Starting phenix.real_space_refine on Sat Mar 16 02:35:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/03_2024/7m74_23708_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/03_2024/7m74_23708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/03_2024/7m74_23708.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/03_2024/7m74_23708.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/03_2024/7m74_23708_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m74_23708/03_2024/7m74_23708_updated.pdb" } 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 Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 438": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G ARG 299": "NH1" <-> "NH2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13457 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3083 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 19, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 736 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 11, 'TRANS': 81} Chain: "G" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2421 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "M" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2834 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain: "L" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Chain: "H" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'TAK': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 7.56, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " GLC D 1 " - " GLC D 2 " Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 2.3 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... running ksdssp... Secondary structure from input PDB file: 46 helices and 22 sheets defined 25.0% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 60 through 72 removed outlier: 3.818A pdb=" N LYS A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 115 through 134 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 162 through 169 removed outlier: 3.541A pdb=" N MET A 165 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 169 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 408 through 421 Processing helix chain 'A' and resid 533 through 542 removed outlier: 3.689A pdb=" N CYS A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'G' and resid 27 through 35 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 38 through 41 Processing helix chain 'G' and resid 57 through 67 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 88 through 97 Processing helix chain 'G' and resid 108 through 111 No H-bonds generated for 'chain 'G' and resid 108 through 111' Processing helix chain 'G' and resid 114 through 121 removed outlier: 3.693A pdb=" N VAL G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'G' and resid 169 through 179 removed outlier: 3.841A pdb=" N LEU G 178 " --> pdb=" O LYS G 174 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE G 179 " --> pdb=" O PHE G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 222 Processing helix chain 'G' and resid 243 through 251 removed outlier: 3.604A pdb=" N ILE G 247 " --> pdb=" O PHE G 244 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN G 248 " --> pdb=" O ASP G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 269 removed outlier: 4.474A pdb=" N HIS G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG G 269 " --> pdb=" O ALA G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 294 Processing helix chain 'G' and resid 315 through 323 removed outlier: 3.573A pdb=" N GLN G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 31 Processing helix chain 'M' and resid 43 through 51 Proline residue: M 48 - end of helix Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 91 through 97 removed outlier: 3.830A pdb=" N VAL M 97 " --> pdb=" O THR M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 139 removed outlier: 3.885A pdb=" N GLU M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 162 Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 186 through 200 removed outlier: 3.688A pdb=" N ILE M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'M' and resid 229 through 238 removed outlier: 4.272A pdb=" N SER M 233 " --> pdb=" O TRP M 230 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR M 237 " --> pdb=" O ASN M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 283 Processing helix chain 'M' and resid 287 through 296 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 305 through 313 removed outlier: 3.899A pdb=" N GLU M 310 " --> pdb=" O SER M 306 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS M 313 " --> pdb=" O GLU M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 315 through 325 Processing helix chain 'M' and resid 334 through 351 removed outlier: 4.145A pdb=" N TRP M 340 " --> pdb=" O SER M 337 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR M 341 " --> pdb=" O ALA M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 357 through 366 Processing helix chain 'L' and resid 185 through 187 No H-bonds generated for 'chain 'L' and resid 185 through 187' Processing helix chain 'H' and resid 