Starting phenix.real_space_refine on Thu Sep 26 19:41:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/09_2024/7m74_23708.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/09_2024/7m74_23708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/09_2024/7m74_23708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/09_2024/7m74_23708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/09_2024/7m74_23708.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/09_2024/7m74_23708.cif" } resolution = 3.93 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 51 5.16 5 C 8589 2.51 5 N 2260 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13457 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3083 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 19, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 736 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 11, 'TRANS': 81} Chain: "G" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2421 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "M" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2834 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain: "L" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Chain: "H" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'TAK': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 7.81, per 1000 atoms: 0.58 Number of scatterers: 13457 At special positions: 0 Unit cell: (101.016, 135.792, 167.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 6 15.00 O 2551 8.00 N 2260 7.00 C 8589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 212 " distance=2.03 Simple disulfide: pdb=" SG CYS N 31 " - pdb=" SG CYS N 105 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " GLC D 1 " - " GLC D 2 " Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 2.0 seconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3184 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 24 sheets defined 29.4% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.687A pdb=" N ILE A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 114 through 135 removed outlier: 3.564A pdb=" N ARG A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 removed outlier: 3.568A pdb=" N GLY A 169 " --> pdb=" O MET A 165 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.999A pdb=" N THR A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.955A pdb=" N ASP A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.646A pdb=" N ILE A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 266 Processing helix chain 'A' and resid 407 through 422 Processing helix chain 'A' and resid 532 through 543 removed outlier: 3.689A pdb=" N CYS A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 removed outlier: 3.791A pdb=" N ILE A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 218 removed outlier: 3.550A pdb=" N LEU B 213 " --> pdb=" O PRO B 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.771A pdb=" N SER G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 42 removed outlier: 3.719A pdb=" N ASP G 40 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE G 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 68 removed outlier: 3.610A pdb=" N ALA G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 98 Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 113 through 122 removed outlier: 3.693A pdb=" N VAL G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 148 removed outlier: 3.967A pdb=" N ALA G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.841A pdb=" N LEU G 178 " --> pdb=" O LYS G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 223 removed outlier: 3.906A pdb=" N ALA G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 252 removed outlier: 3.824A pdb=" N ALA G 250 " --> pdb=" O VAL G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 267 Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 284 through 295 removed outlier: 3.541A pdb=" N ALA G 295 " --> pdb=" O ARG G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 324 removed outlier: 3.573A pdb=" N GLN G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 32 removed outlier: 3.695A pdb=" N LEU M 20 " --> pdb=" O GLY M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 52 Proline residue: M 48 - end of helix Processing helix chain 'M' and resid 66 through 73 removed outlier: 3.819A pdb=" N SER M 73 " --> pdb=" O GLY M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 88 Processing helix chain 'M' and resid 90 through 96 Processing helix chain 'M' and resid 131 through 140 removed outlier: 3.885A pdb=" N GLU M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 