Starting phenix.real_space_refine on Thu Jul 31 23:27:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m74_23708/07_2025/7m74_23708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m74_23708/07_2025/7m74_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/cci-nas-00/data/ceres_data/7m74_23708/07_2025/7m74_23708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m74_23708/07_2025/7m74_23708.map" model { file = "/net/cci-nas-00/data/ceres_data/7m74_23708/07_2025/7m74_23708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m74_23708/07_2025/7m74_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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, 'AMP%rna2p': 1, 'ATP': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 7.82, 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 " TRANS " VAL A 13 " - " PHE M 371 " Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.9 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: 1.56 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: 3.73 Time building geometry restraints manager: 3.96 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: 18596 3.66 - 7.32: 106 7.32 - 10.99: 12 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: 133 47.12 - 70.68: 16 70.68 - 94.24: 4 94.24 - 117.79: 7 Dihedral angle restraints: 8309 sinusoidal: 3347 harmonic: 4962 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 8306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1821 0.073 - 0.145: 245 0.145 - 0.218: 17 0.218 - 0.291: 2 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' AMP G 403 " pdb=" C2' AMP G 403 " pdb=" C4' AMP G 403 " pdb=" O3' AMP G 403 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2084 not shown) Planarity restraints: 2364 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 2361 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4165 2.85 - 3.36: 11214 3.36 - 3.87: 21217 3.87 - 4.39: 23011 4.39 - 4.90: 41111 Nonbonded interactions: 100718 Sorted by model distance: 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 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.365 3.040 nonbonded pdb=" OD2 ASP G 52 " pdb=" OG SER G 54 " model vdw 2.366 3.040 ... (remaining 100713 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: 1.390 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.520 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- 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 13788 Z= 0.210 Angle : 0.757 18.309 18732 Z= 0.422 Chirality : 0.049 0.364 2087 Planarity : 0.007 0.071 2363 Dihedral : 9.736 117.795 5107 Min Nonbonded Distance : 2.337 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 Details of bonding type rmsd link_TRANS : bond 0.00105 ( 1) link_TRANS : angle 0.03163 ( 3) link_ALPHA1-4 : bond 0.00564 ( 1) link_ALPHA1-4 : angle 1.41648 ( 3) hydrogen bonds : bond 0.21995 ( 455) hydrogen bonds : angle 8.63997 ( 1347) SS BOND : bond 0.00351 ( 5) SS BOND : angle 5.44655 ( 10) covalent geometry : bond 0.00353 (13781) covalent geometry : angle 0.74693 (18716) *********************** 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 to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.483 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: 0.3209 time to fit residues: 120.2009 Evaluate side-chains 113 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 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 G 148 ASN G 169 HIS G 197 GLN 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 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.050134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.035221 restraints weight = 105718.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.036364 restraints weight = 61687.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.037127 restraints weight = 43858.977| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 13788 Z= 0.202 Angle : 0.706 12.088 18732 Z= 0.347 Chirality : 0.043 0.169 2087 Planarity : 0.005 0.077 2363 Dihedral : 8.482 119.694 1952 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.91 % Allowed : 9.62 % 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: -1.61 (0.19), residues: 1683 helix: -0.54 (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 0.008 0.001 HIS M 64 PHE 0.020 0.002 PHE A 465 TYR 0.023 0.002 TYR L 50 ARG 0.010 0.001 ARG M 66 Details of bonding type rmsd link_TRANS : bond 0.00306 ( 1) link_TRANS : angle 0.40869 ( 3) link_ALPHA1-4 : bond 0.00638 ( 1) link_ALPHA1-4 : angle 1.06272 ( 3) hydrogen bonds : bond 0.03806 ( 455) hydrogen bonds : angle 5.83176 ( 1347) SS BOND : bond 0.00656 ( 5) SS BOND : angle 1.36042 ( 10) covalent geometry : bond 0.00437 (13781) covalent geometry : angle 0.70567 (18716) *********************** 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 136 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.487 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 52 GLN cc_start: 0.9111 (mt0) cc_final: 0.8663 (mp10) REVERT: A 136 MET cc_start: 0.8872 (mmm) cc_final: 0.8248 (mmp) REVERT: B 257 HIS cc_start: 0.7909 (t70) cc_final: 0.7701 (t70) REVERT: G 225 VAL cc_start: 0.9269 (m) cc_final: 0.8963 (p) REVERT: M 321 MET cc_start: 0.9000 (tmm) cc_final: 0.8386 (tmm) REVERT: H 160 ASP cc_start: 0.9009 (m-30) cc_final: 0.8349 (m-30) REVERT: N 40 ARG cc_start: 0.8787 (mtm110) cc_final: 0.7184 (tpt90) REVERT: N 104 TYR cc_start: 0.8258 (m-80) cc_final: 0.7714 (m-80) outliers start: 28 outliers final: 15 residues processed: 130 average time/residue: 0.2832 time to fit residues: 53.2673 Evaluate side-chains 98 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 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 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 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 76 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 M 124 ASN M 365 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN H 6 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.048081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.033028 restraints weight = 106827.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.034123 restraints weight = 62685.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.034835 restraints weight = 45054.761| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13788 Z= 0.204 Angle : 0.664 12.066 18732 Z= 0.327 Chirality : 0.042 0.166 2087 Planarity : 0.005 0.054 2363 Dihedral : 7.980 121.971 1952 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.25 % Allowed : 9.08 % 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: -1.07 (0.20), residues: 1683 helix: 0.15 (0.24), residues: 453 sheet: -0.51 (0.27), residues: 349 loop : -1.23 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 117 HIS 0.005 0.001 HIS L 199 PHE 0.025 0.002 PHE N 77 TYR 0.020 0.002 TYR A 207 ARG 0.009 0.001 ARG B 197 Details of bonding type rmsd link_TRANS : bond 0.00255 ( 1) link_TRANS : angle 0.54259 ( 3) link_ALPHA1-4 : bond 0.00110 ( 1) link_ALPHA1-4 : angle 1.55629 ( 3) hydrogen bonds : bond 0.03559 ( 455) hydrogen bonds : angle 5.23822 ( 1347) SS BOND : bond 0.00319 ( 5) SS BOND : angle 1.42534 ( 10) covalent geometry : bond 0.00437 (13781) covalent geometry : angle 0.66336 (18716) *********************** 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 118 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 1.496 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: 0.9019 (mmm) cc_final: 0.8547 (mmp) REVERT: A 165 MET cc_start: 0.6323 (mpp) cc_final: 0.6121 (mpp) REVERT: A 256 MET cc_start: 0.8791 (mmp) cc_final: 0.8543 (mmp) REVERT: B 237 MET cc_start: 0.7950 (pmm) cc_final: 0.7536 (pmm) REVERT: B 240 HIS cc_start: 0.8538 (m90) cc_final: 0.8318 (m90) REVERT: B 257 HIS cc_start: 0.8194 (t70) cc_final: 0.7897 (t70) REVERT: M 330 MET cc_start: 0.8439 (mtm) cc_final: 0.8198 (mtt) REVERT: M 336 MET cc_start: 0.8834 (tpt) cc_final: 0.8434 (tpp) REVERT: L 5 MET cc_start: 0.8240 (ptp) cc_final: 0.8035 (pmm) REVERT: N 40 ARG cc_start: 0.8749 (mtm110) cc_final: 0.7306 (tpt170) REVERT: N 53 GLU cc_start: 0.8727 (tp30) cc_final: 0.8510 (tp30) REVERT: N 104 TYR cc_start: 0.8176 (m-80) cc_final: 0.7859 (m-80) outliers start: 33 outliers final: 18 residues processed: 112 average time/residue: 0.2796 time to fit residues: 46.7745 Evaluate side-chains 91 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 157 ILE 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 211 HIS 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 M residue 340 TRP Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 188 SER 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 131 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 104 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 ASN G 96 HIS ** G 248 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.044741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.029764 restraints weight = 110451.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.030774 restraints weight = 65043.