203 through 207 removed outlier: 3.717A pdb=" N GLY H 206 " --> pdb=" O SER H 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 99 No H-bonds generated for 'chain 'N' and resid 97 through 99' Processing sheet with id= A, first strand: chain 'A' and resid 18 through 20 Processing sheet with id= B, 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) Processing sheet with id= C, first strand: chain 'A' and resid 425 through 428 removed outlier: 3.509A pdb=" N ARG A 438 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing sheet with id= D, 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) Processing sheet with id= E, first strand: chain 'G' and resid 50 through 52 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= F, first strand: chain 'G' and resid 300 through 302 removed outlier: 4.311A pdb=" N GLY G 311 " --> pdb=" O VAL G 302 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 7 through 10 Processing sheet with id= H, first strand: chain 'M' and resid 59 through 63 removed outlier: 6.241A pdb=" N ALA M 264 " --> pdb=" O PRO M 107 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE M 266 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA M 105 " --> pdb=" O ILE M 266 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 224 through 227 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= J, first strand: chain 'L' and resid 12 through 14 removed outlier: 4.306A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Processing sheet with id= K, 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= L, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.973A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= M, 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= N, 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= O, 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) Processing sheet with id= P, first strand: chain 'H' and resid 13 through 15 Processing sheet with id= Q, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.589A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 96 through 100 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: 3.516A pdb=" N ILE H 54 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= S, 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= T, first strand: chain 'H' and resid 167 through 170 Processing sheet with id= U, first strand: chain 'N' and resid 12 through 16 removed outlier: 4.662A pdb=" N GLN N 12 " --> pdb=" O SER N 34 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER N 34 " --> pdb=" O GLN N 12 " (cutoff:3.500A) 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= V, first strand: chain 'N' and resid 123 through 126 removed outlier: 3.597A pdb=" N VAL N 126 " --> pdb=" O ALA N 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA N 101 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL N 102 " --> pdb=" O GLN N 48 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER N 44 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET N 43 " --> pdb=" O ALA N 60 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA N 58 " --> pdb=" O TRP N 45 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ARG N 47 " --> pdb=" O PHE N 56 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N PHE N 56 " --> pdb=" O ARG N 47 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE N 68 " --> pdb=" O VAL N 59 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 966 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: 3.50 Time building geometry restraints manager: 5.43 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: 100.48 - 107.64: 604 107.64 - 114.80: 7983 114.80 - 121.97: 7180 121.97 - 129.13: 2849 129.13 - 136.29: 100 Bond angle restraints: 18716 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 121.56 18.31 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP G 401 " pdb=" O3A ATP G 401 " pdb=" PB ATP G 401 " ideal model delta sigma weight residual 136.83 122.34 14.49 1.00e+00 1.00e+00 2.10e+02 angle pdb=" C5 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" N3 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 127.04 134.92 -7.88 1.15e+00 7.59e-01 4.71e+01 angle pdb=" N1 ATP G 401 " pdb=" C2 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 128.69 123.61 5.08 1.00e+00 1.00e+00 2.58e+01 ... (remaining 18711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.56: 8149 23.56 - 47.12: 132 47.12 - 70.68: 15 70.68 - 94.24: 3 94.24 - 117.79: 7 Dihedral angle restraints: 8306 sinusoidal: 3345 harmonic: 4961 Sorted by residual: dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 23.06 69.94 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" C5' AMP G 403 " pdb=" O5' AMP G 403 " pdb=" P AMP G 403 " pdb=" O3P AMP G 403 " ideal model delta sinusoidal sigma weight residual -60.00 57.80 -117.79 1 2.00e+01 2.50e-03 3.52e+01 dihedral pdb=" C2 TAK A 601 " pdb=" C1 TAK A 601 " pdb=" N1 TAK A 601 " pdb=" C5 TAK A 601 " ideal model delta sinusoidal sigma weight residual -59.56 51.63 -111.19 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 8303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1822 