Starting phenix.real_space_refine on Tue Aug 26 01:42:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cg3_45567/08_2025/9cg3_45567.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cg3_45567/08_2025/9cg3_45567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cg3_45567/08_2025/9cg3_45567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cg3_45567/08_2025/9cg3_45567.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cg3_45567/08_2025/9cg3_45567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cg3_45567/08_2025/9cg3_45567.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.036 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 Fe 10 7.16 5 S 156 5.16 5 C 20450 2.51 5 N 5429 2.21 5 O 5799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31844 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 659 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 73} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1506 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 446 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "E" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 541 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 892 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "G" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "H" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1908 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 21, 'TRANS': 217} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3008 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 23, 'TRANS': 354} Chain: "K" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3148 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 404} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3208 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 393} Chain breaks: 2 Chain: "P" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1515 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "Q" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 451 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "R" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 909 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "T" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "U" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1908 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 21, 'TRANS': 217} Chain: "V" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3008 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 23, 'TRANS': 354} Chain: "W" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3162 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 13, 'TRANS': 405} Chain: "Y" Number of atoms: 3228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3228 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 396} Chain breaks: 2 Chain: "N" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 681 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1745 SG CYS C 217 75.964 32.799 127.140 1.00 30.00 S ATOM 1881 SG CYS C 236 73.935 32.900 127.064 1.00 35.05 S ATOM 16831 SG CYS P 217 73.262 96.025 127.117 1.00 30.00 S ATOM 16967 SG CYS P 236 76.701 95.463 127.102 1.00 35.05 S Time building chain proxies: 7.94, per 1000 atoms: 0.25 Number of scatterers: 31844 At special positions: 0 Unit cell: (150.87, 129.47, 167.99, 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) Fe 10 26.01 S 156 16.00 O 5799 8.00 N 5429 7.00 C 20450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 222 " - pdb=" SG CYS C 238 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS E 43 " distance=2.05 Simple disulfide: pdb=" SG CYS P 222 " - pdb=" SG CYS P 238 " distance=1.99 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 301 " pdb="FE2 FES C 301 " - pdb=" SG CYS C 236 " pdb="FE2 FES C 301 " - pdb=" SG CYS C 217 " pdb="FE1 FES C 301 " - pdb=" ND1 HIS C 239 " pdb="FE1 FES C 301 " - pdb=" ND1 HIS C 219 " pdb=" FES P 301 " pdb="FE1 FES P 301 " - pdb=" ND1 HIS P 219 " pdb="FE2 FES P 301 " - pdb=" SG CYS P 236 " pdb="FE2 FES P 301 " - pdb=" SG CYS P 217 " pdb="FE1 FES P 301 " - pdb=" ND1 HIS P 239 " Number of angles added : 6 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7474 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 21 sheets defined 59.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 33 through 47 removed outlier: 4.381A pdb=" N PHE A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 72 removed outlier: 3.737A pdb=" N PHE A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'C' and resid 102 through 140 Processing helix chain 'C' and resid 143 through 149 removed outlier: 3.520A pdb=" N LEU C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 190 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'D' and resid 6 through 14 removed outlier: 4.168A pdb=" N SER D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 48 Processing helix chain 'D' and resid 52 through 57 removed outlier: 3.590A pdb=" N ILE D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.824A pdb=" N THR E 32 " --> pdb=" O ASP E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 60 Processing helix chain 'E' and resid 67 through 85 removed outlier: 3.761A pdb=" N ALA E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 25 Processing helix chain 'F' and resid 26 through 29 Processing helix chain 'F' and resid 33 through 38 removed outlier: 3.657A pdb=" N THR F 37 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 33 through 38' Processing helix chain 'F' and resid 41 through 50 Processing helix chain 'F' and resid 52 through 73 Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.924A pdb=" N GLU F 87 " --> pdb=" O TYR F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 110 removed outlier: 4.675A pdb=" N TYR F 94 " --> pdb=" O TYR F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 37 Proline residue: G 19 - end of helix Processing helix chain 'H' and resid 96 through 100 removed outlier: 3.611A pdb=" N GLY H 100 " --> pdb=" O SER H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 120 Processing helix chain 'H' and resid 121 through 124 Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 181 through 189 Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.663A pdb=" N ARG H 204 " --> pdb=" O VAL H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 217 Processing helix chain 'H' and resid 262 through 279 Processing helix chain 'H' and resid 281 through 316 Proline residue: H 301 - end of helix removed outlier: 4.648A pdb=" N VAL H 313 " --> pdb=" O HIS H 309 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU H 314 " --> pdb=" O LYS H 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 7 Processing helix chain 'J' and resid 8 through 18 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 31 through 53 removed outlier: 4.257A pdb=" N SER J 35 " --> pdb=" O TRP J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 72 Processing helix chain 'J' and resid 75 through 104 Processing helix chain 'J' and resid 105 through 108 removed outlier: 3.523A pdb=" N LEU J 108 " --> pdb=" O GLY J 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 105 through 108' Processing helix chain 'J' and resid 109 through 133 Processing helix chain 'J' and resid 136 through 149 Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 157 through 166 removed outlier: 3.703A pdb=" N VAL J 161 " --> pdb=" O GLY J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 204 Proline residue: J 186 - end of helix removed outlier: 3.700A pdb=" N GLU J 202 " --> pdb=" O LEU J 198 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR J 203 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 215 No H-bonds generated for 'chain 'J' and resid 213 through 215' Processing helix chain 'J' and resid 223 through 245 Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 271 through 273 No H-bonds generated for 'chain 'J' and resid 271 through 273' Processing helix chain 'J' and resid 274 through 284 removed outlier: 3.725A pdb=" N VAL J 284 " --> pdb=" O ILE J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 308 removed outlier: 5.291A pdb=" N LEU J 301 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA J 302 " --> pdb=" O ILE J 298 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Proline residue: J 305 - end of helix Processing helix chain 'J' and resid 318 through 341 Processing helix chain 'J' and resid 344 through 