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.031419 restraints weight = 47102.451| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 13788 Z= 0.346 Angle : 0.822 13.591 18732 Z= 0.408 Chirality : 0.046 0.204 2087 Planarity : 0.005 0.055 2363 Dihedral : 7.501 99.647 1952 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.87 % Allowed : 8.94 % 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: -1.05 (0.20), residues: 1683 helix: 0.14 (0.24), residues: 451 sheet: -0.65 (0.26), residues: 369 loop : -1.12 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 117 HIS 0.007 0.002 HIS A 17 PHE 0.023 0.003 PHE A 279 TYR 0.030 0.003 TYR L 50 ARG 0.009 0.001 ARG B 197 Details of bonding type rmsd link_TRANS : bond 0.00501 ( 1) link_TRANS : angle 0.75950 ( 3) link_ALPHA1-4 : bond 0.00861 ( 1) link_ALPHA1-4 : angle 1.18320 ( 3) hydrogen bonds : bond 0.04151 ( 455) hydrogen bonds : angle 5.55192 ( 1347) SS BOND : bond 0.00596 ( 5) SS BOND : angle 0.98089 ( 10) covalent geometry : bond 0.00728 (13781) covalent geometry : angle 0.82140 (18716) *********************** 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 114 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 72 time to evaluate : 1.682 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: 0.9102 (mmm) cc_final: 0.8700 (mmp) REVERT: B 226 ASP cc_start: 0.5857 (m-30) cc_final: 0.5170 (t70) REVERT: B 237 MET cc_start: 0.8255 (pmm) cc_final: 0.7681 (pmm) REVERT: G 33 MET cc_start: 0.9346 (mtp) cc_final: 0.9140 (ptp) REVERT: M 330 MET cc_start: 0.8431 (mtm) cc_final: 0.8158 (mtt) REVERT: M 336 MET cc_start: 0.9068 (tpt) cc_final: 0.8670 (tpp) REVERT: L 48 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9044 (mp) REVERT: H 114 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8040 (mm-30) REVERT: H 160 ASP cc_start: 0.9173 (m-30) cc_final: 0.8177 (p0) REVERT: N 104 TYR cc_start: 0.8334 (m-80) cc_final: 0.7996 (m-80) outliers start: 42 outliers final: 28 residues processed: 107 average time/residue: 0.2309 time to fit residues: 38.3903 Evaluate side-chains 93 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 LEU 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 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 193 MET 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 271 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 134 VAL 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 96 VAL Chi-restraints excluded: chain H residue 117 ASP 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 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 119 optimal weight: 0.0980 chunk 123 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 0.0060 chunk 147 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 152 optimal weight: 0.2980 overall best weight: 1.4800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.046677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031618 restraints weight = 108009.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.032720 restraints weight = 61581.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.033429 restraints weight = 43968.307| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13788 Z= 0.116 Angle : 0.596 8.008 18732 Z= 0.290 Chirality : 0.042 0.165 2087 Planarity : 0.004 0.051 2363 Dihedral : 6.420 73.748 1952 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.91 % Allowed : 10.17 % 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: -0.65 (0.20), residues: 1683 helix: 0.55 (0.24), residues: 452 sheet: -0.37 (0.26), residues: 368 loop : -0.95 (0.21), residues: 863 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 0.011 0.001 PHE A 122 TYR 0.013 0.001 TYR L 50 ARG 0.003 0.000 ARG B 258 Details of bonding type rmsd link_TRANS : bond 0.00038 ( 1) link_TRANS : angle 0.29871 ( 3) link_ALPHA1-4 : bond 0.00010 ( 1) link_ALPHA1-4 : angle 1.17355 ( 3) hydrogen bonds : bond 0.02960 ( 455) hydrogen bonds : angle 4.93990 ( 1347) SS BOND : bond 0.00390 ( 5) SS BOND : angle 1.04310 ( 10) covalent geometry : bond 0.00261 (13781) covalent geometry : angle 0.59538 (18716) *********************** 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 108 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 1.453 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: 0.9078 (mmm) cc_final: 0.8685 (mmp) REVERT: B 226 ASP cc_start: 0.6006 (m-30) cc_final: 0.5275 (t70) REVERT: M 336 MET cc_start: 0.8975 (tpt) cc_final: 0.8559 (tpp) REVERT: N 62 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.5917 (mtt90) REVERT: N 104 TYR cc_start: 0.8172 (m-80) cc_final: 0.7776 (m-80) outliers start: 28 outliers final: 17 residues processed: 103 average time/residue: 0.2797 time to fit residues: 44.8461 Evaluate side-chains 85 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 3.753 ------------------------------------------------------------------------------- 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 G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL 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 216 HIS Chi-restraints excluded: chain N residue 37 THR 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 8 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 390 HIS ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.045118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.030128 restraints weight = 110200.