Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 09:46:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/08_2023/8eky_28217.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/08_2023/8eky_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_28217/08_2023/8eky_28217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/08_2023/8eky_28217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/08_2023/8eky_28217.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eky_28217/08_2023/8eky_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 7.08, per 1000 atoms: 0.48 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: 5.59 Conformation dependent library (CDL) restraints added in 2.1 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: 1.67 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: 4.02 Time building geometry restraints manager: 6.01 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.010 Extract box with map and model: 7.200 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.790 Find NCS groups from input model: 1.090 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.670 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.684 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.3552 time to fit residues: 147.4935 Evaluate side-chains 244 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3285 ------------------------------------------------------------------------------- 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: 4.9990 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: 4.9990 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: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 14970 Z= 0.231 Angle : 0.558 9.036 20302 Z= 0.288 Chirality : 0.044 0.160 2247 Planarity : 0.004 0.045 2599 Dihedral : 4.038 17.193 1983 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 1.26 % 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: -0.08 (0.20), residues: 1793 helix: 1.12 (0.22), residues: 543 sheet: -1.05 (0.22), residues: 478 loop : -0.04 (0.25), residues: 772 *********************** 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 279 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 259 time to evaluate : 1.766 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 270 average time/residue: 0.3713 time to fit residues: 133.7931 Evaluate side-chains 255 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 1.740 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1275 time to fit residues: 4.8939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 133 optimal weight: 0.0000 chunk 108 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 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: 0.8188 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 0.031 14970 Z= 0.252 Angle : 0.551 8.696 20302 Z= 0.284 Chirality : 0.044 0.192 2247 Planarity : 0.004 0.043 2599 Dihedral : 3.988 18.593 1983 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 1.01 % 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: -0.01 (0.20), residues: 1793 helix: 1.32 (0.22), residues: 543 sheet: -1.06 (0.22), residues: 474 loop : -0.10 (0.24), residues: 776 *********************** 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 274 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 258 time to evaluate : 1.797 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 268 average time/residue: 0.3904 time to fit residues: 138.1310 Evaluate side-chains 248 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 239 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1386 time to fit residues: 4.5958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8187 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 14970 Z= 0.233 Angle : 0.539 7.401 20302 Z= 0.279 Chirality : 0.044 0.160 2247 Planarity : 0.004 0.044 2599 Dihedral : 3.943 21.970 1983 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.94 % 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: 0.09 (0.21), residues: 1793 helix: 1.46 (0.23), residues: 545 sheet: -1.09 (0.22), residues: 478 loop : -0.02 (0.25), residues: 770 *********************** 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 269 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 254 time to evaluate : 1.933 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 262 average time/residue: 0.3853 time to fit residues: 134.3258 Evaluate side-chains 247 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 240 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1411 time to fit residues: 4.3286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 70 optimal weight: 0.0770 chunk 145 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.2980 chunk 152 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.8744 ------------------------------------------------------------------------------- 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** C 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 14970 Z= 0.379 Angle : 0.604 7.328 20302 Z= 0.312 Chirality : 0.046 0.156 2247 Planarity : 0.004 0.045 2599 Dihedral : 4.214 20.727 1983 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 1.32 % 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: -0.11 (0.21), residues: 1793 helix: 1.35 (0.22), residues: 545 sheet: -1.28 (0.22), residues: 476 loop : -0.13 (0.25), residues: 772 *********************** 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 256 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 235 time to evaluate : 1.787 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 248 average time/residue: 0.4033 time to fit residues: 131.9394 Evaluate side-chains 236 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 226 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1363 time to fit residues: 4.8816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 170 optimal weight: 0.2980 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 