc_start: 0.7767 (t70) cc_final: 0.7168 (t0) REVERT: J 184 ILE cc_start: 0.9021 (mp) cc_final: 0.8622 (mt) REVERT: J 190 VAL cc_start: 0.9465 (m) cc_final: 0.9112 (p) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.3459 time to fit residues: 144.2009 Evaluate side-chains 244 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 133 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 ASN C 241 HIS F 233 GLN H 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14970 Z= 0.230 Angle : 0.554 9.110 20302 Z= 0.285 Chirality : 0.044 0.160 2247 Planarity : 0.004 0.045 2599 Dihedral : 4.026 17.447 1983 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.26 % Allowed : 8.67 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1793 helix: 1.11 (0.22), residues: 543 sheet: -1.00 (0.22), residues: 474 loop : -0.06 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 159 HIS 0.007 0.001 HIS M 250 PHE 0.010 0.001 PHE I 114 TYR 0.013 0.001 TYR E 237 ARG 0.007 0.000 ARG E 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 262 time to evaluate : 1.812 Fit side-chains REVERT: A 183 GLN cc_start: 0.8140 (tp40) cc_final: 0.7894 (tp-100) REVERT: A 237 TYR cc_start: 0.8554 (t80) cc_final: 0.8279 (t80) REVERT: B 116 TYR cc_start: 0.9171 (p90) cc_final: 0.8945 (p90) REVERT: B 179 ASP cc_start: 0.7553 (t70) cc_final: 0.6807 (t0) REVERT: C 179 ASP cc_start: 0.7931 (t0) cc_final: 0.7653 (t0) REVERT: D 109 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7664 (mmtt) REVERT: D 116 TYR cc_start: 0.9133 (p90) cc_final: 0.8917 (p90) REVERT: E 227 GLU cc_start: 0.8139 (tp30) cc_final: 0.7861 (tp30) REVERT: G 83 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8685 (mmmt) REVERT: H 142 ASN cc_start: 0.8816 (t0) cc_final: 0.8510 (t0) REVERT: H 227 GLU cc_start: 0.8506 (tp30) cc_final: 0.8300 (tp30) REVERT: J 184 ILE cc_start: 0.9074 (mp) cc_final: 0.8856 (mt) REVERT: J 190 VAL cc_start: 0.9464 (m) cc_final: 0.9126 (p) REVERT: M 251 TYR cc_start: 0.7245 (p90) cc_final: 0.7024 (p90) outliers start: 20 outliers final: 12 residues processed: 273 average time/residue: 0.3604 time to fit residues: 131.5581 Evaluate side-chains 259 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 247 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 217 ASN Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 145 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 0.0470 chunk 172 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS C 75 HIS C 217 ASN C 241 HIS F 233 GLN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 ASN J 153 GLN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14970 Z= 0.270 Angle : 0.554 8.500 20302 Z= 0.285 Chirality : 0.044 0.185 2247 Planarity : 0.004 0.043 2599 Dihedral : 4.012 18.811 1983 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.63 % Allowed : 11.88 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1793 helix: 1.22 (0.22), residues: 547 sheet: -1.09 (0.22), residues: 474 loop : -0.06 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 88 HIS 0.005 0.001 HIS H 197 PHE 0.011 0.001 PHE D 114 TYR 0.011 0.001 TYR B 237 ARG 0.005 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 256 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8597 (t80) cc_final: 0.8327 (t80) REVERT: B 179 ASP cc_start: 0.7667 (t70) cc_final: 0.6856 (t0) REVERT: C 179 ASP cc_start: 0.7899 (t0) cc_final: 0.7612 (t0) REVERT: C 240 LYS cc_start: 0.8599 (tttt) cc_final: 0.8296 (ttmt) REVERT: G 83 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8558 (mmmt) REVERT: G 150 VAL cc_start: 0.8843 (m) cc_final: 0.8500 (t) REVERT: H 142 ASN cc_start: 0.8897 (t0) cc_final: 0.8536 (t0) REVERT: H 227 GLU cc_start: 0.8540 (tp30) cc_final: 0.8299 (tp30) REVERT: J 118 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8224 (mp) REVERT: J 179 ASP cc_start: 0.7935 (t70) cc_final: 0.7201 (t0) REVERT: J 184 ILE cc_start: 0.9102 (mp) cc_final: 0.8672 (mt) REVERT: J 190 VAL cc_start: 0.9478 (m) cc_final: 0.9118 (p) outliers start: 26 outliers final: 20 residues processed: 274 average time/residue: 0.3727 time to fit residues: 135.8690 Evaluate side-chains 256 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 235 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 217 ASN Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 145 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 76 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 GLN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14970 Z= 0.269 Angle : 0.545 8.714 20302 Z= 0.282 Chirality : 0.044 0.164 2247 Planarity : 0.004 0.045 2599 Dihedral : 4.015 22.712 1983 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.95 % Allowed : 13.45 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1793 