0.073 - 0.145: 245 0.145 - 0.218: 17 0.218 - 0.291: 1 0.291 - 0.364: 2 Chirality restraints: 2087 Sorted by residual: chirality pdb=" C1 GLC D 1 " pdb=" C2 GLC D 1 " pdb=" O1 GLC D 1 " pdb=" O5 GLC D 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.40 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE G 106 " pdb=" CA ILE G 106 " pdb=" CG1 ILE G 106 " pdb=" CG2 ILE G 106 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C3 GLC D 2 " pdb=" C2 GLC D 2 " pdb=" C4 GLC D 2 " pdb=" O3 GLC D 2 " both_signs ideal model delta sigma weight residual False 2.34 2.56 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2084 not shown) Planarity restraints: 2363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY L 95 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO L 96 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 143 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO A 144 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO L 9 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " 0.028 5.00e-02 4.00e+02 ... (remaining 2360 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 1290 2.76 - 3.47: 17561 3.47 - 4.19: 30100 4.19 - 4.90: 52114 Nonbonded interactions: 101066 Sorted by model distance: nonbonded pdb=" N VAL A 13 " pdb=" C PHE M 371 " model vdw 1.330 3.350 nonbonded pdb=" N VAL A 13 " pdb=" O PHE M 371 " model vdw 2.251 2.520 nonbonded pdb=" OG1 THR M 53 " pdb=" OD1 ASP M 55 " model vdw 2.337 2.440 nonbonded pdb=" OG SER M 233 " pdb=" O ASP M 296 " model vdw 2.352 2.440 nonbonded pdb=" OD2 ASP M 30 " pdb=" OH TYR M 283 " model vdw 2.357 2.440 ... (remaining 101061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.040 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 36.340 Find NCS groups from input model: 0.380 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 13781 Z= 0.233 Angle : 0.738 18.309 18716 Z= 0.416 Chirality : 0.049 0.364 2087 Planarity : 0.007 0.071 2363 Dihedral : 9.728 117.795 5107 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.16), residues: 1683 helix: -2.70 (0.16), residues: 431 sheet: -1.44 (0.26), residues: 357 loop : -2.16 (0.17), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 119 HIS 0.006 0.001 HIS G 36 PHE 0.024 0.002 PHE A 538 TYR 0.015 0.001 TYR M 341 ARG 0.004 0.000 ARG M 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.386 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: 0.3232 time to fit residues: 121.0546 Evaluate side-chains 113 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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: 10.0000 chunk 127 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 40.0000 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 220 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS B 214 GLN B 235 HIS B 240 HIS G 26 ASN G 36 HIS ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN G 169 HIS G 197 GLN G 290 ASN M 64 HIS M 201 ASN M 218 ASN ** M 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 13781 Z= 0.472 Angle : 0.843 15.100 18716 Z= 0.419 Chirality : 0.045 0.181 2087 Planarity : 0.006 0.095 2363 Dihedral : 8.897 125.424 1952 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.73 % Allowed : 9.56 % Favored : 87.71 % 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: -1.55 (0.19), residues: 1683 helix: -0.51 (0.23), residues: 441 sheet: -1.00 (0.25), residues: 377 loop : -1.26 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 117 HIS 0.012 0.002 HIS M 64 PHE 0.032 0.003 PHE A 279 TYR 0.028 0.003 TYR H 97 ARG 0.012 0.001 ARG M 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 95 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8339 (mmt180) cc_final: 0.8136 (mtt-85) REVERT: A 136 MET cc_start: 0.9101 (mmm) cc_final: 0.8643 (mmp) REVERT: B 237 MET cc_start: 0.7956 (pmm) cc_final: 0.7512 (pmm) REVERT: B 257 HIS cc_start: 0.7970 (t70) cc_final: 0.7696 (t70) REVERT: L 48 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9219 (mp) REVERT: N 43 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7672 (mmm) REVERT: N 104 TYR cc_start: 0.8302 (m-80) cc_final: 0.7896 (m-80) outliers start: 40 outliers final: 20 residues processed: 127 average time/residue: 0.2640 time to fit residues: 49.6542 Evaluate side-chains 96 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 74 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 191 LEU 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 264 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 259 ASP 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 197 VAL Chi-restraints excluded: chain L residue 206 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 Chi-restraints excluded: chain N residue 43 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 151 optimal weight: 50.0000 chunk 52 optimal weight: 8.9990 chunk 122 optimal weight: 0.0770 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 249 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 323 ASN M 365 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN L 190 HIS ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13781 