Starting phenix.real_space_refine on Tue Jun 25 19:40:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/06_2024/8uwl_42676_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/06_2024/8uwl_42676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/06_2024/8uwl_42676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/06_2024/8uwl_42676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/06_2024/8uwl_42676_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/06_2024/8uwl_42676_updated.pdb" } resolution = 2.8 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= 0.001 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5495 2.51 5 N 1470 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8626 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2084 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1792 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2592 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 396 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1737 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H8G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.17, per 1000 atoms: 0.83 Number of scatterers: 8626 At special positions: 0 Unit cell: (115.886, 100.548, 134.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1604 8.00 N 1470 7.00 C 5495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.34 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=1.90 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 2.5 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 12 sheets defined 34.6% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 78 through 100 removed outlier: 3.570A pdb=" N LEU A 87 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 89 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 91 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 92 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 125 removed outlier: 3.529A pdb=" N PHE A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.673A pdb=" N MET A 132 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 178 removed outlier: 4.085A pdb=" N CYS A 148 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA A 149 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 159 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 172 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 173 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 191 through 208 removed outlier: 3.671A pdb=" N SER A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 213 No H-bonds generated for 'chain 'A' and resid 210 through 213' Processing helix chain 'A' and resid 218 through 221 Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.533A pdb=" N PHE A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 265 Processing helix chain 'A' and resid 313 through 348 Proline residue: A 338 - end of helix removed outlier: 3.657A pdb=" N THR A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 removed outlier: 3.519A pdb=" N LEU A 362 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 376 " --> pdb=" O SER A 373 " (cutoff:3.500A) Proline residue: A 377 - end of helix removed outlier: 3.571A pdb=" N TYR A 380 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU A 382 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.512A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 184 through 203 removed outlier: 3.750A pdb=" N GLU B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 242 Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'D' and resid 10 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 7.140A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.975A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.954A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.742A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.879A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.827A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.509A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.708A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 3.695A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.385A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 148 375 hydrogen bonds defined for protein. 