164 optimal weight: 0.0670 overall best weight: 1.0724 ------------------------------------------------------------------------------- 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** F 233 GLN ** F 241 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: 0.8185 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14970 Z= 0.186 Angle : 0.552 8.183 20302 Z= 0.284 Chirality : 0.044 0.168 2247 Planarity : 0.004 0.046 2599 Dihedral : 3.980 20.246 1983 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 1.32 % 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: 0.15 (0.21), residues: 1793 helix: 1.58 (0.23), residues: 545 sheet: -1.13 (0.22), residues: 474 loop : 0.00 (0.25), residues: 774 *********************** 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 274 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 253 time to evaluate : 1.803 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 268 average time/residue: 0.3824 time to fit residues: 136.0979 Evaluate side-chains 248 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 1.767 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1407 time to fit residues: 5.6168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN B 241 HIS C 241 HIS F 156 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.047 14970 Z= 0.531 Angle : 0.704 8.654 20302 Z= 0.366 Chirality : 0.049 0.188 2247 Planarity : 0.005 0.045 2599 Dihedral : 4.604 21.068 1983 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.20 % Rotamer Outliers : 1.38 % 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: -0.43 (0.20), residues: 1793 helix: 1.00 (0.22), residues: 562 sheet: -1.48 (0.23), residues: 452 loop : -0.32 (0.24), residues: 779 *********************** 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 248 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 1.802 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 240 average time/residue: 0.4106 time to fit residues: 129.3540 Evaluate side-chains 230 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 218 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1730 time to fit residues: 5.7174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 HIS C 241 HIS F 233 GLN G 182 HIS ** M 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1970 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= 0.203 Angle : 0.593 10.003 20302 Z= 0.308 Chirality : 0.045 0.184 2247 Planarity : 0.004 0.047 2599 Dihedral : 4.173 20.315 1983 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.69 % 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: -0.03 (0.21), residues: 1793 helix: 1.49 (0.23), residues: 545 sheet: -1.36 (0.22), residues: 478 loop : -0.04 (0.25), residues: 770 *********************** 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 253 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 242 time to evaluate : 1.720 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 245 average time/residue: 0.3959 time to fit residues: 128.4265 Evaluate side-chains 234 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 228 time to evaluate : 1.729 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1905 time to fit residues: 4.0414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 HIS C 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 14970 Z= 0.376 Angle : 0.638 10.722 20302 Z= 0.330 Chirality : 0.046 0.176 2247 Planarity : 0.004 0.047 2599 Dihedral : 4.313 20.437 1983 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.63 % 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: -0.25 (0.21), residues: 1793 helix: 1.18 (0.22), residues: 563 sheet: -1.38 (0.23), residues: 438 loop : -0.26 (0.24), residues: 792 *********************** 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 233 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 223 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 227 average time/residue: 0.4147 time to fit residues: 123.8102 Evaluate side-chains 226 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3076 time to fit residues: 4.8736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 79 optimal weight: 0.0770 chunk 116 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 236 GLN B 241 HIS C 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 14970 Z= 0.189 Angle : 0.595 8.789 20302 Z= 0.309 Chirality : 0.044 0.172 2247 Planarity : 0.004 0.048 2599 Dihedral : 4.048 19.789 1983 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.31 % 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: 1.55 (0.23), residues: 545 sheet: -1.26 (0.23), residues: 474 loop : -0.02 (0.25), residues: 774 ********************** 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 250 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 1.979 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 248 average time/residue: 0.4025 time to fit residues: 132.8957 Evaluate side-chains 234 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 1.872 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1802 time to fit residues: 3.0910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 143 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN B 241 HIS C 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.075787 restraints weight = 30478.639| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.89 r_work: 0.2865 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 14970 Z= 0.311 Angle : 0.624 9.434 20302 Z= 0.325 Chirality : 0.046 0.206 2247 Planarity : 0.004 0.048 2599 Dihedral : 4.155 19.992 1983 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.38 % 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: -0.14 (0.21), residues: 1793 helix: 1.29 (0.22), residues: 563 sheet: -1.32 (0.24), residues: 438 loop : -0.23 (0.24), residues: 792 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.60 seconds wall clock time: 59 minutes 1.08 seconds (3541.08 seconds total)