163 removed outlier: 4.019A pdb=" N THR M 157 " --> pdb=" O GLU M 153 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 185 through 201 removed outlier: 3.688A pdb=" N ILE M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 209 through 219 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 231 through 239 Processing helix chain 'M' and resid 272 through 284 Processing helix chain 'M' and resid 286 through 297 removed outlier: 3.632A pdb=" N LEU M 290 " --> pdb=" O THR M 286 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU M 291 " --> pdb=" O ASP M 287 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA M 292 " --> pdb=" O GLU M 288 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL M 293 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 312 removed outlier: 3.899A pdb=" N GLU M 310 " --> pdb=" O SER M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 314 through 326 Processing helix chain 'M' and resid 334 through 352 removed outlier: 4.055A pdb=" N ALA M 338 " --> pdb=" O PRO M 334 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR M 341 " --> pdb=" O SER M 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA M 342 " --> pdb=" O ALA M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 356 through 367 Processing helix chain 'L' and resid 185 through 188 removed outlier: 3.982A pdb=" N GLU L 188 " --> pdb=" O ALA L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 185 through 188' Processing helix chain 'H' and resid 203 through 208 removed outlier: 4.515A pdb=" N THR H 207 " --> pdb=" O SER H 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 100 removed outlier: 4.044A pdb=" N THR N 100 " --> pdb=" O PRO N 97 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.757A pdb=" N VAL A 34 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR A 23 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL A 32 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY A 25 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY A 30 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASP A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER A 86 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE A 92 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL A 84 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 94 " --> pdb=" O TYR A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 404 removed outlier: 3.690A pdb=" N ILE A 402 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 438 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 241 through 243 removed outlier: 3.802A pdb=" N ALA B 255 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL G 49 " --> pdb=" O PRO G 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N TRP G 75 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE G 51 " --> pdb=" O TRP G 75 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY G 84 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP G 76 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE G 82 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 154 through 156 removed outlier: 7.077A pdb=" N VAL G 155 " --> pdb=" O LEU G 164 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 164 " --> pdb=" O VAL G 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'G' and resid 278 through 279 removed outlier: 4.311A pdb=" N GLY G 311 " --> pdb=" O VAL G 302 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.460A pdb=" N LEU M 7 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU M 38 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE M 9 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL M 8 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE M 61 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP M 10 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ALA M 63 " --> pdb=" O TRP M 10 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA M 264 " --> pdb=" O PRO M 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.460A pdb=" N LEU M 7 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU M 38 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE M 9 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL M 8 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE M 61 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP M 10 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ALA M 63 " --> pdb=" O TRP M 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AB2, first strand: chain 'M' and resid 145 through 147 removed outlier: 8.142A pdb=" N SER M 145 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR M 225 " --> pdb=" O SER M 145 