364 removed outlier: 3.736A pdb=" N ILE J 349 " --> pdb=" O TYR J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 377 Processing helix chain 'K' and resid 68 through 72 Processing helix chain 'K' and resid 78 through 84 removed outlier: 3.748A pdb=" N LEU K 82 " --> pdb=" O GLY K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 107 Processing helix chain 'K' and resid 129 through 142 removed outlier: 4.413A pdb=" N LEU K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 155 Processing helix chain 'K' and resid 155 through 166 removed outlier: 4.253A pdb=" N LYS K 159 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE K 160 " --> pdb=" O PRO K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 182 removed outlier: 3.925A pdb=" N HIS K 172 " --> pdb=" O ASN K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 197 Processing helix chain 'K' and resid 201 through 213 Processing helix chain 'K' and resid 214 through 216 No H-bonds generated for 'chain 'K' and resid 214 through 216' Processing helix chain 'K' and resid 226 through 237 Processing helix chain 'K' and resid 280 through 294 Processing helix chain 'K' and resid 307 through 317 Processing helix chain 'K' and resid 346 through 364 Processing helix chain 'K' and resid 367 through 388 removed outlier: 3.845A pdb=" N VAL K 371 " --> pdb=" O SER K 367 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER K 388 " --> pdb=" O MET K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 403 Processing helix chain 'K' and resid 408 through 419 removed outlier: 3.543A pdb=" N VAL K 419 " --> pdb=" O GLN K 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 434 Processing helix chain 'L' and resid 37 through 45 removed outlier: 3.583A pdb=" N VAL L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 88 through 98 removed outlier: 4.702A pdb=" N PHE L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 117 Processing helix chain 'L' and resid 139 through 152 Processing helix chain 'L' and resid 157 through 176 removed outlier: 3.689A pdb=" N GLN L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 193 Processing helix chain 'L' and resid 204 through 210 Processing helix chain 'L' and resid 212 through 224 Processing helix chain 'L' and resid 238 through 250 Processing helix chain 'L' and resid 299 through 311 removed outlier: 4.456A pdb=" N ALA L 303 " --> pdb=" O PRO L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 364 through 382 Processing helix chain 'L' and resid 384 through 403 removed outlier: 3.507A pdb=" N LEU L 403 " --> pdb=" O LEU L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 420 Processing helix chain 'L' and resid 425 through 436 Processing helix chain 'L' and resid 437 through 449 Processing helix chain 'L' and resid 467 through 475 Processing helix chain 'P' and resid 102 through 140 Processing helix chain 'P' and resid 143 through 149 Processing helix chain 'P' and resid 180 through 190 Processing helix chain 'P' and resid 201 through 205 Processing helix chain 'Q' and resid 5 through 14 Processing helix chain 'Q' and resid 17 through 48 Processing helix chain 'Q' and resid 52 through 58 removed outlier: 4.028A pdb=" N ILE Q 56 " --> pdb=" O LEU Q 52 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 removed outlier: 3.599A pdb=" N THR R 32 " --> pdb=" O ASP R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 60 Processing helix chain 'R' and resid 67 through 86 Processing helix chain 'S' and resid 11 through 25 removed outlier: 3.759A pdb=" N ASP S 15 " --> pdb=" O GLY S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 29 Processing helix chain 'S' and resid 33 through 38 removed outlier: 3.676A pdb=" N THR S 37 " --> pdb=" O MET S 33 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE S 38 " --> pdb=" O ARG S 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 33 through 38' Processing helix chain 'S' and resid 41 through 50 Processing helix chain 'S' and resid 52 through 72 Processing helix chain 'S' and resid 77 through 81 Processing helix chain 'S' and resid 91 through 111 Processing helix chain 'T' and resid 7 through 37 Proline residue: T 19 - end of helix Processing helix chain 'T' and resid 38 through 43 Processing helix chain 'T' and resid 48 through 52 Processing helix chain 'U' and resid 96 through 100 removed outlier: 4.159A pdb=" N GLY U 100 " --> pdb=" O SER U 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 120 Processing helix chain 'U' and resid 121 through 124 Processing helix chain 'U' and resid 141 through 151 removed outlier: 3.612A pdb=" N GLU U 151 " --> pdb=" O GLU U 147 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 163 removed outlier: 4.020A pdb=" N GLU U 163 " --> pdb=" O GLU U 160 " (cutoff:3.500A) Processing helix chain 'U' and resid 181 through 189 Processing helix chain 'U' and resid 199 through 204 Processing helix chain 'U' and resid 207 through 217 Processing helix chain 'U' and resid 262 through 279 Processing helix chain 'U' and resid 281 through 317 Proline residue: U 301 - end of helix removed outlier: 4.722A pdb=" N VAL U 313 " --> pdb=" O HIS U 309 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU U 314 " --> pdb=" O LYS U 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 7 Processing helix chain 'V' and resid 8 through 18 Processing helix chain 'V' and resid 28 through 31 Processing helix chain 'V' and resid 32 through 53 Processing helix chain 'V' and resid 61 through 72 Processing helix chain 'V' and resid 75 through 104 removed outlier: 3.702A pdb=" N ILE V 79 " --> pdb=" O TYR V 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 108 Processing helix chain 'V' and resid 109 through 133 Processing helix chain 'V' and resid 136 through 149 Processing helix chain 'V' and resid 150 through 153 Processing helix chain 'V' and resid 157 through 166 Processing helix chain 'V' and resid 171 through 204 Proline residue: V 186 - end of helix removed outlier: 3.684A pdb=" N GLU V 202 " --> pdb=" O LEU V 198 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR V 203 " --> pdb=" O PHE V 199 " (cutoff:3.500A) Processing helix chain 'V' and resid 213 through 215 No H-bonds generated for 'chain 'V' and resid 213 through 215' Processing helix chain 'V' and resid 223 through 245 Processing helix chain 'V' and resid 271 through 273 No H-bonds generated for 'chain 'V' and resid 271 through 273' Processing helix chain 'V' and resid 274 through 284 Processing helix chain 'V' and resid 286 through 304 removed outlier: 5.360A pdb=" N LEU V 301 " --> pdb=" O SER V 297 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA V 302 " --> pdb=" O ILE V 298 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET V 303 " --> pdb=" O LEU V 299 " (cutoff:3.500A) Processing helix chain 'V' and resid 305 through 308 Processing helix chain 'V' and resid 318 through 341 Processing helix chain 'V' and resid 344 through 362 removed outlier: 3.671A pdb=" N ILE V 349 " --> pdb=" O TYR V 345 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE V 362 " --> pdb=" O TYR V 358 " (cutoff:3.500A) Processing helix chain 'V' and resid 364 through 377 Processing helix chain 'W' and resid 68 through 72 Processing helix chain 'W' and resid 78 through 86 removed outlier: 3.824A pdb=" N LEU W 82 " --> pdb=" O GLY W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 107 Processing helix chain 'W' and resid 129 through 143 removed outlier: 3.958A pdb=" N LEU W 133 " --> pdb=" O ASP W 129 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA W 143 " --> pdb=" O ASN W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 166 Proline residue: W 156 - end of helix removed outlier: 4.259A pdb=" N LYS W 159 " --> pdb=" O GLN W 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE W 160 " --> pdb=" O PRO W 156 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 182 removed outlier: 3.752A pdb=" N HIS W 172 " --> pdb=" O ASN W 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 193 through 197 Processing helix chain 'W' and resid 201 through 213 Processing helix chain 'W' and resid 214 through 216 No H-bonds generated for 'chain 'W' and resid 214 through 216' Processing helix chain 'W' and resid 226 through 238 removed outlier: 3.810A pdb=" N GLN W 236 " --> pdb=" O GLN W 232 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE W 237 " --> pdb=" O VAL