Z= 0.146 Angle : 0.571 9.675 18716 Z= 0.276 Chirality : 0.041 0.212 2087 Planarity : 0.004 0.051 2363 Dihedral : 6.909 100.755 1952 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.18 % Allowed : 10.24 % Favored : 87.58 % 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: -1.11 (0.20), residues: 1683 helix: 0.03 (0.24), residues: 436 sheet: -0.63 (0.26), residues: 377 loop : -1.14 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 45 HIS 0.005 0.001 HIS A 77 PHE 0.016 0.001 PHE N 77 TYR 0.018 0.001 TYR L 50 ARG 0.005 0.000 ARG L 212 *********************** 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 122 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9153 (mmm) cc_final: 0.8794 (mmp) REVERT: B 197 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5712 (mmp80) REVERT: B 237 MET cc_start: 0.7779 (pmm) cc_final: 0.6796 (pmm) REVERT: M 72 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8960 (tm-30) REVERT: M 330 MET cc_start: 0.8485 (mtm) cc_final: 0.8138 (mtt) REVERT: M 336 MET cc_start: 0.8628 (tpt) cc_final: 0.8281 (tpp) REVERT: N 104 TYR cc_start: 0.8091 (m-80) cc_final: 0.7756 (m-80) outliers start: 32 outliers final: 16 residues processed: 113 average time/residue: 0.2476 time to fit residues: 42.2032 Evaluate side-chains 94 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 0.2980 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 30.0000 chunk 162 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13781 Z= 0.258 Angle : 0.602 10.944 18716 Z= 0.293 Chirality : 0.041 0.227 2087 Planarity : 0.004 0.051 2363 Dihedral : 6.795 97.318 1952 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.66 % Allowed : 9.69 % Favored : 87.65 % 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: -0.83 (0.20), residues: 1683 helix: 0.27 (0.25), residues: 445 sheet: -0.50 (0.26), residues: 383 loop : -0.95 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 117 HIS 0.005 0.001 HIS A 77 PHE 0.015 0.002 PHE A 279 TYR 0.025 0.002 TYR H 97 ARG 0.004 0.001 ARG G 70 *********************** 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 117 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 78 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9135 (mmm) cc_final: 0.8852 (mmp) REVERT: B 197 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6039 (mmp80) REVERT: M 330 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8107 (mtt) REVERT: M 336 MET cc_start: 0.8845 (tpt) cc_final: 0.8546 (tpp) REVERT: N 104 TYR cc_start: 0.8155 (m-80) cc_final: 0.7882 (m-80) outliers start: 39 outliers final: 23 residues processed: 110 average time/residue: 0.2443 time to fit residues: 40.5844 Evaluate side-chains 95 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain M residue 330 MET Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 96 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 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 135 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN L 90 GLN N 10 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13781 Z= 0.236 Angle : 0.584 8.894 18716 Z= 0.287 Chirality : 0.041 0.207 2087 Planarity : 0.004 0.050 2363 Dihedral : 6.623 90.732 1952 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.59 % Allowed : 9.76 % Favored : 87.65 % 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: -0.72 (0.21), residues: 1683 helix: 0.35 (0.25), residues: 447 sheet: -0.48 (0.26), residues: 389 loop : -0.86 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 117 HIS 0.009 0.001 HIS B 240 PHE 0.011 0.001 PHE G 91 TYR 0.021 0.001 TYR L 50 ARG 0.008 0.001 ARG L 212 *********************** 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 114 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 76 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9169 (mmm) cc_final: 0.8899 (mmp) REVERT: G 189 MET cc_start: 0.8924 (mpp) cc_final: 0.8422 (pmm) REVERT: M 336 MET cc_start: 0.8976 (tpt) cc_final: 0.8667 (tpp) REVERT: L 48 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9078 (mp) REVERT: H 114 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8023 (mm-30) REVERT: N 104 TYR cc_start: 0.8108 (m-80) cc_final: 0.7799 (m-80) outliers start: 38 outliers final: 28 residues processed: 107 average time/residue: 0.2632 time to fit residues: 41.7030 Evaluate side-chains 100 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 71 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 40 optimal weight: 0.0870 chunk 162 optimal weight: 0.3980 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 overall best weight: 1.