903 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: 2.94 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1619 1.32 - 1.45: 2212 1.45 - 1.57: 4890 1.57 - 1.69: 0 1.69 - 1.82: 85 Bond restraints: 8806 Sorted by residual: bond pdb=" N VAL E 135 " pdb=" CA VAL E 135 " ideal model delta sigma weight residual 1.454 1.497 -0.043 7.70e-03 1.69e+04 3.08e+01 bond pdb=" N ILE C 93 " pdb=" CA ILE C 93 " ideal model delta sigma weight residual 1.456 1.497 -0.041 8.70e-03 1.32e+04 2.19e+01 bond pdb=" N VAL E 48 " pdb=" CA VAL E 48 " ideal model delta sigma weight residual 1.458 1.495 -0.037 9.00e-03 1.23e+04 1.71e+01 bond pdb=" N VAL B 5 " pdb=" CA VAL B 5 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.19e-02 7.06e+03 1.70e+01 bond pdb=" N MET A 128 " pdb=" CA MET A 128 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.04e-02 9.25e+03 1.61e+01 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.67: 273 106.67 - 113.89: 4737 113.89 - 121.11: 4392 121.11 - 128.32: 2493 128.32 - 135.54: 63 Bond angle restraints: 11958 Sorted by residual: angle pdb=" N ASN B 43 " pdb=" CA ASN B 43 " pdb=" C ASN B 43 " ideal model delta sigma weight residual 113.17 104.43 8.74 1.26e+00 6.30e-01 4.81e+01 angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 112.59 104.16 8.43 1.22e+00 6.72e-01 4.78e+01 angle pdb=" CA GLY E 114 " pdb=" C GLY E 114 " pdb=" O GLY E 114 " ideal model delta sigma weight residual 122.22 117.75 4.47 6.50e-01 2.37e+00 4.73e+01 angle pdb=" N THR A 190 " pdb=" CA THR A 190 " pdb=" C THR A 190 " ideal model delta sigma weight residual 113.41 105.26 8.15 1.22e+00 6.72e-01 4.46e+01 angle pdb=" C PRO B 184 " pdb=" CA PRO B 184 " pdb=" CB PRO B 184 " ideal model delta sigma weight residual 112.62 102.02 10.60 1.65e+00 3.67e-01 4.13e+01 ... (remaining 11953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 5149 35.54 - 71.07: 74 71.07 - 106.60: 1 106.60 - 142.14: 0 142.14 - 177.67: 2 Dihedral angle restraints: 5226 sinusoidal: 1970 harmonic: 3256 Sorted by residual: dihedral pdb=" C THR E 198 " pdb=" N THR E 198 " pdb=" CA THR E 198 " pdb=" CB THR E 198 " ideal model delta harmonic sigma weight residual -122.00 -137.73 15.73 0 2.50e+00 1.60e-01 3.96e+01 dihedral pdb=" N THR E 198 " pdb=" C THR E 198 " pdb=" CA THR E 198 " pdb=" CB THR E 198 " ideal model delta harmonic sigma weight residual 123.40 137.37 -13.97 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C PRO B 184 " pdb=" N PRO B 184 " pdb=" CA PRO B 184 " pdb=" CB PRO B 184 " ideal model delta harmonic sigma weight residual -120.70 -107.32 -13.38 0 2.50e+00 1.60e-01 2.87e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 839 0.113 - 0.226: 459 0.226 - 0.339: 71 0.339 - 0.452: 2 0.452 - 0.565: 1 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA THR E 198 " pdb=" N THR E 198 " pdb=" C THR E 198 " pdb=" CB THR E 198 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.56 2.00e-01 2.50e+01 7.98e+00 chirality pdb=" CA HIS B 209 " pdb=" N HIS B 209 " pdb=" C HIS B 209 " pdb=" CB HIS B 209 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ASP C 153 " pdb=" N ASP C 153 " pdb=" C ASP C 153 " pdb=" CB ASP C 153 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 1369 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAF H8G A 501 " -0.113 2.00e-02 2.50e+03 8.88e-02 2.17e+02 pdb=" CAG H8G A 501 " -0.078 2.00e-02 2.50e+03 pdb=" CAH H8G A 501 " -0.012 2.00e-02 2.50e+03 pdb=" CAI H8G A 501 " -0.015 2.00e-02 2.50e+03 pdb=" CAL H8G A 501 " -0.179 2.00e-02 2.50e+03 pdb=" CAQ H8G A 501 " 0.116 2.00e-02 2.50e+03 pdb=" CAR H8G A 501 " 0.007 2.00e-02 2.50e+03 pdb=" CAS H8G A 501 " 0.067 2.00e-02 2.50e+03 pdb=" CAT H8G A 501 " 0.081 2.00e-02 2.50e+03 pdb=" CAU H8G A 501 " 0.101 2.00e-02 2.50e+03 pdb=" NAO H8G A 501 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAJ H8G A 501 " 0.058 2.00e-02 2.50e+03 1.04e-01 1.89e+02 pdb=" CAK H8G A 501 " 0.024 2.00e-02 2.50e+03 pdb=" CAP H8G A 501 " -0.065 2.00e-02 2.50e+03 pdb=" CAV H8G A 501 " 0.160 2.00e-02 2.50e+03 pdb=" NAN H8G A 501 " -0.203 2.00e-02 2.50e+03 pdb=" NAY H8G A 501 " 0.017 2.00e-02 2.50e+03 pdb=" OAD H8G A 501 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAE H8G A 501 " -0.036 2.00e-02 2.50e+03 2.26e-02 6.37e+00 pdb=" CAQ H8G A 501 " -0.008 2.00e-02 2.50e+03 pdb=" CAS H8G A 501 " 0.021 2.00e-02 2.50e+03 pdb=" CAV H8G A 501 " 0.027 2.00e-02 2.50e+03 pdb=" CAW H8G A 501 " -0.005 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 72 2.64 - 3.21: 7228 3.21 - 3.77: 11703 3.77 - 4.34: 16678 4.34 - 4.90: 28161 Nonbonded interactions: 63842 Sorted by model distance: nonbonded pdb=" O SER A 131 " pdb=" OG1 THR A 134 " model vdw 2.079 2.440 nonbonded pdb=" O ASN A 233 " pdb=" ND2 ASN A 233 " model vdw 2.286 2.520 nonbonded pdb=" O ALA A 78 " pdb=" OG1 THR A 81 " model vdw 2.310 2.440 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.310 2.440 nonbonded pdb=" OD1 ASP B 147 " pdb=" N LEU B 148 " model vdw 2.325 2.520 ... (remaining 63837 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 9.