W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 294 Processing helix chain 'W' and resid 307 through 315 Processing helix chain 'W' and resid 346 through 364 Processing helix chain 'W' and resid 367 through 388 removed outlier: 3.844A pdb=" N VAL W 371 " --> pdb=" O SER W 367 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER W 388 " --> pdb=" O MET W 384 " (cutoff:3.500A) Processing helix chain 'W' and resid 388 through 403 Processing helix chain 'W' and resid 408 through 419 removed outlier: 3.550A pdb=" N VAL W 419 " --> pdb=" O GLN W 415 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 434 Processing helix chain 'Y' and resid 37 through 43 removed outlier: 3.918A pdb=" N GLN Y 43 " --> pdb=" O ALA Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 82 Processing helix chain 'Y' and resid 83 through 87 removed outlier: 3.975A pdb=" N ASN Y 87 " --> pdb=" O GLU Y 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 98 removed outlier: 4.721A pdb=" N PHE Y 98 " --> pdb=" O GLU Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 116 Processing helix chain 'Y' and resid 139 through 152 removed outlier: 3.655A pdb=" N GLU Y 145 " --> pdb=" O PRO Y 141 " (cutoff:3.500A) Processing helix chain 'Y' and resid 157 through 178 removed outlier: 3.779A pdb=" N GLN Y 173 " --> pdb=" O LEU Y 169 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA Y 177 " --> pdb=" O GLN Y 173 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER Y 178 " --> pdb=" O GLU Y 174 " (cutoff:3.500A) Processing helix chain 'Y' and resid 178 through 193 Processing helix chain 'Y' and resid 195 through 199 removed outlier: 3.717A pdb=" N GLN Y 199 " --> pdb=" O PRO Y 196 " (cutoff:3.500A) Processing helix chain 'Y' and resid 204 through 210 Processing helix chain 'Y' and resid 212 through 224 Processing helix chain 'Y' and resid 238 through 250 Processing helix chain 'Y' and resid 299 through 311 removed outlier: 4.412A pdb=" N ALA Y 303 " --> pdb=" O PRO Y 299 " (cutoff:3.500A) Processing helix chain 'Y' and resid 364 through 382 Processing helix chain 'Y' and resid 384 through 403 Processing helix chain 'Y' and resid 405 through 420 Processing helix chain 'Y' and resid 425 through 436 Processing helix chain 'Y' and resid 437 through 449 Processing helix chain 'Y' and resid 467 through 474 Processing helix chain 'N' and resid 33 through 71 removed outlier: 4.150A pdb=" N PHE N 47 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG N 48 " --> pdb=" O GLU N 44 " (cutoff:3.500A) Proline residue: N 51 - end of helix removed outlier: 3.545A pdb=" N LYS N 71 " --> pdb=" O PHE N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 80 Processing sheet with id=AA1, first strand: chain 'H' and resid 318 through 321 removed outlier: 6.536A pdb=" N ILE L 275 " --> pdb=" O GLY L 458 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER L 340 " --> pdb=" O VAL L 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'C' and resid 164 through 167 removed outlier: 4.053A pdb=" N LEU C 174 " --> pdb=" O PHE C 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 225 through 226 Processing sheet with id=AA5, first strand: chain 'H' and resid 154 through 158 removed outlier: 4.075A pdb=" N PHE H 165 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 232 through 233 Processing sheet with id=AA7, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=AA8, first strand: chain 'K' and resid 41 through 42 removed outlier: 3.528A pdb=" N VAL K 48 " --> pdb=" O MET K 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 257 through 261 removed outlier: 6.520A pdb=" N ILE K 258 " --> pdb=" O ALA K 440 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N GLY K 442 " --> pdb=" O ILE K 258 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU K 260 " --> pdb=" O GLY K 442 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY K 334 " --> pdb=" O SER K 275 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 257 through 261 removed outlier: 6.520A pdb=" N ILE K 258 " --> pdb=" O ALA K 440 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N GLY K 442 " --> pdb=" O ILE K 258 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU K 260 " --> pdb=" O GLY K 442 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY K 334 " --> pdb=" O SER K 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 49 through 52 Processing sheet with id=AB3, first strand: chain 'P' and resid 153 through 156 removed outlier: 4.344A pdb=" N GLU P 153 " --> pdb=" O VAL P 273 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL P 273 " --> pdb=" O GLU P 153 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET P 270 " --> pdb=" O THR P 266 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR P 266 " --> pdb=" O MET P 270 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU P 264 " --> pdb=" O ILE P 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 164 through 169 Processing sheet with id=AB5, first strand: chain 'P' and resid 225 through 226 removed outlier: 3.517A pdb=" N LEU P 251 " --> pdb=" O HIS P 242 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'U' and resid 232 through 233 Processing sheet with id=AB8, first strand: chain 'U' and resid 318 through 321 removed outlier: 6.645A pdb=" N ILE Y 275 " --> pdb=" O GLY Y 458 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL Y 359 " --> pdb=" O SER Y 340 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER Y 340 " --> pdb=" O VAL Y 359 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'V' and resid 23 through 24 Processing sheet with id=AC1, first strand: chain 'W' and resid 41 through 42 removed outlier: 6.278A pdb=" N VAL W 48 " --> pdb=" O LEU W 220 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY W 222 " --> pdb=" O VAL W 48 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA W 50 " --> pdb=" O GLY W 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 257 through 259 removed outlier: 6.508A pdb=" N ILE W 258 " --> pdb=" O ALA W 440 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Y' and resid 49 through 52 removed outlier: 4.319A pdb=" N ALA Y 234 " --> pdb=" O THR Y 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR Y 70 " --> pdb=" O ALA Y 234 " (cutoff:3.500A) 1871 hydrogen bonds defined for protein. 5349 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: 6.98 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 13718 1.42 - 1.62: 18670 1.62 - 1.82: 244 1.82 - 2.03: 4 2.03 - 2.23: 30 Bond restraints: 32666 Sorted by residual: bond pdb=" C2B HEC H 401 " pdb=" C3B HEC H 401 " ideal model delta sigma weight residual 1.334 1.478 -0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C2A HEC H 401 " pdb=" C3A HEC H 401 " ideal model delta sigma weight residual 1.334 1.476 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C2C HEC H 401 " pdb=" C3C HEC H 401 " ideal model delta sigma weight residual 1.334 1.475 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C4D HEC H 401 " pdb=" CHA HEC H 401 " ideal model delta sigma weight residual 1.378 1.483 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C4C HEC H 401 " pdb=" CHD HEC H 401 " ideal model delta sigma weight residual 1.378 1.482 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 32661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 44241 3.54 - 7.08: 164 7.08 - 10.61: 9 10.61 - 14.15: 4 14.15 - 17.69: 8 Bond angle restraints: 44426 Sorted by residual: angle pdb=" S1 FES C 301 " pdb="FE2 FES C 301 " pdb=" S2 FES C 301 " ideal model delta sigma weight residual 104.33 86.87 17.46 1.14e+00 7.69e-01 2.35e+02 angle pdb=" S1 FES C 301 " pdb="FE1 FES C 301 " pdb=" S2 FES C 301 " ideal model delta sigma weight residual 104.33 86.89 17.44 1.20e+00 6.94e-01 2.11e+02 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 88.68 15.65 1.14e+00 7.69e-01 1.88e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 88.70 15.63 1.20e+00 6.94e-01 1.70e+02 angle pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " pdb="FE2 FES P 301 " ideal model delta sigma weight residual 75.66 88.89 -13.23 1.14e+00 7.69e-01 1.35e+02 ... (remaining 44421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 18095 17.58 - 35.17: 939 35.17 - 52.75: 179 52.75 - 70.33: 40 70.33 - 87.92: 16 Dihedral angle restraints: 19269 sinusoidal: 7663 harmonic: 11606 Sorted by residual: dihedral pdb=" C2B HEM V 401 " pdb=" C3B HEM V 401 " pdb=" CAB HEM V 401 " pdb=" CBB HEM V 401 " ideal model delta sinusoidal sigma weight residual 0.00 -71.62 71.62 2 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" C2C HEC H 401 " pdb=" C3C HEC H 401 " pdb=" CAC HEC H 401 " pdb=" CBC HEC H 401 " ideal model delta sinusoidal sigma weight residual 60.00 -1.01 61.01 2 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" C2B HEC H 401 " pdb=" C3B HEC H 401 " pdb=" CAB HEC H 401 " pdb=" CBB HEC H 401 " ideal model delta sinusoidal sigma weight residual 60.00 -0.01 60.01 2 1.00e+01 1.00e-02 3.60e+01 ... (remaining 19266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3590 0.041 - 0.082: 944 0.082 - 0.123: 275 0.123 - 0.164: 49 0.164 - 0.205: 9 Chirality restraints: 4867 Sorted by residual: chirality pdb=" CA ILE V 211 " pdb=" N ILE V 211 " pdb=" C ILE V 211 " pdb=" CB ILE V 211 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA MET S 33 " pdb=" N MET S 33 " pdb=" C MET S 33 " pdb=" CB MET S 33 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA ILE H 242 " pdb=" N ILE H 242 " pdb=" C ILE H 242 " pdb=" CB ILE H 242 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 4864 not shown) Planarity restraints: 5656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC U 401 " -0.023 2.00e-02 2.50e+03 6.36e-02 9.10e+01 pdb=" C2C HEC U 401 " 0.174 2.00e-02 2.50e+03 pdb=" C3C HEC U 401 " -0.019 2.00e-02 2.50e+03 pdb=" C4C HEC U 401 " -0.009 2.00e-02 2.50e+03 pdb=" CAC HEC U 401 " -0.039 2.00e-02 2.50e+03 pdb=" CHC HEC U 401 " -0.033 2.00e-02 2.50e+03 pdb=" CHD HEC U 401 " 0.006 2.00e-02 2.50e+03 pdb=" CMC HEC U 401 " -0.049 2.00e-02 2.50e+03 pdb=" NC HEC U 401 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 34 " 0.501 9.50e-02 1.11e+02 2.25e-01 3.10e+01 pdb=" NE ARG S 34 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG S 34 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG S 34 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG S 34 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 177 " 0.242 9.50e-02 1.11e+02 1.09e-01 7.31e+00 pdb=" NE ARG J 177 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG J 177 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG J 177 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 177 " 0.007 2.00e-02 2.50e+03 ... (remaining 5653 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1218 2.72 - 3.26: 33811 3.26 - 3.81: 55345 3.81 - 4.35: 67970 4.35 - 4.90: 115062 Nonbonded interactions: 273406 Sorted by model distance: nonbonded pdb=" NE2 HIS V 182 " pdb="FE HEM V 401 " model vdw 2.175 3.080 nonbonded pdb=" OD1 ASP F 36 " pdb=" OH TYR F 90 " model vdw 2.197 3.040 nonbonded pdb=" O TRP V 165 " pdb=" OG1 THR V 174 " model vdw 2.220 3.040 nonbonded pdb=" NH2 ARG C 204 " pdb=" O LEU C 258 " model vdw 2.223 3.120 nonbonded pdb=" O GLN W 357 " pdb=" OG1 THR W 360 " model vdw 2.227 3.040 ... (remaining 273401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 80) selection = (chain 'N' and (resid 3 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 77 or (resid 78 through 80 and (nam \ e N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'C' selection = (chain 'P' and (resid 80 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 273 or resid 301)) } ncs_group { reference = chain 'D' selection = (chain 'Q' and resid 5 through 58) } ncs_group { reference = (chain 'E' and resid 24 through 90) selection = (chain 'R' and (resid 24 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 90)) } ncs_group { reference = chain 'F' selection = (chain 'S' and resid 11 through 111) } ncs_group { reference = chain 'G' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = (chain 'W' and (resid 36 through 108 or (resid 109 and (name N or name CA or nam \ e C or name O or name CB )) or resid 110 through 452 or (resid 453 and (name N o \ r name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'L' selection = (chain 'Y' and (resid 36 through 256 or resid 267 through 311 or resid 336 throu \ gh 480)) } 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: 3.160 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 35.740 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 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:9.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 1.298 32683 Z= 0.349 Angle : 0.704 36.116 44438 Z= 0.385 Chirality : 0.042 0.205 4867 Planarity : 0.006 0.225 5656 Dihedral : 11.484 87.917 11786 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.20 % Allowed : 6.04 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.14), residues: 3947 helix: 2.19 (0.11), residues: 2084 sheet: -0.29 (0.27), residues: 359 loop : -0.46 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 177 TYR 0.023 0.001 TYR J 224 PHE 0.013 0.001 PHE V 91 TRP 0.017 0.001 TRP J 141 HIS 0.006 0.001 HIS W 227 Details of bonding type rmsd covalent geometry : bond 0.00461 (32666) covalent geometry : angle 0.66508 (44426) SS BOND : bond 0.02375 ( 3) SS BOND : angle 3.47161 ( 6) hydrogen bonds : bond 0.12587 ( 1856) hydrogen bonds : angle 5.43394 ( 5349) metal coordination : bond 0.73095 ( 8) metal coordination : angle 19.63246 ( 6) Misc. bond : bond 0.21290 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 922 time to evaluate : 1.275 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: D 56 ILE cc_start: 0.6919 (mt) cc_final: 0.6714 (mt) REVERT: E 59 SER cc_start: 0.8461 (m) cc_final: 0.8025 (p) REVERT: F 35 ASP cc_start: 0.8058 (m-30) cc_final: 0.7850 (m-30) REVERT: J 273 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.8037 (p90) REVERT: K 310 HIS cc_start: 0.6682 (m-70) cc_final: 0.6223 (t-170) REVERT: Q 56 ILE cc_start: 0.6432 (mt) cc_final: 0.6086 (mt) REVERT: R 81 CYS cc_start: 0.7189 (m) cc_final: 0.6970 (t) REVERT: T 39 ARG cc_start: 0.7657 (tpp80) cc_final: 0.7305 (pmt170) outliers start: 108 outliers final: 18 residues processed: 990 average time/residue: 0.7418 time to fit residues: 861.0258 Evaluate side-chains 496 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 477 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 273 TYR Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain V residue 32 ASN Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain Y residue 271 THR Chi-restraints excluded: chain Y residue 286 HIS Chi-restraints excluded: chain Y residue 419 THR Chi-restraints excluded: chain N residue 13 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN C 181 GLN C 186 GLN C 200 HIS C 242 HIS E 39 GLN F 54 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN ** H 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 282 HIS H 309 HIS ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 260 ASN J 286 ASN K 36 GLN K 81 HIS ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 HIS K 212 HIS ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN K 291 HIS K 310 HIS K 319 GLN K 363 GLN K 435 GLN L 40 GLN L 63 GLN ** L 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 HIS L 207 ASN L 239 HIS L 249 HIS ** L 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 ASN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 452 GLN P 164 ASN ** P 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 HIS Q 48 ASN R 39 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** T 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 107 HIS ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 265 GLN U 282 HIS V 32 ASN V 44 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 312 GLN W 54 ASN W 81 HIS W 178 HIS W 212 HIS W 291 HIS W 298 HIS W 310 HIS W 363 GLN W 421 ASN W 426 ASN Y 66 GLN ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 160 GLN Y 207 ASN Y 239 HIS ** Y 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 301 ASN ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.079781 restraints weight = 58546.317| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.38 r_work: 0.2912 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.499 32683 Z= 0.417 Angle : 0.820 22.546 44438 Z= 0.400 Chirality : 0.050 0.220 4867 Planarity : 0.006 0.067 5656 Dihedral : 7.386 94.855 4440 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.34 % Allowed : 16.17 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.13), residues: 3947 helix: 1.80 (0.11), residues: 2109 sheet: -0.12 (0.28), residues: 350 loop : -0.52 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 47 TYR 0.020 0.002 TYR K 