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13781 Z= 0.157 Angle : 0.552 8.083 18716 Z= 0.267 Chirality : 0.040 0.209 2087 Planarity : 0.004 0.106 2363 Dihedral : 6.190 74.487 1952 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.12 % Allowed : 10.24 % Favored : 87.65 % 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: 0.42 (0.25), residues: 450 sheet: -0.38 (0.26), residues: 388 loop : -0.80 (0.22), residues: 845 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 0.018 0.001 PHE G 91 TYR 0.017 0.001 TYR L 50 ARG 0.006 0.000 ARG M 354 *********************** 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 109 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 78 time to evaluate : 1.431 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 65 ARG cc_start: 0.8448 (mmt180) cc_final: 0.8232 (mpt-90) REVERT: A 136 MET cc_start: 0.9121 (mmm) cc_final: 0.8863 (mmp) REVERT: B 226 ASP cc_start: 0.6132 (m-30) cc_final: 0.5386 (t70) REVERT: G 189 MET cc_start: 0.9014 (mpp) cc_final: 0.8538 (pmm) REVERT: M 336 MET cc_start: 0.8983 (tpt) cc_final: 0.8710 (tpp) REVERT: H 114 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7966 (mm-30) REVERT: N 104 TYR cc_start: 0.8101 (m-80) cc_final: 0.7782 (m-80) REVERT: N 113 TYR cc_start: 0.6683 (t80) cc_final: 0.6336 (t80) outliers start: 31 outliers final: 26 residues processed: 103 average time/residue: 0.2453 time to fit residues: 38.6394 Evaluate side-chains 100 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 74 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain L residue 49 ILE 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 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 188 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 0.1980 chunk 91 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 98 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13781 Z= 0.201 Angle : 0.572 8.452 18716 Z= 0.277 Chirality : 0.040 0.178 2087 Planarity : 0.004 0.051 2363 Dihedral : 5.648 51.737 1952 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.32 % Allowed : 9.90 % 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: -0.49 (0.21), residues: 1683 helix: 0.42 (0.25), residues: 451 sheet: -0.17 (0.26), residues: 381 loop : -0.75 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 117 HIS 0.006 0.001 HIS A 77 PHE 0.009 0.001 PHE N 77 TYR 0.018 0.001 TYR L 50 ARG 0.005 0.000 ARG B 197 *********************** 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 110 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 76 time to evaluate : 1.534 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 65 ARG cc_start: 0.8488 (mmt180) cc_final: 0.8148 (mpt-90) REVERT: A 136 MET cc_start: 0.9072 (mmm) cc_final: 0.8858 (mmp) REVERT: B 226 ASP cc_start: 0.6022 (m-30) cc_final: 0.5298 (t70) REVERT: G 33 MET cc_start: 0.9374 (mtp) cc_final: 0.9171 (ptp) REVERT: G 189 MET cc_start: 0.8974 (mpp) cc_final: 0.8554 (pmm) REVERT: M 336 MET cc_start: 0.9052 (tpt) cc_final: 0.8780 (tpp) REVERT: H 114 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7963 (mm-30) REVERT: N 104 TYR cc_start: 0.8079 (m-80) cc_final: 0.7775 (m-80) REVERT: N 113 TYR cc_start: 0.6707 (t80) cc_final: 0.6369 (t80) outliers start: 34 outliers final: 30 residues processed: 104 average time/residue: 0.2529 time to fit residues: 39.8978 Evaluate side-chains 104 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 74 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain 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 188 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 323 ASN ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13781 Z= 0.211 Angle : 0.575 8.291 18716 Z= 0.280 Chirality : 0.040 0.171 2087 Planarity : 0.004 0.052 2363 Dihedral : 5.702 55.547 1952 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.46 % Allowed : 10.24 % Favored : 87.30 % 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: -0.42 (0.21), residues: 1683 helix: 0.47 (0.25), residues: 451 sheet: -0.10 (0.27), residues: 381 loop : -0.71 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 117 HIS 0.006 0.001 HIS A 77 PHE 0.019 0.001 PHE G 91 TYR 0.018 0.001 TYR L 50 ARG 0.006 0.000 ARG B 197 *********************** 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 116 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 80 time to evaluate : 1.664 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 65 ARG cc_start: 0.8497 (mmt180) cc_final: 0.8129 (mpt-90) REVERT: A 107 ILE cc_start: 0.9329 (mm) cc_final: 0.9041 (tp) REVERT: A 136 MET cc_start: 0.9067 (mmm) cc_final: 0.8825 (mmp) REVERT: A 256 MET cc_start: 0.8896 (mmm) cc_final: 0.8631 (mmm) REVERT: B 218 ASN cc_start: 0.7915 (t0) cc_final: 0.7680 (p0) REVERT: B 226 ASP cc_start: 0.6004 (m-30) cc_final: 0.5271 (t70) REVERT: G 33 MET cc_start: 0.9349 (mtp) cc_final: 0.9140 (ptp) REVERT: G 189 MET cc_start: 0.8983 (mpp) cc_final: 0.8590 (pmm) REVERT: M 336 MET cc_start: 0.9093 (tpt) cc_final: 0.8855 (tpp) REVERT: H 114 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7927 (mm-30) REVERT: N 104 TYR cc_start: 0.8101 (m-80) cc_final: 0.7793 (m-80) REVERT: N 113 TYR cc_start: 0.6819 (t80) cc_final: 0.6468 (t80) outliers start: 36 outliers final: 35 residues processed: 109 average time/residue: 0.2497 time to fit residues: 41.2995 Evaluate side-chains 113 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 78 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 188 PHE Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR 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 188 