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 30.550 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.013 0.056 8806 Z= 0.859 Angle : 1.689 10.601 11958 Z= 1.290 Chirality : 0.121 0.565 1372 Planarity : 0.006 0.104 1517 Dihedral : 12.383 177.669 3113 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.43 % Allowed : 3.07 % Favored : 95.50 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 2.94 % 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: 1.81 (0.23), residues: 1105 helix: 2.54 (0.25), residues: 377 sheet: 2.30 (0.37), residues: 173 loop : -0.11 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 82 HIS 0.008 0.003 HIS E 35 PHE 0.033 0.003 PHE C 151 TYR 0.020 0.003 TYR E 102 ARG 0.005 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 226 time to evaluate : 0.951 Fit side-chains REVERT: A 219 SER cc_start: 0.6894 (p) cc_final: 0.6665 (m) REVERT: A 222 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6477 (t80) REVERT: A 227 CYS cc_start: 0.6529 (t) cc_final: 0.6278 (t) REVERT: A 345 MET cc_start: 0.7399 (ttm) cc_final: 0.7193 (ttt) REVERT: C 37 ILE cc_start: 0.7653 (mm) cc_final: 0.7348 (pt) REVERT: C 246 ASP cc_start: 0.7566 (p0) cc_final: 0.7327 (p0) REVERT: C 325 MET cc_start: 0.8526 (mmt) cc_final: 0.7856 (mmt) REVERT: E 34 MET cc_start: 0.9209 (mmm) cc_final: 0.8933 (mmt) REVERT: E 211 ASP cc_start: 0.7828 (m-30) cc_final: 0.7548 (m-30) outliers start: 13 outliers final: 3 residues processed: 234 average time/residue: 1.1622 time to fit residues: 289.2651 Evaluate side-chains 159 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 113 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 313 GLN A 317 ASN B 146 GLN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8806 Z= 0.238 Angle : 0.627 7.796 11958 Z= 0.355 Chirality : 0.046 0.169 1372 Planarity : 0.005 0.038 1517 Dihedral : 9.371 167.720 1245 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.40 % Allowed : 12.62 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.70 (0.24), residues: 1105 helix: 2.31 (0.26), residues: 377 sheet: 1.68 (0.29), residues: 278 loop : -0.25 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.005 0.002 HIS E 35 PHE 0.027 0.002 PHE C 151 TYR 0.014 0.002 TYR A 370 ARG 0.007 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 0.870 Fit side-chains REVERT: A 171 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8578 (tt) REVERT: A 203 SER cc_start: 0.8723 (m) cc_final: 0.8468 (m) REVERT: A 222 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6822 (t80) REVERT: A 345 MET cc_start: 0.7442 (ttm) cc_final: 0.7215 (ttt) REVERT: C 175 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: C 325 MET cc_start: 0.8382 (mmt) cc_final: 0.8070 (mmt) outliers start: 31 outliers final: 6 residues processed: 170 average time/residue: 1.1857 time to fit residues: 214.6841 Evaluate side-chains 148 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN D 18 GLN E 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8806 Z= 0.290 Angle : 0.621 7.558 11958 Z= 0.346 Chirality : 0.046 0.162 1372 Planarity : 0.005 0.044 1517 Dihedral : 9.199 168.738 1242 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.17 % Allowed : 15.92 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.19 (0.24), residues: 1105 helix: 1.93 (0.27), residues: 378 sheet: 1.35 (0.29), residues: 285 loop : -0.61 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 47 HIS 0.006 0.002 HIS E 35 PHE 0.025 0.002 PHE C 151 TYR 0.015 0.002 TYR E 95 ARG 0.007 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 2.484 Fit side-chains REVERT: A 345 MET cc_start: 0.7466 (ttm) cc_final: 0.7251 (ttt) REVERT: B 185 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6702 (mtm-85) REVERT: C 258 ASP cc_start: 0.7079 (t0) cc_final: 0.6528 (t0) REVERT: C 318 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8840 (mt) REVERT: C 325 MET cc_start: 0.8451 (mmt) cc_final: 0.8025 (mmt) outliers start: 38 outliers final: 15 residues processed: 172 average time/residue: 1.3111 time to fit residues: 239.8335 Evaluate side-chains 159 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 74 optimal weight: 0.0060 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 0.0070 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 0.4614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 98 GLN C 44 GLN C 237 ASN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8806 Z= 0.155 Angle : 0.502 6.013 11958 Z= 0.276 Chirality : 0.041 0.133 1372 Planarity : 0.004 0.041 1517 Dihedral : 8.885 172.146 1240 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.73 % Allowed : 18.00 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.27 (0.25), residues: 1105 helix: 2.05 (0.28), residues: 379 sheet: 1.29 (0.30), residues: 286 loop : -0.55 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 141 