71 PHE 0.035 0.002 PHE P 231 TRP 0.030 0.002 TRP V 379 HIS 0.028 0.002 HIS L 95 Details of bonding type rmsd covalent geometry : bond 0.00990 (32666) covalent geometry : angle 0.81440 (44426) SS BOND : bond 0.01452 ( 3) SS BOND : angle 3.96982 ( 6) hydrogen bonds : bond 0.05682 ( 1856) hydrogen bonds : angle 4.84406 ( 5349) metal coordination : bond 0.04769 ( 8) metal coordination : angle 6.88561 ( 6) Misc. bond : bond 0.41706 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 502 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 LEU cc_start: 0.8544 (mp) cc_final: 0.8217 (pp) REVERT: C 153 GLU cc_start: 0.7016 (pt0) cc_final: 0.6416 (pm20) REVERT: C 172 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7819 (mtmm) REVERT: C 207 LYS cc_start: 0.4656 (OUTLIER) cc_final: 0.4409 (mttp) REVERT: C 242 HIS cc_start: 0.6768 (m90) cc_final: 0.6548 (m170) REVERT: C 250 ARG cc_start: 0.7544 (mtp85) cc_final: 0.6997 (ptp-110) REVERT: C 260 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8532 (t) REVERT: D 49 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8696 (pp20) REVERT: E 39 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8455 (pp30) REVERT: E 66 ASP cc_start: 0.8845 (p0) cc_final: 0.8625 (p0) REVERT: F 17 ILE cc_start: 0.9242 (mm) cc_final: 0.8956 (mp) REVERT: F 60 MET cc_start: 0.8932 (tpt) cc_final: 0.8683 (mmp) REVERT: G 12 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8326 (tt0) REVERT: H 99 ARG cc_start: 0.8712 (tpt170) cc_final: 0.7828 (tpm170) REVERT: H 164 MET cc_start: 0.9190 (mmm) cc_final: 0.8896 (mmm) REVERT: J 11 MET cc_start: 0.8501 (tpp) cc_final: 0.8269 (tpp) REVERT: J 273 TYR cc_start: 0.9607 (OUTLIER) cc_final: 0.8913 (p90) REVERT: J 306 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8448 (mp) REVERT: K 157 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: K 351 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8700 (mt) REVERT: L 85 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8663 (mtpt) REVERT: L 360 CYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6981 (p) REVERT: L 368 MET cc_start: 0.6276 (mtt) cc_final: 0.6059 (mtt) REVERT: P 93 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8310 (mtm-85) REVERT: P 155 LYS cc_start: 0.6120 (tptp) cc_final: 0.5807 (tptp) REVERT: P 169 TRP cc_start: 0.7431 (t60) cc_final: 0.6876 (t60) REVERT: P 170 ARG cc_start: 0.6826 (mtt180) cc_final: 0.6383 (ttm170) REVERT: P 270 MET cc_start: 0.5852 (ttm) cc_final: 0.5600 (tpt) REVERT: Q 56 ILE cc_start: 0.7345 (mt) cc_final: 0.7069 (mt) REVERT: R 47 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8281 (ttm-80) REVERT: R 81 CYS cc_start: 0.8181 (m) cc_final: 0.7889 (t) REVERT: T 12 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8305 (tt0) REVERT: T 39 ARG cc_start: 0.8481 (tpp80) cc_final: 0.6668 (pmt170) REVERT: T 47 TYR cc_start: 0.9084 (t80) cc_final: 0.8732 (t80) REVERT: U 244 MET cc_start: 0.9400 (ttp) cc_final: 0.8331 (ttp) REVERT: V 11 MET cc_start: 0.8568 (mmt) cc_final: 0.8324 (tpp) REVERT: V 148 ASN cc_start: 0.8489 (t0) cc_final: 0.8251 (t0) REVERT: V 306 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8574 (mp) REVERT: V 366 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8379 (mtm) REVERT: W 173 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8727 (p) REVERT: W 218 MET cc_start: 0.9487 (mtm) cc_final: 0.9276 (mtm) REVERT: Y 157 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: Y 305 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8901 (mt0) REVERT: Y 364 LYS cc_start: 0.8838 (mttt) cc_final: 0.8593 (mttt) REVERT: N 47 PHE cc_start: 0.9003 (m-10) cc_final: 0.7818 (t80) outliers start: 214 outliers final: 85 residues processed: 650 average time/residue: 0.6782 time to fit residues: 526.5431 Evaluate side-chains 544 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 443 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 16 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 164 ILE Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 264 THR Chi-restraints excluded: chain J residue 273 TYR Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 351 ILE Chi-restraints excluded: chain K residue 402 VAL Chi-restraints excluded: chain L residue 85 LYS Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain L residue 124 SER Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 360 CYS Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain S residue 33 MET Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain U residue 298 LEU Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain U residue 319 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain V residue 295 LEU Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 306 ILE Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain V residue 353 VAL Chi-restraints excluded: chain V residue 366 MET Chi-restraints excluded: chain V residue 376 MET Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 154 LEU Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain W residue 197 ILE Chi-restraints excluded: chain W residue 317 THR Chi-restraints excluded: chain W residue 402 VAL Chi-restraints excluded: chain W residue 413 LEU Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain Y residue 124 SER Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 157 GLU Chi-restraints excluded: chain Y residue 271 THR Chi-restraints excluded: chain Y residue 286 HIS Chi-restraints excluded: chain Y residue 305 GLN Chi-restraints excluded: chain Y residue 419 THR Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 85 optimal weight: 0.5980 chunk 381 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 360 optimal weight: 7.9990 chunk 226 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 355 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN C 181 GLN E 39 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 HIS K 239 ASN K 268 HIS ** L 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 186 GLN R 39 GLN S 28 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** T 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 284 HIS V 114 ASN V 137 GLN V 148 ASN ** V 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 172 HIS W 176 ASN ** W 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 43 GLN ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 HIS Y 223 HIS ** Y 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.084203 restraints weight = 56681.289| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.38 r_work: 0.2997 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.362 32683 Z= 0.140 Angle : 0.618 15.507 44438 Z= 0.302 Chirality : 0.041 0.199 4867 Planarity : 0.004 0.059 5656 Dihedral : 6.883 89.383 4434 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.68 % Allowed : 17.71 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.14), residues: 3947 helix: 2.14 (0.11), residues: 2104 sheet: -0.37 (0.27), residues: 366 loop : -0.35 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG V 177 TYR 0.020 0.001 TYR Q 11 PHE 0.025 0.001 PHE P 231 TRP 0.017 0.001 TRP V 141 HIS 0.012 0.001 HIS L 95 Details of bonding type rmsd covalent geometry : bond 0.00313 (32666) covalent geometry : angle 0.61220 (44426) SS BOND : bond 0.01656 ( 3) SS BOND : angle 3.08757 ( 6) hydrogen bonds : bond 0.04545 ( 1856) hydrogen bonds : angle 4.46539 ( 5349) metal coordination : bond 0.01500 ( 8) metal coordination : angle 6.76601 ( 6) Misc. bond : bond 0.27573 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 513 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8917 (m-80) cc_final: 0.8693 (m-80) REVERT: A 74 ASN cc_start: 0.9161 (p0) cc_final: 0.8425 (t0) REVERT: C 149 LEU cc_start: 0.8425 (mp) cc_final: 0.8111 (pp) REVERT: C 153 GLU cc_start: 0.7019 (pt0) cc_final: 0.6494 (pm20) REVERT: C 168 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7764 (mtpt) REVERT: C 231 PHE cc_start: 0.6305 (m-80) cc_final: 0.5703 (m-80) REVERT: C 242 HIS cc_start: 0.7019 (m90) cc_final: 0.6739 (m90) REVERT: C 250 ARG cc_start: 0.7533 (mtp85) cc_final: 0.7105 (ptp-110) REVERT: D 13 LEU cc_start: 0.8886 (tp) cc_final: 0.8556 (pp) REVERT: D 49 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8612 (pp20) REVERT: E 66 ASP cc_start: 0.8759 (p0) cc_final: 0.8488 (p0) REVERT: F 71 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8932 (tp) REVERT: G 12 