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.031182 restraints weight = 63820.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.031871 restraints weight = 45804.432| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 13788 Z= 0.244 Angle : 0.696 11.490 18732 Z= 0.339 Chirality : 0.042 0.198 2087 Planarity : 0.004 0.052 2363 Dihedral : 6.058 50.814 1952 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.05 % Allowed : 10.17 % Favored : 87.78 % 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: -0.61 (0.21), residues: 1683 helix: 0.63 (0.25), residues: 452 sheet: -0.53 (0.26), residues: 372 loop : -0.85 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 117 HIS 0.007 0.001 HIS A 249 PHE 0.024 0.002 PHE L 210 TYR 0.021 0.002 TYR L 193 ARG 0.006 0.001 ARG G 70 Details of bonding type rmsd link_TRANS : bond 0.00350 ( 1) link_TRANS : angle 0.56818 ( 3) link_ALPHA1-4 : bond 0.00175 ( 1) link_ALPHA1-4 : angle 1.16276 ( 3) hydrogen bonds : bond 0.03380 ( 455) hydrogen bonds : angle 5.10088 ( 1347) SS BOND : bond 0.00225 ( 5) SS BOND : angle 0.72244 ( 10) covalent geometry : bond 0.00524 (13781) covalent geometry : angle 0.69562 (18716) *********************** 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 100 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 1.556 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: 0.9039 (mmm) cc_final: 0.8643 (mmp) REVERT: A 256 MET cc_start: 0.8855 (mmp) cc_final: 0.8377 (mmp) REVERT: B 226 ASP cc_start: 0.5796 (m-30) cc_final: 0.5097 (t70) REVERT: G 85 MET cc_start: 0.9184 (tpp) cc_final: 0.8901 (tpp) REVERT: M 336 MET cc_start: 0.9124 (tpt) cc_final: 0.8721 (tpp) REVERT: H 113 MET cc_start: 0.8102 (ttt) cc_final: 0.7586 (ttp) REVERT: H 114 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7965 (mm-30) REVERT: N 104 TYR cc_start: 0.8195 (m-80) cc_final: 0.7860 (m-80) outliers start: 30 outliers final: 21 residues processed: 96 average time/residue: 0.2354 time to fit residues: 35.3409 Evaluate side-chains 86 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 205 ILE 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 464 ASP Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 301 VAL 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 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 22 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 156 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 0.4980 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** 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 = 0.3434 r_free = 0.3434 target = 0.045176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.030036 restraints weight = 110310.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.031099 restraints weight = 63355.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031804 restraints weight = 45507.337| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13788 Z= 0.211 Angle : 0.652 10.197 18732 Z= 0.320 Chirality : 0.042 0.236 2087 Planarity : 0.005 0.119 2363 Dihedral : 6.023 56.156 1952 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.84 % Allowed : 11.13 % Favored : 87.03 % 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: -0.61 (0.21), residues: 1683 helix: 0.65 (0.24), residues: 457 sheet: -0.59 (0.26), residues: 374 loop : -0.84 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 117 HIS 0.005 0.001 HIS A 77 PHE 0.011 0.002 PHE L 210 TYR 0.017 0.002 TYR L 50 ARG 0.009 0.001 ARG N 61 Details of bonding type rmsd link_TRANS : bond 0.00267 ( 1) link_TRANS : angle 0.55876 ( 3) link_ALPHA1-4 : bond 0.00135 ( 1) link_ALPHA1-4 : angle 1.11714 ( 3) hydrogen bonds : bond 0.03197 ( 455) hydrogen bonds : angle 5.04283 ( 1347) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.73428 ( 10) covalent geometry : bond 0.00452 (13781) covalent geometry : angle 0.65141 (18716) *********************** 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 96 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 2.060 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: 0.9056 (mmm) cc_final: 0.8692 (mmp) REVERT: B 226 ASP cc_start: 0.5485 (m-30) cc_final: 0.4842 (t70) REVERT: G 85 MET cc_start: 0.9200 (tpp) cc_final: 0.8949 (tpp) REVERT: M 336 MET cc_start: 0.9151 (tpt) cc_final: 0.8671 (tpp) REVERT: H 