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N LEU M 147 " --> pdb=" O THR M 225 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N ASN M 227 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA M 223 " --> pdb=" O ASN M 118 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN M 227 " --> pdb=" O SER M 114 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER M 114 " --> pdb=" O ASN M 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 170 through 171 removed outlier: 3.914A pdb=" N LYS M 170 " --> pdb=" O ASP M 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.591A pdb=" N SER L 68 " --> pdb=" O ASP L 71 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER L 66 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.963A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.963A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.696A pdb=" N PHE L 119 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA L 131 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 146 through 149 removed outlier: 3.689A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.699A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER H 10 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA H 82 " --> pdb=" O CYS H 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.560A pdb=" N THR H 123 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR H 98 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL H 40 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 136 through 139 removed outlier: 6.450A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 136 through 139 removed outlier: 6.450A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 167 through 170 Processing sheet with id=AC5, first strand: chain 'N' and resid 14 through 16 removed outlier: 3.696A pdb=" N GLN N 14 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA N 32 " --> pdb=" O GLN N 14 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS N 31 " --> pdb=" O VAL N 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 67 through 69 removed outlier: 3.636A pdb=" N PHE N 68 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP N 45 " --> pdb=" O VAL N 57 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL N 59 " --> pdb=" O MET N 43 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET N 43 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER N 44 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL N 102 " --> pdb=" O GLN N 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA N 101 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL N 126 " --> pdb=" O ALA N 101 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS N 105 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN N 122 " --> pdb=" O CYS N 105 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE N 107 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP N 120 " --> pdb=" O ILE N 107 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1347 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: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4254 1.34 - 1.46: 3217 1.46 - 1.58: 6220 1.58 - 1.70: 9 1.70 - 1.82: 81 Bond restraints: 13781 Sorted by residual: bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C5 ATP G 401 " pdb=" C6 ATP G 401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C8 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.24e+01 bond pdb=" C PHE G 183 " pdb=" N PRO G 184 " ideal model delta sigma weight residual 1.334 1.437 -0.104 2.34e-02 1.83e+03 1.96e+01 bond pdb=" C5 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.387 1.346 0.041 1.00e-02 1.00e+04 1.66e+01 ... (remaining 13776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 18601 3.66 - 7.32: 103 7.32 - 10.99: 10 10.99 - 14.65: 1 14.65 - 18.31: 1 Bond angle restraints: 18716 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 121.56 18.31 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP G 401 " pdb=" O3A ATP G 401 " pdb=" PB ATP G 401 " ideal model delta sigma weight residual 136.83 122.34 14.49 1.00e+00 1.00e+00 2.10e+02 angle pdb=" C5 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" N3 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 127.04 134.92 -7.88 1.15e+00 7.59e-01 4.71e+01 angle pdb=" N1 ATP G 401 " pdb=" C2 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 128.69 123.61 5.08 1.00e+00 1.00e+00 2.58e+01 ... (remaining 18711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.56: 8149 23.56 - 47.12: 132 47.12 - 70.68: 15 70.68 - 94.24: 3 94.24 - 117.79: 7 Dihedral angle restraints: 8306 sinusoidal: 3345 harmonic: 4961 Sorted by residual: dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 23.06 69.94 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" C5' AMP G 403 " pdb=" O5' AMP G 403 " pdb=" P AMP G 403 " pdb=" O3P AMP G 403 " ideal model delta sinusoidal sigma weight residual -60.00 57.80 -117.79 1 2.00e+01 2.50e-03 3.52e+01 dihedral pdb=" C2 TAK A 601 " pdb=" C1 TAK A 601 " pdb=" N1 TAK A 601 " pdb=" C5 TAK A 601 " ideal model delta sinusoidal sigma weight residual -59.56 51.63 -111.19 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 8303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1822 0.073 - 0.145: 245 0.145 - 0.218: 17 0.218 - 0.291: 1 0.291 - 0.364: 2 Chirality restraints: 2087 Sorted by residual: chirality pdb=" C1 GLC D 1 " pdb=" C2 GLC D 1 " pdb=" O1 GLC D 1 " pdb=" O5 GLC D 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.40 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE G 106 " pdb=" CA ILE G 106 " pdb=" CG1 ILE G 106 " pdb=" CG2 ILE G 106 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C3 GLC D 2 " pdb=" C2 GLC D 2 " pdb=" C4 GLC D 2 " pdb=" O3 GLC D 2 " both_signs ideal model delta sigma weight residual False 2.34 2.56 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2084 not shown) Planarity restraints: 2363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY L 95 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO L 96 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 143 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO A 144 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO L 9 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " 0.028 5.00e-02 4.00e+02 ... (remaining 2360 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 1276 2.76 - 3.47: 17472 3.47 - 4.19: 29905 4.19 - 4.90: 52068 Nonbonded interactions: 100722 Sorted by model distance: nonbonded pdb=" N VAL A 13 " pdb=" C PHE M 371 " model vdw 1.330 3.350 nonbonded pdb=" N VAL A 13 " pdb=" O PHE M 371 " model vdw 2.251 3.120 nonbonded pdb=" OG1 THR M 53 " pdb=" OD1 ASP M 55 " model vdw 2.337 3.040 nonbonded pdb=" OG SER M 233 " pdb=" O ASP M 296 " model vdw 2.352 3.040 nonbonded pdb=" OD2 ASP M 30 " pdb=" OH TYR M 283 " model vdw 2.357 3.040 ... (remaining 100717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.120 Find NCS groups from input model: 0.170 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 0.104 13781 Z= 0.233 Angle : 0.738 18.309 18716 Z= 0.416 Chirality : 0.049 0.364 2087 Planarity : 0.007 0.071 2363 Dihedral : 9.728 117.795 5107 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.16), residues: 1683 helix: -2.70 (0.16), residues: 431 sheet: -1.44 (0.26), residues: 357 loop : -2.16 (0.17), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 119 HIS 0.006 0.001 HIS G 36 PHE 0.024 0.002 PHE A 538 TYR 0.015 0.001 TYR M 341 ARG 0.004 0.000 ARG M 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9005 (mt0) cc_final: 0.8582 (mp10) REVERT: A 446 TYR cc_start: 0.6632 (p90) cc_final: 0.6115 (p90) REVERT: B 257 HIS cc_start: 0.8211 (t70) cc_final: 0.7748 (t-90) REVERT: G 41 LEU cc_start: 0.8261 (mm) cc_final: 0.8030 (mm) REVERT: G 98 TYR cc_start: 0.8081 (m-80) cc_final: 0.7533 (m-10) REVERT: M 148 MET cc_start: 0.8562 (mtp) cc_final: 0.8062 (mmm) REVERT: M 354 ARG cc_start: 0.8510 (ttm110) cc_final: 0.7960 (mtm-85) REVERT: L 146 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8309 (tptp) REVERT: N 37 THR cc_start: 0.8138 (m) cc_final: 0.7351 (p) REVERT: N 104 TYR cc_start: 0.8133 (m-80) cc_final: 0.7808 (m-80) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3365 time to fit residues: 126.9335 Evaluate side-chains 113 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 0.0970 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 40.0000 chunk 98 optimal weight: 10.0000 chunk 152 optimal weight: 0.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 HIS A 164 ASN A 220 HIS A 249 HIS A 390 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 240 HIS G 36 HIS G 80 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN G 169 HIS G 197 GLN ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 HIS M 335 GLN ** M 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 156 GLN L 190 HIS L 199 HIS ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13781 Z= 0.287 Angle : 0.698 11.945 18716 Z= 0.344 Chirality : 0.043 0.182 2087 Planarity : 0.005 0.075 2363 Dihedral : 8.620 119.775 1952 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.05 % Allowed : 9.49 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.19), residues: 1683 helix: -0.58 (0.23), residues: 451 sheet: -0.74 (0.27), residues: 