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8431 (mt-10) REVERT: H 99 ARG cc_start: 0.8720 (tpt170) cc_final: 0.7863 (tpm170) REVERT: J 11 MET cc_start: 0.8179 (tpp) cc_final: 0.7705 (tpt) REVERT: J 78 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8915 (tp) REVERT: J 218 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7929 (pt) REVERT: J 306 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8407 (mp) REVERT: K 157 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: K 238 LEU cc_start: 0.8862 (pp) cc_final: 0.8657 (pt) REVERT: K 266 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9222 (tp) REVERT: K 401 LEU cc_start: 0.8940 (mt) cc_final: 0.8708 (mt) REVERT: L 146 LEU cc_start: 0.9100 (mt) cc_final: 0.8891 (mt) REVERT: L 157 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: L 360 CYS cc_start: 0.7245 (p) cc_final: 0.6868 (p) REVERT: P 172 LYS cc_start: 0.8362 (mtpt) cc_final: 0.7792 (mtmt) REVERT: Q 56 ILE cc_start: 0.7167 (mt) cc_final: 0.6880 (mt) REVERT: R 55 GLU cc_start: 0.8814 (tp30) cc_final: 0.8511 (tp30) REVERT: R 56 ARG cc_start: 0.8991 (ttp-110) cc_final: 0.8545 (ttp80) REVERT: R 66 ASP cc_start: 0.8580 (p0) cc_final: 0.8373 (p0) REVERT: R 81 CYS cc_start: 0.7837 (m) cc_final: 0.7593 (t) REVERT: T 12 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8304 (tt0) REVERT: T 39 ARG cc_start: 0.8341 (tpp80) cc_final: 0.6812 (pmt170) REVERT: T 47 TYR cc_start: 0.9015 (t80) cc_final: 0.8698 (t80) REVERT: V 11 MET cc_start: 0.8525 (mmt) cc_final: 0.8262 (tpp) REVERT: V 68 HIS cc_start: 0.8774 (OUTLIER) cc_final: 0.8081 (t-90) REVERT: V 124 MET cc_start: 0.9391 (mtp) cc_final: 0.9153 (mtp) REVERT: V 148 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8136 (t0) REVERT: V 255 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.8067 (t0) REVERT: V 306 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8487 (mp) REVERT: V 366 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8220 (mtm) REVERT: W 384 MET cc_start: 0.8890 (mtt) cc_final: 0.8662 (mtt) REVERT: Y 157 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: Y 368 MET cc_start: 0.8532 (mmm) cc_final: 0.8252 (tpp) REVERT: Y 472 ARG cc_start: 0.8962 (tpt90) cc_final: 0.8658 (tpt90) REVERT: N 47 PHE cc_start: 0.8922 (m-10) cc_final: 0.7760 (t80) outliers start: 158 outliers final: 46 residues processed: 619 average time/residue: 0.6868 time to fit residues: 506.9641 Evaluate side-chains 512 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 451 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain G residue 16 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 278 TYR Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 316 MET Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 268 HIS Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 438 MET Chi-restraints excluded: chain L residue 157 GLU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 68 HIS Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain V residue 148 ASN Chi-restraints excluded: chain V residue 255 ASN Chi-restraints excluded: chain V residue 306 ILE Chi-restraints excluded: chain V residue 366 MET Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain W residue 197 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 157 GLU Chi-restraints excluded: chain Y residue 271 THR Chi-restraints excluded: chain Y residue 286 HIS Chi-restraints excluded: chain Y residue 360 CYS Chi-restraints excluded: chain Y residue 419 THR Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 137 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 0.1980 chunk 316 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 355 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 GLN H 265 GLN ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 HIS ** L 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 GLN ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 GLN R 39 GLN S 28 ASN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** T 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 148 ASN ** V 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.084500 restraints weight = 56535.891| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.37 r_work: 0.3000 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.362 32683 Z= 0.142 Angle : 0.602 15.848 44438 Z= 0.292 Chirality : 0.041 0.192 4867 Planarity : 0.004 0.047 5656 Dihedral : 6.716 89.384 4432 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.15 % Allowed : 18.86 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.14), residues: 3947 helix: 2.19 (0.11), residues: 2122 sheet: -0.34 (0.27), residues: 365 loop : -0.30 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 49 TYR 0.018 0.001 TYR V 224 PHE 0.026 0.001 PHE P 231 TRP 0.015 0.001 TRP V 141 HIS 0.007 0.001 HIS L 95 Details of bonding type rmsd covalent geometry : bond 0.00326 (32666) covalent geometry : angle 0.59679 (44426) SS BOND : bond 0.01250 ( 3) SS BOND : angle 2.95455 ( 6) hydrogen bonds : bond 0.04323 ( 1856) hydrogen bonds : angle 4.35878 ( 5349) metal coordination : bond 0.01070 ( 8) metal coordination : angle 6.20253 ( 6) Misc. bond : bond 0.26615 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 492 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8633 (mtpm) REVERT: A 74 ASN cc_start: 0.9209 (p0) cc_final: 0.8401 (t0) REVERT: C 149 LEU cc_start: 0.8426 (mp) cc_final: 0.8105 (pp) REVERT: C 153 GLU cc_start: 0.6896 (pt0) cc_final: 0.6378 (pm20) REVERT: C 163 LYS cc_start: 0.6881 (mmtt) cc_final: 0.6591 (mmtm) REVERT: C 168 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7874 (mtpt) REVERT: C 172 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7573 (mppt) REVERT: C 177 ARG cc_start: 0.4196 (OUTLIER) cc_final: 0.1954 (ttp-170) REVERT: C 231 PHE cc_start: 0.6982 (m-80) cc_final: 0.6748 (m-80) REVERT: D 49 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8631 (pp20) REVERT: E 57 VAL cc_start: 0.8175 (t) cc_final: 0.7964 (p) REVERT: E 66 ASP cc_start: 0.8778 (p0) cc_final: 0.8517 (p0) REVERT: F 17 ILE cc_start: 0.9220 (mm) cc_final: 0.8914 (mp) REVERT: F 40 GLU cc_start: 0.8373 (mp0) cc_final: 0.8114 (mt-10) REVERT: F 79 GLU cc_start: 0.8616 (mp0) cc_final: 0.8399 (mp0) REVERT: H 99 ARG cc_start: 0.8710 (tpt170) cc_final: 0.7866 (tpm170) REVERT: H 164 MET cc_start: 0.9174 (mmm) cc_final: 0.8903 (mmm) REVERT: H 190 ASN cc_start: 0.8553 (t0) cc_final: 0.8322 (t0) REVERT: H 240 GLN cc_start: 0.8072 (mp10) cc_final: 0.7862 (mp10) REVERT: J 11 MET cc_start: 0.8193 (tpp) cc_final: 0.7733 (tpt) REVERT: J 218 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8058 (pt) REVERT: J 306 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8406 (mp) REVERT: K 113 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8557 (p) REVERT: K 157 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: K 203 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8907 (mp0) REVERT: K 238 LEU cc_start: 0.8777 (pp) cc_final: 0.8416 (mt) REVERT: K 266 LEU cc_start: 0.9508 (mp) cc_final: 0.9244 (tp) REVERT: K 301 ARG cc_start: 0.9110 (mtm180) cc_final: 0.8473 (mtm180) REVERT: L 146 LEU cc_start: 0.9088 (mt) cc_final: 0.8876 (mt) REVERT: L 157 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: L 360 CYS cc_start: 0.7210 (p) cc_final: 0.6913 (p) REVERT: P 92 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.7968 (mtp-110) REVERT: P 172 LYS cc_start: 0.8454 (mtpt) cc_final: 0.7928 (mtmt) REVERT: P 231 PHE cc_start: 0.7932 (m-10) cc_final: 0.7476 (m-10) REVERT: P 242 HIS cc_start: 0.7177 (m-70) cc_final: 0.6941 (m-70) REVERT: P 250 ARG cc_start: 0.7023 (mtp85) cc_final: 0.6680 (ptp-110) REVERT: Q 56 ILE cc_start: 0.7236 (mt) cc_final: 0.6965 (mt) REVERT: R 37 CYS cc_start: 0.8605 (m) cc_final: 0.8372 (m) REVERT: R 55 GLU cc_start: 0.8874 (tp30) cc_final: 0.8510 (tp30) REVERT: R 66 ASP cc_start: 0.8498 (p0) cc_final: 0.8282 (p0) REVERT: R 81 CYS cc_start: 0.7814 (m) cc_final: 0.7239 (t) REVERT: R 85 LYS cc_start: 0.8739 (ptmt) cc_final: 0.8507 (ptmt) REVERT: T 12 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8331 (tt0) REVERT: T 39 ARG cc_start: 0.8507 (tpp80) cc_final: 0.6766 (pmt170) REVERT: T 47 TYR cc_start: 0.9014 (t80) cc_final: 0.8669 (t80) REVERT: V 11 MET cc_start: 0.8573 (mmt) cc_final: 0.8311 (tpp) REVERT: V 68 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.8160 (t-90) REVERT: V 148 