helix: 1.33 (0.22), residues: 549 sheet: -1.12 (0.22), residues: 474 loop : -0.02 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 88 HIS 0.005 0.001 HIS B 182 PHE 0.010 0.001 PHE D 114 TYR 0.013 0.001 TYR E 237 ARG 0.005 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 244 time to evaluate : 2.055 Fit side-chains revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8624 (t80) cc_final: 0.8343 (t80) REVERT: B 179 ASP cc_start: 0.7693 (t70) cc_final: 0.6947 (t0) REVERT: C 179 ASP cc_start: 0.7885 (t0) cc_final: 0.7676 (t0) REVERT: C 240 LYS cc_start: 0.8609 (tttt) cc_final: 0.8298 (ttmt) REVERT: D 109 LYS cc_start: 0.8360 (mmmt) cc_final: 0.7872 (mmtt) REVERT: F 144 GLU cc_start: 0.7575 (mp0) cc_final: 0.7280 (mp0) REVERT: G 83 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8643 (mmmt) REVERT: G 150 VAL cc_start: 0.8831 (m) cc_final: 0.8511 (t) REVERT: H 142 ASN cc_start: 0.8901 (t0) cc_final: 0.8508 (t0) REVERT: J 118 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8292 (mp) REVERT: J 179 ASP cc_start: 0.7852 (t70) cc_final: 0.7135 (t0) REVERT: J 184 ILE cc_start: 0.9109 (mp) cc_final: 0.8615 (mt) REVERT: J 190 VAL cc_start: 0.9480 (m) cc_final: 0.9111 (p) outliers start: 31 outliers final: 23 residues processed: 264 average time/residue: 0.3792 time to fit residues: 134.2712 Evaluate side-chains 262 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 217 ASN Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 241 HIS Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 145 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.0270 chunk 152 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 GLN ** F 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14970 Z= 0.320 Angle : 0.578 9.450 20302 Z= 0.298 Chirality : 0.045 0.188 2247 Planarity : 0.004 0.045 2599 Dihedral : 4.100 20.194 1983 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.33 % Allowed : 14.90 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1793 helix: 1.33 (0.22), residues: 549 sheet: -1.22 (0.22), residues: 474 loop : -0.06 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 88 HIS 0.006 0.001 HIS B 182 PHE 0.012 0.001 PHE D 114 TYR 0.012 0.001 TYR B 237 ARG 0.006 0.000 ARG E 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 242 time to evaluate : 1.833 Fit side-chains revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8625 (t80) cc_final: 0.8342 (t80) REVERT: B 179 ASP cc_start: 0.7777 (t70) cc_final: 0.7066 (t0) REVERT: C 166 GLN cc_start: 0.8395 (pm20) cc_final: 0.8018 (pm20) REVERT: C 179 ASP cc_start: 0.7909 (t0) cc_final: 0.7709 (t0) REVERT: C 210 ILE cc_start: 0.9265 (mm) cc_final: 0.8563 (tt) REVERT: C 240 LYS cc_start: 0.8633 (tttt) cc_final: 0.8340 (ttmt) REVERT: D 179 ASP cc_start: 0.8177 (t0) cc_final: 0.7875 (t0) REVERT: E 143 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8469 (p) REVERT: E 227 GLU cc_start: 0.8191 (tp30) cc_final: 0.7979 (tp30) REVERT: F 144 GLU cc_start: 0.7668 (mp0) cc_final: 0.7328 (mp0) REVERT: G 83 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8637 (mmmt) REVERT: H 208 LYS cc_start: 0.8975 (mppt) cc_final: 0.8614 (mppt) REVERT: J 118 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8276 (mp) REVERT: J 179 ASP cc_start: 0.7870 (t70) cc_final: 0.7297 (t0) REVERT: J 184 ILE cc_start: 0.9133 (mp) cc_final: 0.8684 (mt) outliers start: 37 outliers final: 29 residues processed: 266 average time/residue: 0.3799 time to fit residues: 134.3749 Evaluate side-chains 265 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 217 ASN Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 241 HIS Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 145 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 233 GLN ** F 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14970 Z= 0.203 Angle : 0.544 9.228 20302 Z= 0.279 Chirality : 0.044 0.290 2247 Planarity : 0.004 0.046 2599 Dihedral : 3.960 19.481 1983 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.39 % Allowed : 15.59 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1793 helix: 1.47 (0.23), residues: 549 sheet: -1.10 (0.22), residues: 474 loop : 0.03 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 88 HIS 0.005 0.001 HIS B 241 PHE 0.008 0.001 PHE A 122 TYR 0.015 0.001 TYR E 237 ARG 0.006 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 252 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.8229 (mtp85) REVERT: A 237 TYR cc_start: 0.8611 (t80) cc_final: 0.8318 (t80) REVERT: B 179 ASP cc_start: 0.7643 (t70) cc_final: 0.6938 (t0) REVERT: C 166 GLN cc_start: 0.8348 (pm20) cc_final: 0.7991 (pm20) REVERT: C 210 ILE cc_start: 0.9256 (mm) cc_final: 0.8582 (tt) REVERT: C 240 LYS cc_start: 0.8597 (tttt) cc_final: 0.8288 (ttmt) REVERT: D 179 ASP cc_start: 0.8092 (t0) cc_final: 0.7756 (t0) REVERT: D 213 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8625 (tm-30) REVERT: E 143 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8486 (p) REVERT: F 144 GLU cc_start: 0.7625 (mp0) cc_final: 0.7255 (mp0) REVERT: G 83 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8655 (mmmt) REVERT: H 142 ASN cc_start: 0.8929 (t0) cc_final: 0.8525 (t0) REVERT: J 179 ASP cc_start: 0.7849 (t70) cc_final: 0.7271 (t0) REVERT: J 184 ILE cc_start: 0.9117 (mp) cc_final: 0.8658 (mt) outliers start: 38 outliers final: 26 residues processed: 278 average time/residue: 0.3650 time to fit residues: 135.6059 Evaluate side-chains 267 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 131 PHE Chi-restraints excluded: chain G residue 217 ASN Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain M residue 274 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.0170 chunk 97 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 HIS F 233 GLN ** F 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14970 Z= 0.302 Angle : 0.583 10.979 20302 Z= 0.301 Chirality : 0.045 0.259 2247 Planarity : 0.004 0.046 2599 Dihedral : 4.066 19.192 1983 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.58 % Allowed : 16.59 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1793 helix: 1.43 (0.22), residues: 549 sheet: -1.17 (0.22), residues: 476 loop : -0.00 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 88 HIS 0.007 0.001 HIS B 241 PHE 0.012 0.001 PHE D 114 TYR 0.011 0.001 TYR H 110 ARG 0.006 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 239 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8249 (tp-100) cc_final: 0.8027 (tp40) REVERT: A 237 TYR cc_start: 0.8645 (t80) cc_final: 0.8348 (t80) REVERT: B 179 ASP cc_start: 0.7751 (t70) cc_final: 0.7004 (t0) REVERT: C 166 GLN cc_start: 0.8341 (pm20) cc_final: 0.7959 (pm20) REVERT: C 240 LYS cc_start: 0.8633 (tttt) cc_final: 0.8337 (ttmt) REVERT: D 179 ASP cc_start: 0.8089 (t0) cc_final: 0.7752 (t0) REVERT: E 143 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8472 (p) REVERT: G 83 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8654 (mmmt) REVERT: J 179 ASP cc_start: 0.7868 (t70) cc_final: 0.7335 (t0) REVERT: J 184 ILE cc_start: 0.9136 (mp) cc_final: 0.8695 (mt) outliers start: 41 outliers final: 34 residues processed: 267 average time/residue: 0.3744 time to fit residues: 133.1025 Evaluate side-chains 269 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 234 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 131 PHE Chi-restraints excluded: chain G residue 217 ASN Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 241 HIS Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 138 PHE Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain M residue 274 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 0.0000 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 HIS F 233 GLN ** F 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14970 Z= 0.215 Angle : 0.559 10.009 20302 Z= 0.288 Chirality : 0.044 0.231 2247 Planarity : 0.004 0.047 2599 Dihedral : 3.936 18.960 1983 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.51 % Allowed : 17.41 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1793 helix: 1.53 (0.23), residues: 549 sheet: -1.07 (0.23), residues: 474 loop : 0.07 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 88 HIS 0.008 0.001 HIS B 241 PHE 0.008 0.001 PHE D 114 TYR 0.018 0.001 TYR E 237 ARG 0.006 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 241 time to evaluate : 1.905 Fit side-chains revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8607 (t80) cc_final: 0.8339 (t80) REVERT: B 179 ASP cc_start: 0.7594 (t70) cc_final: 0.6961 (t70) REVERT: C 166 GLN cc_start: 0.8342 (pm20) cc_final: 0.7921 (pm20) REVERT: C 240 LYS cc_start: 0.8615 (tttt) cc_final: 0.8315 (ttmt) REVERT: D 179 ASP cc_start: 0.8024 (t0) cc_final: 0.7707 (t0) REVERT: D 213 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8688 (tm-30) REVERT: E 143 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8480 (p) REVERT: H 208 LYS cc_start: 0.8906 (mppt) cc_final: 0.8543 (mppt) REVERT: J 179 ASP cc_start: 0.7853 (t70) cc_final: 0.7324 (t0) REVERT: J 184 ILE cc_start: 0.9113 (mp) cc_final: 0.8664 (mt) outliers start: 40 outliers final: 32 residues processed: 266 average time/residue: 0.3704 time to fit residues: 131.8428 Evaluate side-chains 267 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 131 PHE Chi-restraints excluded: chain G residue 217 ASN Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain M residue 274 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 HIS F 233 