358 loop : -1.46 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 45 HIS 0.009 0.001 HIS M 64 PHE 0.020 0.002 PHE A 465 TYR 0.023 0.002 TYR L 50 ARG 0.008 0.001 ARG M 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9082 (mt0) cc_final: 0.8631 (mp10) REVERT: A 136 MET cc_start: 0.8890 (mmm) cc_final: 0.8279 (mmp) REVERT: B 237 MET cc_start: 0.7909 (pmm) cc_final: 0.7697 (pmm) REVERT: G 225 VAL cc_start: 0.9247 (m) cc_final: 0.8931 (p) REVERT: L 48 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9169 (mp) REVERT: H 160 ASP cc_start: 0.8818 (m-30) cc_final: 0.8180 (m-30) REVERT: N 40 ARG cc_start: 0.8767 (mtm110) cc_final: 0.7187 (tpt90) REVERT: N 104 TYR cc_start: 0.8091 (m-80) cc_final: 0.7655 (m-80) outliers start: 30 outliers final: 16 residues processed: 133 average time/residue: 0.2921 time to fit residues: 56.4225 Evaluate side-chains 101 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain M residue 340 TRP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 216 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 40.0000 chunk 42 optimal weight: 0.0770 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 0.0050 overall best weight: 2.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 GLN M 124 ASN M 365 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN H 6 GLN H 85 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13781 Z= 0.197 Angle : 0.601 10.456 18716 Z= 0.292 Chirality : 0.041 0.161 2087 Planarity : 0.004 0.055 2363 Dihedral : 8.136 119.159 1952 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.84 % Allowed : 9.42 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.20), residues: 1683 helix: 0.12 (0.24), residues: 451 sheet: -0.44 (0.27), residues: 342 loop : -1.31 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 45 HIS 0.004 0.001 HIS L 199 PHE 0.012 0.001 PHE A 279 TYR 0.014 0.001 TYR N 113 ARG 0.005 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.8951 (mmm) cc_final: 0.8410 (mmp) REVERT: A 153 MET cc_start: 0.8794 (mmp) cc_final: 0.8561 (tpp) REVERT: A 256 MET cc_start: 0.8687 (mmp) cc_final: 0.8318 (mmp) REVERT: B 208 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7407 (pp) REVERT: B 237 MET cc_start: 0.7891 (pmm) cc_final: 0.7183 (pmm) REVERT: H 160 ASP cc_start: 0.8766 (m-30) cc_final: 0.8249 (m-30) REVERT: N 40 ARG cc_start: 0.8692 (mtm110) cc_final: 0.7025 (tpt90) REVERT: N 104 TYR cc_start: 0.7965 (m-80) cc_final: 0.7722 (m-80) outliers start: 27 outliers final: 13 residues processed: 108 average time/residue: 0.2516 time to fit residues: 40.6277 Evaluate side-chains 89 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain M residue 340 TRP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 153 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 80 optimal weight: 30.0000 chunk 145 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS G 26 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 13781 Z= 0.450 Angle : 0.791 13.943 18716 Z= 0.394 Chirality : 0.045 0.205 2087 Planarity : 0.005 0.055 2363 Dihedral : 7.626 109.800 1952 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.66 % Allowed : 8.67 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1683 helix: 0.21 (0.24), residues: 455 sheet: -0.72 (0.26), residues: 370 loop : -1.07 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 117 HIS 0.011 0.002 HIS B 240 PHE 0.024 0.003 PHE A 279 TYR 0.033 0.003 TYR H 97 ARG 0.007 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 76 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9137 (mmm) cc_final: 0.8707 (mmp) REVERT: B 208 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7669 (pp) REVERT: M 330 MET cc_start: 0.8276 (mtp) cc_final: 0.6929 (ttp) REVERT: M 336 MET cc_start: 0.8965 (tpp) cc_final: 0.8503 (tpp) REVERT: H 114 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7956 (mm-30) REVERT: N 40 ARG cc_start: 0.8859 (mtm110) cc_final: 0.7463 (tpt170) REVERT: N 77 PHE cc_start: 0.8589 (m-10) cc_final: 0.7911 (m-80) REVERT: N 104 TYR cc_start: 0.8180 (m-80) cc_final: 0.7929 (m-80) outliers start: 39 outliers final: 27 residues processed: 109 average time/residue: 0.2421 time to fit residues: 40.2147 Evaluate side-chains 97 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 69 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 40 optimal weight: 30.