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7984 (t0) REVERT: V 366 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8208 (mtm) REVERT: W 218 MET cc_start: 0.9542 (mtm) cc_final: 0.9268 (mtm) REVERT: W 268 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.8072 (p-80) REVERT: W 384 MET cc_start: 0.8918 (mtt) cc_final: 0.8698 (mtt) REVERT: Y 157 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: Y 368 MET cc_start: 0.8573 (mmm) cc_final: 0.8250 (tpp) REVERT: Y 472 ARG cc_start: 0.8896 (tpt90) cc_final: 0.8580 (tpt90) REVERT: N 47 PHE cc_start: 0.8888 (m-10) cc_final: 0.7750 (t80) outliers start: 140 outliers final: 51 residues processed: 584 average time/residue: 0.6833 time to fit residues: 475.8319 Evaluate side-chains 525 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 459 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 16 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 316 MET Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 240 MET Chi-restraints excluded: chain L residue 157 GLU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 68 HIS Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain V residue 148 ASN Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 171 ASP Chi-restraints excluded: chain V residue 278 TYR Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain V residue 366 MET Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain W residue 197 ILE Chi-restraints excluded: chain W residue 268 HIS Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 157 GLU Chi-restraints excluded: chain Y residue 271 THR Chi-restraints excluded: chain Y residue 286 HIS Chi-restraints excluded: chain Y residue 360 CYS Chi-restraints excluded: chain Y residue 419 THR Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 39 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 316 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 287 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 270 optimal weight: 0.1980 chunk 139 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 GLN ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 HIS ** L 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 GLN R 39 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** U 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 452 GLN N 13 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.084390 restraints weight = 56819.596| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.38 r_work: 0.3001 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.341 32683 Z= 0.144 Angle : 0.597 16.247 44438 Z= 0.289 Chirality : 0.041 0.217 4867 Planarity : 0.004 0.045 5656 Dihedral : 6.630 88.994 4430 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.65 % Allowed : 19.01 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.14), residues: 3947 helix: 2.25 (0.11), residues: 2114 sheet: -0.38 (0.27), residues: 379 loop : -0.23 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 47 TYR 0.019 0.001 TYR V 224 PHE 0.023 0.001 PHE Y 341 TRP 0.022 0.001 TRP J 141 HIS 0.007 0.001 HIS L 95 Details of bonding type rmsd covalent geometry : bond 0.00336 (32666) covalent geometry : angle 0.59262 (44426) SS BOND : bond 0.01421 ( 3) SS BOND : angle 2.29183 ( 6) hydrogen bonds : bond 0.04238 ( 1856) hydrogen bonds : angle 4.30749 ( 5349) metal coordination : bond 0.00855 ( 8) metal coordination : angle 5.80255 ( 6) Misc. bond : bond 0.25324 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 494 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8648 (mtpm) REVERT: A 74 ASN cc_start: 0.9193 (p0) cc_final: 0.8413 (t0) REVERT: C 149 LEU cc_start: 0.8434 (mp) cc_final: 0.8229 (pp) REVERT: C 163 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6803 (mmtm) REVERT: C 172 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7552 (mppt) REVERT: C 177 ARG cc_start: 0.4046 (OUTLIER) cc_final: 0.1858 (ttp-170) REVERT: D 13 LEU cc_start: 0.8896 (tp) cc_final: 0.8528 (pp) REVERT: D 49 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8634 (pp20) REVERT: E 55 GLU cc_start: 0.8943 (tp30) cc_final: 0.8695 (tt0) REVERT: E 57 VAL cc_start: 0.8173 (t) cc_final: 0.7851 (p) REVERT: E 66 ASP cc_start: 0.8712 (p0) cc_final: 0.8495 (p0) REVERT: F 40 GLU cc_start: 0.8301 (mp0) cc_final: 0.8094 (mt-10) REVERT: F 79 GLU cc_start: 0.8613 (mp0) cc_final: 0.8403 (mp0) REVERT: G 12 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8197 (tt0) REVERT: H 99 ARG cc_start: 0.8718 (tpt170) cc_final: 0.7860 (tpm170) REVERT: H 142 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: H 164 MET cc_start: 0.9164 (mmm) cc_final: 0.8898 (mmm) REVERT: H 166 MET cc_start: 0.8986 (mmt) cc_final: 0.8556 (mmt) REVERT: H 190 ASN cc_start: 0.8592 (t0) cc_final: 0.8322 (t0) REVERT: J 11 MET cc_start: 0.8219 (tpp) cc_final: 0.7738 (tpt) REVERT: J 53 MET cc_start: 0.9547 (OUTLIER) cc_final: 0.9337 (mtp) REVERT: J 306 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8410 (mp) REVERT: K 113 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8567 (p) REVERT: K 157 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: K 203 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8904 (mp0) REVERT: K 238 LEU cc_start: 0.8773 (pp) cc_final: 0.8359 (mt) REVERT: K 266 LEU cc_start: 0.9514 (mp) cc_final: 0.9305 (tp) REVERT: K 301 ARG cc_start: 0.9127 (mtm180) cc_final: 0.8367 (mtm180) REVERT: L 146 LEU cc_start: 0.9079 (mt) cc_final: 0.8851 (mt) REVERT: L 157 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: P 172 LYS cc_start: 0.8471 (mtpt) cc_final: 0.7972 (mtmt) REVERT: P 231 PHE cc_start: 0.7854 (m-10) cc_final: 0.7452 (m-10) REVERT: P 250 ARG cc_start: 0.7034 (mtp85) cc_final: 0.6726 (ptp-110) REVERT: Q 56 ILE cc_start: 0.7501 (mt) cc_final: 0.7225 (mt) REVERT: R 55 GLU cc_start: 0.8836 (tp30) cc_final: 0.8447 (tp30) REVERT: R 66 ASP cc_start: 0.8529 (p0) cc_final: 0.8267 (p0) REVERT: R 81 CYS cc_start: 0.7757 (m) cc_final: 0.7225 (t) REVERT: T 39 ARG cc_start: 0.8396 (tpp80) cc_final: 0.6746 (pmt170) REVERT: T 47 TYR cc_start: 0.9007 (t80) cc_final: 0.8667 (t80) REVERT: U 142 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: V 11 MET cc_start: 0.8567 (mmt) cc_final: 0.8316 (tpp) REVERT: V 68 HIS cc_start: 0.8769 (OUTLIER) cc_final: 0.8156 (t-90) REVERT: V 102 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8776 (tt) REVERT: V 148 ASN cc_start: 0.8266 (t0) cc_final: 0.7981 (t0) REVERT: V 306 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8455 (mp) REVERT: V 366 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8191 (mtm) REVERT: W 203 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8882 (mp0) REVERT: W 218 MET cc_start: 0.9550 (mtm) cc_final: 0.9326 (mtm) REVERT: W 268 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7945 (p-80) REVERT: Y 157 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: Y 368 MET cc_start: 0.8575 (mmm) cc_final: 0.8248 (tpp) REVERT: N 47 PHE cc_start: 0.8926 (m-10) cc_final: 0.7761 (t80) outliers start: 157 outliers final: 65 residues processed: 602 average time/residue: 0.6649 time to fit residues: 479.1235 Evaluate side-chains 533 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 450 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain G residue 16 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 316 MET Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain K residue 438 MET Chi-restraints excluded: chain L residue 157 GLU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 14 ILE Chi-restraints excluded: chain V residue 68 HIS Chi-restraints excluded: chain V residue 74 ASN Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 171 ASP Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 278 TYR Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 306 ILE Chi-restraints excluded: chain V residue 316 MET Chi-restraints excluded: chain V residue 333 LEU Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain V residue 366 MET Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain W residue 197 ILE Chi-restraints excluded: chain W residue 203 GLU Chi-restraints excluded: chain W residue 268 HIS Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain Y residue 85 LYS Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 157 GLU Chi-restraints excluded: chain Y residue 179 MET Chi-restraints excluded: chain Y residue 271 THR Chi-restraints excluded: chain Y residue 286 HIS