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 5.9990 chunk 141 optimal weight: 0.0040 chunk 150 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 0.0870 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 overall best weight: 1.0176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13781 Z= 0.136 Angle : 0.569 8.827 18716 Z= 0.273 Chirality : 0.041 0.164 2087 Planarity : 0.003 0.051 2363 Dihedral : 5.587 59.113 1952 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.91 % Allowed : 10.92 % Favored : 87.17 % 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: -0.36 (0.21), residues: 1683 helix: 0.56 (0.25), residues: 448 sheet: -0.03 (0.26), residues: 381 loop : -0.71 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 269 HIS 0.006 0.001 HIS A 77 PHE 0.020 0.001 PHE G 91 TYR 0.013 0.001 TYR L 50 ARG 0.004 0.000 ARG B 197 *********************** 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 110 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8483 (mmt180) cc_final: 0.8125 (mpt-90) REVERT: A 107 ILE cc_start: 0.9308 (mm) cc_final: 0.8975 (tp) REVERT: A 136 MET cc_start: 0.9045 (mmm) cc_final: 0.8804 (mmp) REVERT: B 193 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7873 (pmm) REVERT: B 226 ASP cc_start: 0.5999 (m-30) cc_final: 0.5272 (t70) REVERT: G 33 MET cc_start: 0.9330 (mtp) cc_final: 0.9124 (ptp) REVERT: G 189 MET cc_start: 0.8966 (mpp) cc_final: 0.8684 (pmm) REVERT: M 336 MET cc_start: 0.9059 (tpt) cc_final: 0.8639 (tpp) REVERT: H 114 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7945 (mm-30) REVERT: N 104 TYR cc_start: 0.8073 (m-80) cc_final: 0.7750 (m-80) REVERT: N 113 TYR cc_start: 0.6797 (t80) cc_final: 0.6430 (t80) outliers start: 28 outliers final: 25 residues processed: 103 average time/residue: 0.2429 time to fit residues: 38.1367 Evaluate side-chains 102 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain 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 207 THR Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 13781 Z= 0.298 Angle : 0.653 8.933 18716 Z= 0.319 Chirality : 0.041 0.163 2087 Planarity : 0.004 0.061 2363 Dihedral : 5.952 56.440 1952 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.98 % Allowed : 11.19 % Favored : 86.83 % 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: -0.41 (0.21), residues: 1683 helix: 0.51 (0.25), residues: 451 sheet: -0.10 (0.26), residues: 385 loop : -0.72 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 117 HIS 0.006 0.001 HIS B 240 PHE 0.028 0.002 PHE G 91 TYR 0.024 0.002 TYR L 50 ARG 0.007 0.001 ARG B 197 ********************** 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 103 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 74 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8482 (mmt180) cc_final: 0.8148 (mpt-90) REVERT: A 136 MET cc_start: 0.9053 (mmm) cc_final: 0.8779 (mmp) REVERT: A 256 MET cc_start: 0.8963 (mmm) cc_final: 0.8704 (mmm) REVERT: B 218 ASN cc_start: 0.8241 (t0) cc_final: 0.7788 (p0) REVERT: B 226 ASP cc_start: 0.5757 (m-30) cc_final: 0.5058 (t70) REVERT: B 237 MET cc_start: 0.7687 (pmm) cc_final: 0.7450 (pmm) REVERT: G 189 MET cc_start: 0.8989 (mpp) cc_final: 0.8680 (pmm) REVERT: M 336 MET cc_start: 0.9191 (tpt) cc_final: 0.8789 (tpp) REVERT: H 114 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8083 (mm-30) REVERT: H 160 ASP cc_start: 0.9091 (m-30) cc_final: 0.8257 (p0) REVERT: N 77 PHE cc_start: 0.8811 (m-10) cc_final: 0.8520 (m-10) REVERT: N 92 MET cc_start: 0.8728 (pmm) cc_final: 0.8377 (pmm) REVERT: N 104 TYR cc_start: 0.8139 (m-80) cc_final: 0.7842 (m-80) REVERT: N 113 TYR cc_start: 0.7014 (t80) cc_final: 0.6631 (t80) outliers start: 29 outliers final: 28 residues processed: 98 average time/residue: 0.2475 time to fit residues: 36.5251 Evaluate side-chains 101 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 206 MET Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 7 optimal weight: 0.4980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 GLN ** 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 = 0.3452 r_free = 0.3452 target = 0.045883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.030957 restraints weight = 107271.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.031982 restraints weight = 62495.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.032657 restraints weight = 45035.561| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13781 Z= 0.224 Angle : 0.605 8.979 18716 Z= 0.293 Chirality : 0.041 0.166 2087 Planarity : 0.004 0.050 2363 Dihedral : 5.923 55.610 1952 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.77 % Allowed : 11.47 % Favored : 86.76 % 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: -0.35 (0.21), residues: 1683 helix: 0.52 (0.26), residues: 450 sheet: -0.04 (0.26), residues: 384 loop : -0.68 (0.23), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 426 HIS 0.006 0.001 HIS A 77 PHE 0.031 0.001 PHE G 91 TYR 0.039 0.001 TYR B 189 ARG 0.007 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2377.34 seconds wall clock time: 45 minutes 23.97 seconds (2723.97 seconds total)