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13781 Z= 0.182 Angle : 0.588 9.306 18716 Z= 0.288 Chirality : 0.042 0.190 2087 Planarity : 0.004 0.052 2363 Dihedral : 6.759 92.149 1952 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.71 % Allowed : 9.90 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.68 (0.20), residues: 1683 helix: 0.50 (0.24), residues: 458 sheet: -0.42 (0.27), residues: 362 loop : -0.94 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 269 HIS 0.006 0.001 HIS A 77 PHE 0.009 0.001 PHE N 77 TYR 0.022 0.001 TYR N 113 ARG 0.004 0.000 ARG G 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9101 (mmm) cc_final: 0.8684 (mmp) REVERT: A 141 ASP cc_start: 0.8231 (m-30) cc_final: 0.7786 (p0) REVERT: G 33 MET cc_start: 0.8852 (ptp) cc_final: 0.8649 (ptp) REVERT: G 252 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8741 (pm20) REVERT: M 336 MET cc_start: 0.8968 (tpp) cc_final: 0.8749 (tpt) REVERT: N 62 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.5916 (mtt90) REVERT: N 104 TYR cc_start: 0.8012 (m-80) cc_final: 0.7703 (m-80) outliers start: 25 outliers final: 14 residues processed: 97 average time/residue: 0.2409 time to fit residues: 35.7934 Evaluate side-chains 83 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain N residue 62 ARG Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 40 optimal weight: 0.2980 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13781 Z= 0.229 Angle : 0.594 9.466 18716 Z= 0.289 Chirality : 0.041 0.221 2087 Planarity : 0.004 0.052 2363 Dihedral : 6.516 83.054 1952 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.12 % Allowed : 9.83 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.54 (0.21), residues: 1683 helix: 0.69 (0.25), residues: 459 sheet: -0.52 (0.26), residues: 377 loop : -0.81 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 117 HIS 0.005 0.001 HIS A 77 PHE 0.016 0.001 PHE G 91 TYR 0.017 0.001 TYR L 50 ARG 0.003 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 73 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9059 (mmm) cc_final: 0.8643 (mmp) REVERT: B 226 ASP cc_start: 0.6027 (m-30) cc_final: 0.5289 (t70) REVERT: G 85 MET cc_start: 0.9199 (tpp) cc_final: 0.8909 (tpp) REVERT: G 252 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8724 (pm20) REVERT: M 336 MET cc_start: 0.9009 (tpp) cc_final: 0.8772 (tpt) REVERT: L 48 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9038 (mp) REVERT: H 113 MET cc_start: 0.7994 (ttt) cc_final: 0.7585 (ttp) REVERT: H 114 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7980 (mm-30) REVERT: N 104 TYR cc_start: 0.8024 (m-80) cc_final: 0.7743 (m-80) outliers start: 31 outliers final: 20 residues processed: 101 average time/residue: 0.2372 time to fit residues: 36.6208 Evaluate side-chains 88 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 92 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 235 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13781 Z= 0.226 Angle : 0.602 9.044 18716 Z= 0.293 Chirality : 0.041 0.221 2087 Planarity : 0.005 0.148 2363 Dihedral : 5.958 59.523 1952 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.84 % Allowed : 10.03 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.44 (0.21), residues: 1683 helix: 0.79 (0.25), residues: 459 sheet: -0.45 (0.26), residues: 377 loop : -0.76 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 117 HIS 0.005 0.001 HIS A 77 PHE 0.020 0.001 PHE G 91 TYR 0.016 0.001 TYR L 50 ARG 0.012 0.001 ARG N 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 70 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9067 (mmm) cc_final: 0.8667 (mmp) REVERT: B 226 ASP cc_start: 0.5997 (m-30) cc_final: 0.5253 (t70) REVERT: G 85 MET cc_start: 0.9212 (tpp) cc_final: 0.8927 (tpp) REVERT: M 336 MET cc_start: 0.9033 (tpp) cc_final: 0.8826 (tpp) REVERT: L 48 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8982 (mp) REVERT: H 113 MET cc_start: 0.8037 (ttt) cc_final: 0.7718 (ttp) REVERT: N 104 TYR cc_start: 0.8004 (m-80) cc_final: 0.7702 (m-80) REVERT: N 113 TYR cc_start: 0.6821 (t80) cc_final: 0.6578 (t80) outliers start: 27 outliers final: 22 residues processed: 94 average time/residue: 0.2420 time to fit residues: 35.1162 Evaluate side-chains 89 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 40.0000 chunk 15 optimal weight: 0.0870 chunk 127 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 153 ASN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13781 Z= 0.168 Angle : 0.578 7.642 18716 Z= 0.281 Chirality : 0.041 0.181 2087 Planarity : 0.004 0.052 2363 Dihedral : 5.672 53.546 1952 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.71 % Allowed : 10.31 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.37 (0.21), residues: 1683 helix: 0.90 (0.25), residues: 460 sheet: -0.35 (0.26), residues: 367 loop : -0.78 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.005 