113 MET cc_start: 0.8124 (ttt) cc_final: 0.7585 (ttp) REVERT: H 114 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7962 (mm-30) REVERT: N 104 TYR cc_start: 0.8262 (m-80) cc_final: 0.7906 (m-80) REVERT: N 113 TYR cc_start: 0.7164 (t80) cc_final: 0.6925 (t80) outliers start: 27 outliers final: 21 residues processed: 92 average time/residue: 0.3119 time to fit residues: 45.6356 Evaluate side-chains 85 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 464 ASP Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 301 VAL 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 89 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 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 109 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.045659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.030630 restraints weight = 110002.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.031708 restraints weight = 63137.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.032424 restraints weight = 45233.331| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13788 Z= 0.138 Angle : 0.602 8.985 18732 Z= 0.292 Chirality : 0.042 0.192 2087 Planarity : 0.004 0.054 2363 Dihedral : 5.798 56.861 1952 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.37 % Allowed : 11.26 % Favored : 87.37 % 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: -0.47 (0.21), residues: 1683 helix: 0.79 (0.25), residues: 456 sheet: -0.47 (0.26), residues: 371 loop : -0.79 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 398 HIS 0.006 0.001 HIS A 77 PHE 0.009 0.001 PHE A 122 TYR 0.015 0.001 TYR L 50 ARG 0.003 0.000 ARG N 62 Details of bonding type rmsd link_TRANS : bond 0.00123 ( 1) link_TRANS : angle 0.40925 ( 3) link_ALPHA1-4 : bond 0.00083 ( 1) link_ALPHA1-4 : angle 1.11288 ( 3) hydrogen bonds : bond 0.02911 ( 455) hydrogen bonds : angle 4.82132 ( 1347) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.70326 ( 10) covalent geometry : bond 0.00306 (13781) covalent geometry : angle 0.60169 (18716) *********************** 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 91 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9023 (mmm) cc_final: 0.8652 (mmp) REVERT: B 226 ASP cc_start: 0.5474 (m-30) cc_final: 0.4840 (t70) REVERT: G 85 MET cc_start: 0.9238 (tpp) cc_final: 0.8957 (tpp) REVERT: M 336 MET cc_start: 0.9130 (tpt) cc_final: 0.8861 (tpp) REVERT: H 114 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7903 (mm-30) REVERT: N 104 TYR cc_start: 0.8224 (m-80) cc_final: 0.7878 (m-80) REVERT: N 113 TYR cc_start: 0.7195 (t80) cc_final: 0.6818 (t80) outliers start: 20 outliers final: 17 residues processed: 88 average time/residue: 0.2839 time to fit residues: 40.3801 Evaluate side-chains 83 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 464 ASP 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 139 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 160 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.045912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.030907 restraints weight = 106562.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.031977 restraints weight = 61701.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.032674 restraints weight = 44323.508| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13788 Z= 0.120 Angle : 0.592 8.437 18732 Z= 0.286 Chirality : 0.041 0.178 2087 Planarity : 0.004 0.052 2363 Dihedral : 5.613 56.394 1952 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.50 % Allowed : 11.13 % Favored : 87.37 % 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: -0.34 (0.21), residues: 1683 helix: 0.93 (0.25), residues: 453 sheet: -0.40 (0.26), residues: 382 loop : -0.72 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 398 HIS 0.006 0.001 HIS A 77 PHE 0.010 0.001 PHE A 122 TYR 0.013 0.001 TYR L 50 ARG 0.003 0.000 ARG N 62 Details of bonding type rmsd link_TRANS : bond 0.00099 ( 1) link_TRANS : angle 0.37195 ( 3) link_ALPHA1-4 : bond 0.00100 ( 1) link_ALPHA1-4 : angle 1.06925 ( 3) hydrogen bonds : bond 0.02754 ( 455) hydrogen bonds : angle 4.72289 ( 1347) SS BOND : bond 0.00187 ( 5) SS BOND : angle 0.66826 ( 10) covalent geometry : bond 0.00269 (13781) covalent geometry : angle 0.59202 (18716) *********************** 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 90 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 1.483 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: 0.8984 (mmm) cc_final: 0.8619 (mmp) REVERT: B 226 ASP cc_start: 0.5512 (m-30) cc_final: 0.4865 (t70) REVERT: M 336 MET cc_start: 0.9134 (tpt) cc_final: 0.8882 (tpp) REVERT: H 114 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7858 (mm-30) REVERT: N 104 TYR cc_start: 0.8188 (m-80) cc_final: 0.7827 (m-80) REVERT: N 113 TYR cc_start: 0.7199 (t80) cc_final: 0.6805 (t80) outliers start: 22 outliers final: 19 residues processed: 87 average time/residue: 0.2392 time to fit residues: 32.9677 Evaluate side-chains 83 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 464 ASP 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 59 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 89 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 95 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 0.0050 chunk 136 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.044813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.029862 restraints weight = 109944.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.030909 restraints weight = 63830.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.031569 restraints weight = 45960.270| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 13788 Z= 0.232 Angle : 0.685 10.197 18732 Z= 0.334 Chirality : 0.042 0.175 2087 Planarity : 0.005 0.089 2363 Dihedral : 5.962 60.543 1952 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.30 % Allowed : 11.74 % Favored : 86.96 % 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: -0.45 (0.21), residues: 1683 helix: 0.80 (0.25), residues: 457 sheet: -0.48 (0.26), residues: 369 loop : -0.77 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 117 HIS 0.006 0.001 HIS A 249 PHE 0.011 0.002 PHE H 182 TYR 0.019 0.002 TYR L 50 ARG 0.011 0.001 ARG B 201 Details of bonding type rmsd link_TRANS : bond 0.00197 ( 1) link_TRANS : angle 0.09392 ( 3) link_ALPHA1-4 : bond 0.00819 ( 1) link_ALPHA1-4 : angle 1.06263 ( 3) hydrogen bonds : bond 0.03149 ( 455) hydrogen bonds : angle 4.96031 ( 1347) SS BOND : bond 0.00193 ( 5) SS BOND : angle 0.69041 ( 10) covalent geometry : bond 0.00498 (13781) covalent geometry : angle 0.68483 (18716) ********************** 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 to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 2.697 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: 0.9025 (mmm) cc_final: 0.8639 (mmp) REVERT: B 226 ASP cc_start: 0.5537 (m-30) cc_final: 0.4885 (t70) REVERT: M 336 MET cc_start: 0.9235 (tpt) cc_final: 0.8786 (tpp) REVERT: H 114 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7922 (mm-30) REVERT: N 104 TYR cc_start: 0.8276 (m-80) cc_final: 0.7939 (m-80) REVERT: N 113 TYR cc_start: 0.7330 (t80) cc_final: 0.6924 (t80) outliers start: 19 outliers final: 18 residues processed: 81 average time/residue: 0.2982 time to fit residues: 39.4656 Evaluate side-chains 81 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 2.340 ------------------------------------------------------------------------------- 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 464 ASP 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 59 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 89 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 167 optimal weight: 20.0000 chunk 137 optimal weight: 0.0980 chunk 133 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 136 optimal weight: 0.0270 chunk 143 optimal weight: 0.9990 overall best weight: 3.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.045203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.030244 restraints weight = 108562.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.031291 restraints weight = 62815.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.031989 restraints weight = 45018.492| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13788 Z= 0.156 Angle : 0.628 8.866 18732 Z= 0.303 Chirality : 0.042 0.174 2087 Planarity : 0.004 0.051 2363 Dihedral : 5.790 62.069 1952 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.57 % Allowed : 11.54 % Favored : 86.89 % 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: -0.40 (0.21), residues: 1683 helix: 0.90 (0.25), residues: 463 sheet: -0.44 (0.26), residues: 367 loop : -0.78 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 398 HIS 0.006 0.001 HIS A 77 PHE 0.008 0.001 PHE M 92 TYR 0.015 0.001 TYR L 50 ARG 0.009 0.001 ARG B 201 Details of bonding type rmsd link_TRANS : bond 0.00185 ( 1) link_TRANS : angle 0.38527 ( 3) link_ALPHA1-4 : bond 0.00073 ( 1) link_ALPHA1-4 : angle 1.14444 ( 3) hydrogen bonds : bond 0.02873 ( 455) hydrogen bonds : angle 4.82926 ( 1347) SS BOND : bond 0.00198 ( 5) SS BOND : angle 0.67125 ( 10) covalent geometry : bond 0.00343 (13781) covalent geometry : angle 0.62774 (18716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5617.84 seconds wall clock time: 104 minutes 3.15 seconds (6243.15 seconds total)