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.008 0.001 TYR E 95 ARG 0.011 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 0.846 Fit side-chains REVERT: C 256 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7536 (mtp180) REVERT: C 258 ASP cc_start: 0.7047 (t0) cc_final: 0.6569 (t0) REVERT: C 325 MET cc_start: 0.8463 (mmt) cc_final: 0.8062 (mmt) outliers start: 34 outliers final: 11 residues processed: 157 average time/residue: 1.2562 time to fit residues: 208.8925 Evaluate side-chains 146 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 0.1980 chunk 0 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8806 Z= 0.162 Angle : 0.498 5.823 11958 Z= 0.274 Chirality : 0.041 0.133 1372 Planarity : 0.004 0.040 1517 Dihedral : 8.792 171.798 1240 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.62 % Allowed : 18.77 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.17 (0.25), residues: 1105 helix: 2.07 (0.28), residues: 373 sheet: 1.21 (0.30), residues: 285 loop : -0.65 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 141 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.010 0.001 TYR E 95 ARG 0.011 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 0.902 Fit side-chains REVERT: B 185 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6473 (mtm-85) REVERT: C 175 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: C 256 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7478 (mtp180) REVERT: C 258 ASP cc_start: 0.7019 (t0) cc_final: 0.6563 (t0) REVERT: C 325 MET cc_start: 0.8467 (mmt) cc_final: 0.8052 (mmt) outliers start: 33 outliers final: 17 residues processed: 159 average time/residue: 1.2368 time to fit residues: 208.6933 Evaluate side-chains 150 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8806 Z= 0.154 Angle : 0.492 6.348 11958 Z= 0.268 Chirality : 0.041 0.131 1372 Planarity : 0.004 0.044 1517 Dihedral : 8.736 171.680 1240 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.18 % Allowed : 19.32 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.16 (0.25), residues: 1105 helix: 2.12 (0.28), residues: 371 sheet: 1.18 (0.30), residues: 285 loop : -0.68 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 141 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE C 151 TYR 0.009 0.001 TYR E 95 ARG 0.011 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.879 Fit side-chains REVERT: B 185 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6454 (mtm-85) REVERT: B 221 THR cc_start: 0.7105 (p) cc_final: 0.6791 (t) REVERT: C 175 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: C 256 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7517 (mtp180) REVERT: C 258 ASP cc_start: 0.7010 (t0) cc_final: 0.6556 (t0) REVERT: C 325 MET cc_start: 0.8466 (mmt) cc_final: 0.8027 (mmt) outliers start: 29 outliers final: 16 residues processed: 148 average time/residue: 1.2584 time to fit residues: 197.6399 Evaluate side-chains 147 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8806 Z= 0.228 Angle : 0.546 7.595 11958 Z= 0.299 Chirality : 0.043 0.141 1372 Planarity : 0.005 0.050 1517 Dihedral : 8.797 170.131 1240 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.06 % Allowed : 18.33 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.95 (0.25), residues: 1105 helix: 1.96 (0.28), residues: 368 sheet: 1.18 (0.30), residues: 281 loop : -0.86 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 141 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.002 PHE C 151 TYR 0.011 0.001 TYR E 95 ARG 0.012 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 0.968 Fit side-chains REVERT: A 384 ASN cc_start: 0.7721 (t0) cc_final: 0.7471 (t0) REVERT: B 185 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6582 (mtm-85) REVERT: B 221 THR cc_start: 0.7148 (p) cc_final: 0.6827 (t) REVERT: C 32 GLN cc_start: 0.8512 (mt0) cc_final: 0.8251 (mt0) REVERT: C 42 ARG cc_start: 0.7327 (ttm110) cc_final: 0.6958 (ttp-110) REVERT: C 175 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: C 256 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7563 (mtp180) REVERT: C 258 ASP cc_start: 0.7081 (t0) cc_final: 0.6587 (t0) REVERT: C 325 MET cc_start: 0.8465 (mmt) cc_final: 0.7981 (mmt) outliers start: 37 outliers final: 17 residues processed: 154 average time/residue: 1.2083 time to fit residues: 197.7927 Evaluate side-chains 153 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8806 Z= 0.206 Angle : 0.530 6.859 11958 Z= 0.288 Chirality : 0.042 0.140 1372 Planarity : 0.005 0.052 1517 Dihedral : 8.804 170.469 1240 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.07 % Allowed : 19.98 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.86 (0.25), residues: 1105 helix: 1.90 (0.28), residues: 368 sheet: 1.08 (0.30), residues: 285 loop : -0.92 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 141 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE C 151 TYR 0.010 0.001 TYR E 95 ARG 0.014 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.965 Fit side-chains REVERT: B 185 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6577 (mtm-85) REVERT: B 221 THR cc_start: 0.7159 (p) cc_final: 0.6833 (t) REVERT: C 32 GLN cc_start: 0.8512 (mt0) cc_final: 0.8252 (mt0) REVERT: C 79 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8976 (mp) REVERT: C 175 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: C 256 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7561 (mtp180) REVERT: C 258 ASP cc_start: 0.7058 (t0) cc_final: 0.6588 (t0) REVERT: C 325 MET cc_start: 0.8455 (mmt) cc_final: 0.7960 (mmt) outliers start: 28 outliers final: 20 residues processed: 150 average time/residue: 1.1832 time to fit residues: 189.1413 Evaluate side-chains 150 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8806 Z= 0.156 Angle : 0.489 6.254 11958 Z= 0.267 Chirality : 0.041 0.130 1372 Planarity : 0.004 0.049 1517 Dihedral : 8.736 171.416 1240 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.29 % Allowed : 19.76 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.94 (0.25), residues: 1105 helix: 2.02 (0.28), residues: 366 sheet: 1.05 (0.30), residues: 289 loop : -0.86 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 141 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE C 151 TYR 0.008 0.001 TYR E 95 ARG 0.012 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.015 Fit side-chains REVERT: A 208 MET cc_start: 0.8103 (tpp) cc_final: 0.7619 (tpt) REVERT: B 185 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6508 (mtm-85) REVERT: B 221 THR cc_start: 0.7087 (p) cc_final: 0.6822 (t) REVERT: C 42 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7117 (ttp80) REVERT: C 175 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: C 215 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: C 256 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7525 (mtp180) REVERT: C 258 ASP cc_start: 0.7014 (t0) cc_final: 0.6633 (t0) REVERT: C 325 MET cc_start: 0.8460 (mmt) cc_final: 0.7919 (mmt) outliers start: 30 outliers final: 19 residues processed: 147 average time/residue: 1.1181 time to fit residues: 175.2195 Evaluate side-chains 149 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.0470 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8806 Z= 0.178 Angle : 0.510 6.727 11958 Z= 0.276 Chirality : 0.041 0.131 1372 Planarity : 0.005 0.046 1517 Dihedral : 8.713 170.417 1240 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.74 % Allowed : 20.31 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.88 (0.25), residues: 1105 helix: 1.98 (0.28), residues: 366 sheet: 1.06 (0.30), residues: 288 loop : -0.94 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 141 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.010 0.001 TYR E 95 ARG 0.012 0.001 ARG B 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.876 Fit side-chains REVERT: B 185 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6543 (mtm-85) REVERT: B 221 THR cc_start: 0.7123 (p) cc_final: 0.6846 (t) REVERT: C 42 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7083 (ttp80) REVERT: C 175 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: C 256 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7527 (mtp180) REVERT: C 258 ASP cc_start: 0.7038 (t0) cc_final: 0.6582 (t0) REVERT: C 325 MET cc_start: 0.8467 (mmt) cc_final: 0.7938 (mmt) outliers start: 25 outliers final: 19 residues processed: 140 average time/residue: 1.2035 time to fit residues: 179.0729 Evaluate side-chains 147 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.102947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089372 restraints weight = 14423.410| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.96 r_work: 0.3139 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8806 Z= 0.193 Angle : 0.518 7.037 11958 Z= 0.281 Chirality : 0.042 0.135 1372 Planarity : 0.005 0.044 1517 Dihedral : 8.729 170.177 1240 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.96 % Allowed : 19.98 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.82 (0.25), residues: 1105 helix: 1.93 (0.28), residues: 366 sheet: 1.03 (0.30), residues: 288 loop : -0.98 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 141 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.010 0.001 TYR E 95 ARG 0.011 0.001 ARG B 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3896.23 seconds wall clock time: 68 minutes 15.65 seconds (4095.65 seconds total)