0.001 HIS A 77 PHE 0.021 0.001 PHE G 91 TYR 0.013 0.001 TYR L 50 ARG 0.005 0.000 ARG N 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 71 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9020 (mmm) cc_final: 0.8660 (mmp) REVERT: A 141 ASP cc_start: 0.8188 (m-30) cc_final: 0.7796 (p0) REVERT: B 226 ASP cc_start: 0.5940 (m-30) cc_final: 0.5216 (t70) REVERT: G 267 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9094 (tm-30) REVERT: L 48 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8986 (mp) REVERT: H 113 MET cc_start: 0.7911 (ttt) cc_final: 0.7558 (ttp) REVERT: H 114 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8132 (mm-30) REVERT: N 77 PHE cc_start: 0.8630 (m-10) cc_final: 0.8357 (m-10) REVERT: N 104 TYR cc_start: 0.7964 (m-80) cc_final: 0.7669 (m-80) REVERT: N 113 TYR cc_start: 0.6719 (t80) cc_final: 0.6426 (t80) outliers start: 25 outliers final: 19 residues processed: 91 average time/residue: 0.2465 time to fit residues: 34.7776 Evaluate side-chains 88 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 68 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 118 optimal weight: 0.0370 chunk 46 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13781 Z= 0.171 Angle : 0.589 8.526 18716 Z= 0.284 Chirality : 0.041 0.178 2087 Planarity : 0.004 0.050 2363 Dihedral : 5.613 49.543 1952 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.37 % Allowed : 10.44 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.30 (0.21), residues: 1683 helix: 0.95 (0.25), residues: 460 sheet: -0.31 (0.26), residues: 366 loop : -0.73 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 117 HIS 0.005 0.001 HIS A 77 PHE 0.020 0.001 PHE G 91 TYR 0.012 0.001 TYR L 50 ARG 0.005 0.000 ARG M 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9000 (mmm) cc_final: 0.8623 (mmp) REVERT: B 226 ASP cc_start: 0.5941 (m-30) cc_final: 0.5220 (t70) REVERT: M 336 MET cc_start: 0.8911 (tpp) cc_final: 0.8588 (tpp) REVERT: L 48 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8982 (mp) REVERT: H 114 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8134 (mm-30) REVERT: N 104 TYR cc_start: 0.7920 (m-80) cc_final: 0.7656 (m-80) REVERT: N 113 TYR cc_start: 0.6707 (t80) cc_final: 0.6413 (t80) outliers start: 20 outliers final: 18 residues processed: 88 average time/residue: 0.2374 time to fit residues: 32.8393 Evaluate side-chains 87 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13781 Z= 0.282 Angle : 0.661 9.803 18716 Z= 0.320 Chirality : 0.042 0.174 2087 Planarity : 0.004 0.060 2363 Dihedral : 5.937 59.798 1952 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.23 % Allowed : 10.58 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.32 (0.21), residues: 1683 helix: 1.00 (0.25), residues: 453 sheet: -0.40 (0.26), residues: 378 loop : -0.74 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 117 HIS 0.004 0.001 HIS A 249 PHE 0.021 0.002 PHE G 91 TYR 0.019 0.002 TYR L 50 ARG 0.006 0.001 ARG N 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9030 (mmm) cc_final: 0.8635 (mmp) REVERT: B 226 ASP cc_start: 0.5547 (m-30) cc_final: 0.4905 (t70) REVERT: M 336 MET cc_start: 0.8983 (tpp) cc_final: 0.8683 (tpp) REVERT: L 48 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9034 (mp) REVERT: H 114 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8169 (mm-30) REVERT: N 113 TYR cc_start: 0.6855 (t80) cc_final: 0.6493 (t80) outliers start: 18 outliers final: 15 residues processed: 81 average time/residue: 0.2479 time to fit residues: 31.4739 Evaluate side-chains 79 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.046958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.032135 restraints weight = 106321.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.033255 restraints weight = 61003.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.033991 restraints weight = 43342.020| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13781 Z= 0.143 Angle : 0.592 8.887 18716 Z= 0.285 Chirality : 0.042 0.170 2087 Planarity : 0.004 0.051 2363 Dihedral : 5.641 60.318 1952 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.89 % Allowed : 11.19 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.20 (0.21), residues: 1683 helix: 1.18 (0.25), residues: 447 sheet: -0.31 (0.26), residues: 366 loop : -0.70 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 398 HIS 0.006 0.001 HIS A 77 PHE 0.019 0.001 PHE G 91 TYR 0.013 0.001 TYR M 341 ARG 0.005 0.000 ARG M 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.02 seconds wall clock time: 46 minutes 57.66 seconds (2817.66 seconds total)