GLN ** F 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14970 Z= 0.236 Angle : 0.573 8.340 20302 Z= 0.295 Chirality : 0.045 0.363 2247 Planarity : 0.004 0.047 2599 Dihedral : 3.936 19.027 1983 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.51 % Allowed : 17.66 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1793 helix: 1.51 (0.23), residues: 549 sheet: -1.06 (0.23), residues: 474 loop : 0.08 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 88 HIS 0.009 0.001 HIS B 241 PHE 0.009 0.001 PHE D 114 TYR 0.010 0.001 TYR D 116 ARG 0.006 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 242 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8620 (t80) cc_final: 0.8347 (t80) REVERT: C 240 LYS cc_start: 0.8619 (tttt) cc_final: 0.8325 (ttmt) REVERT: D 179 ASP cc_start: 0.8018 (t0) cc_final: 0.7677 (t0) REVERT: D 213 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8694 (tm-30) REVERT: E 143 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8477 (p) REVERT: E 183 GLN cc_start: 0.8332 (tp40) cc_final: 0.7937 (tp40) REVERT: E 227 GLU cc_start: 0.8111 (tp30) cc_final: 0.7798 (tp30) REVERT: F 173 ARG cc_start: 0.7779 (mtm180) cc_final: 0.7314 (mtm180) REVERT: J 179 ASP cc_start: 0.7873 (t70) cc_final: 0.7348 (t0) REVERT: J 184 ILE cc_start: 0.9121 (mp) cc_final: 0.8675 (mt) outliers start: 40 outliers final: 33 residues processed: 269 average time/residue: 0.3995 time to fit residues: 143.5562 Evaluate side-chains 269 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 131 PHE Chi-restraints excluded: chain G residue 217 ASN Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 138 PHE Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain M residue 274 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 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 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 HIS F 233 GLN ** F 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14970 Z= 0.167 Angle : 0.561 8.389 20302 Z= 0.288 Chirality : 0.044 0.338 2247 Planarity : 0.004 0.047 2599 Dihedral : 3.814 18.372 1983 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.20 % Allowed : 18.16 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1793 helix: 1.63 (0.23), residues: 545 sheet: -0.83 (0.23), residues: 450 loop : 0.02 (0.25), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 88 HIS 0.007 0.001 HIS B 241 PHE 0.007 0.001 PHE D 113 TYR 0.021 0.001 TYR E 237 ARG 0.008 0.000 ARG M 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8588 (t80) cc_final: 0.8309 (t80) REVERT: C 240 LYS cc_start: 0.8629 (tttt) cc_final: 0.8316 (ttmt) REVERT: D 179 ASP cc_start: 0.7926 (t0) cc_final: 0.7583 (t0) REVERT: D 213 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8730 (tm-30) REVERT: E 143 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8480 (p) REVERT: E 183 GLN cc_start: 0.8250 (tp40) cc_final: 0.7943 (tp40) REVERT: E 227 GLU cc_start: 0.8028 (tp30) cc_final: 0.7773 (tp30) REVERT: F 173 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7299 (mtm180) REVERT: H 142 ASN cc_start: 0.8904 (t0) cc_final: 0.8526 (t0) REVERT: J 179 ASP cc_start: 0.7811 (t70) cc_final: 0.7343 (t0) REVERT: J 184 ILE cc_start: 0.9077 (mp) cc_final: 0.8744 (mt) outliers start: 35 outliers final: 24 residues processed: 277 average time/residue: 0.3576 time to fit residues: 133.4375 Evaluate side-chains 266 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 241 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 131 PHE Chi-restraints excluded: chain G residue 241 HIS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 138 PHE Chi-restraints excluded: chain I residue 153 GLN Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain M residue 274 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 HIS F 233 GLN ** F 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 HIS H 217 ASN ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.078356 restraints weight = 29958.954| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.95 r_work: 0.2912 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14970 Z= 0.185 Angle : 0.574 8.327 20302 Z= 0.295 Chirality : 0.044 0.324 2247 Planarity : 0.004 0.047 2599 Dihedral : 3.799 18.222 1983 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.14 % Allowed : 18.48 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1793 helix: 1.63 (0.23), residues: 545 sheet: -0.91 (0.23), residues: 472 loop : 0.11 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 88 HIS 0.008 0.001 HIS B 241 PHE 0.007 0.001 PHE D 114 TYR 0.016 0.001 TYR C 110 ARG 0.007 0.000 ARG B 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3352.76 seconds wall clock time: 61 minutes 45.74 seconds (3705.74 seconds total)