Chi-restraints excluded: chain Y residue 360 CYS Chi-restraints excluded: chain Y residue 419 THR Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 236 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 chunk 325 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 339 optimal weight: 1.9990 chunk 327 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 373 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN E 39 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 GLN ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** T 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.080354 restraints weight = 57400.850| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.34 r_work: 0.2925 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.394 32683 Z= 0.296 Angle : 0.707 19.283 44438 Z= 0.341 Chirality : 0.045 0.209 4867 Planarity : 0.005 0.050 5656 Dihedral : 6.822 88.867 4427 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.95 % Allowed : 19.13 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.14), residues: 3947 helix: 2.01 (0.11), residues: 2117 sheet: -0.37 (0.27), residues: 380 loop : -0.30 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 49 TYR 0.021 0.002 TYR V 224 PHE 0.025 0.002 PHE C 231 TRP 0.020 0.001 TRP V 379 HIS 0.014 0.002 HIS J 196 Details of bonding type rmsd covalent geometry : bond 0.00710 (32666) covalent geometry : angle 0.70206 (44426) SS BOND : bond 0.01311 ( 3) SS BOND : angle 2.87553 ( 6) hydrogen bonds : bond 0.04904 ( 1856) hydrogen bonds : angle 4.51606 ( 5349) metal coordination : bond 0.01386 ( 8) metal coordination : angle 6.48835 ( 6) Misc. bond : bond 0.34208 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 449 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8804 (mtpt) REVERT: C 153 GLU cc_start: 0.7047 (pt0) cc_final: 0.6574 (pm20) REVERT: C 163 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6783 (mmtm) REVERT: C 168 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7840 (mtpt) REVERT: C 172 LYS cc_start: 0.8075 (mtmm) cc_final: 0.7495 (mppt) REVERT: C 177 ARG cc_start: 0.4171 (OUTLIER) cc_final: 0.1883 (ttp-170) REVERT: C 231 PHE cc_start: 0.7774 (m-10) cc_final: 0.7293 (m-10) REVERT: D 13 LEU cc_start: 0.8991 (tp) cc_final: 0.8583 (pp) REVERT: D 49 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8613 (pp20) REVERT: F 17 ILE cc_start: 0.9211 (mm) cc_final: 0.8891 (mp) REVERT: F 40 GLU cc_start: 0.8258 (mp0) cc_final: 0.7963 (mt-10) REVERT: F 79 GLU cc_start: 0.8678 (mp0) cc_final: 0.8452 (mp0) REVERT: G 12 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8165 (tt0) REVERT: H 99 ARG cc_start: 0.8728 (tpt170) cc_final: 0.7870 (tpm170) REVERT: H 142 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8613 (tt0) REVERT: H 164 MET cc_start: 0.9116 (mmm) cc_final: 0.8885 (mmm) REVERT: H 190 ASN cc_start: 0.8670 (t0) cc_final: 0.8451 (t0) REVERT: H 244 MET cc_start: 0.9299 (ttp) cc_final: 0.8312 (ttp) REVERT: J 11 MET cc_start: 0.8288 (tpp) cc_final: 0.8014 (tpp) REVERT: J 68 HIS cc_start: 0.8847 (OUTLIER) cc_final: 0.7893 (t-90) REVERT: J 306 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8421 (mp) REVERT: K 157 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: K 203 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8877 (mp0) REVERT: K 238 LEU cc_start: 0.8818 (pp) cc_final: 0.8398 (mt) REVERT: K 266 LEU cc_start: 0.9530 (mp) cc_final: 0.9267 (tp) REVERT: P 92 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.7927 (mtp-110) REVERT: P 95 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6957 (mt-10) REVERT: P 172 LYS cc_start: 0.8421 (mtpt) cc_final: 0.7931 (mtmt) REVERT: Q 56 ILE cc_start: 0.7182 (mt) cc_final: 0.6905 (mt) REVERT: R 55 GLU cc_start: 0.8878 (tp30) cc_final: 0.8509 (tp30) REVERT: R 66 ASP cc_start: 0.8513 (p0) cc_final: 0.8296 (p0) REVERT: R 81 CYS cc_start: 0.8292 (m) cc_final: 0.7923 (t) REVERT: S 33 MET cc_start: 0.8867 (mmt) cc_final: 0.8377 (mtt) REVERT: T 12 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8143 (tt0) REVERT: T 39 ARG cc_start: 0.8393 (tpp80) cc_final: 0.6726 (pmt170) REVERT: T 47 TYR cc_start: 0.9108 (t80) cc_final: 0.8643 (t80) REVERT: U 142 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8023 (tp30) REVERT: U 190 ASN cc_start: 0.8565 (t0) cc_final: 0.8350 (t0) REVERT: V 11 MET cc_start: 0.8623 (mmt) cc_final: 0.8345 (tpp) REVERT: V 68 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.7970 (t-90) REVERT: V 148 ASN cc_start: 0.8317 (t0) cc_final: 0.7999 (t0) REVERT: V 218 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7999 (pt) REVERT: V 306 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8487 (mp) REVERT: V 366 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8239 (mtm) REVERT: W 157 GLN cc_start: 0.9151 (tp40) cc_final: 0.8950 (tm-30) REVERT: W 203 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8890 (mp0) REVERT: W 218 MET cc_start: 0.9574 (mtm) cc_final: 0.9368 (mtm) REVERT: Y 157 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: Y 368 MET cc_start: 0.8770 (mmm) cc_final: 0.8442 (tpp) REVERT: N 47 PHE cc_start: 0.8960 (m-10) cc_final: 0.7743 (t80) outliers start: 167 outliers final: 74 residues processed: 566 average time/residue: 0.6612 time to fit residues: 446.8927 Evaluate side-chains 518 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 426 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain G residue 16 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain J residue 68 HIS Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain K residue 438 MET Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 16 ASN Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 216 THR Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 298 LEU Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 68 HIS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 278 TYR Chi-restraints excluded: chain V residue 306 ILE Chi-restraints excluded: chain V residue 332 LEU Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain V residue 366 MET Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain W residue 197 ILE Chi-restraints excluded: chain W residue 203 GLU Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 85 LYS Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 157 GLU Chi-restraints excluded: chain Y residue 271 THR Chi-restraints excluded: chain Y residue 286 HIS Chi-restraints excluded: chain Y residue 360 CYS Chi-restraints excluded: chain Y residue 419 THR Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 64 optimal weight: 0.7980 chunk 210 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 chunk 253 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 GLN J 114 ASN ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** L 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 373 GLN ** P 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** T 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 74 ASN ** V 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 119 HIS ** Y 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.083765 restraints weight = 57129.423| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.36 r_work: 0.2988 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.325 32683 Z= 0.135 Angle : 0.613 14.792 44438 Z= 0.298 Chirality : 0.041 0.197 4867 Planarity : 0.004 0.046 5656 Dihedral : 6.634 88.852 4425 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.58 % Allowed : 20.91 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.14), residues: 3947 helix: 2.19 (0.11), residues: 2115 sheet: -0.10 (0.29), residues: 354 loop : -0.24 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 49 TYR 0.018 0.001 TYR V 224 PHE 0.026 0.001 PHE Y 341 TRP 0.020 0.001 TRP J 141 HIS 0.007 0.001 HIS K 268 Details of bonding type rmsd covalent geometry : bond 0.00311 (32666) covalent geometry : angle 0.60824 (44426) SS BOND : bond 0.01061 ( 3) SS BOND : angle 2.33525 ( 6) hydrogen bonds : bond 0.04203 ( 1856) hydrogen bonds : angle 4.34256 ( 5349) metal coordination : bond 0.00788 ( 8) metal coordination : angle 6.03145 ( 6) Misc. bond : bond 0.24834 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 471 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8517 (mtpm) REVERT: A 74 ASN cc_start: 0.9044 (p0) cc_final: 0.8331 (t0) REVERT: C 154 ILE cc_start: 0.4425 (OUTLIER) cc_final: 0.3750 (tp) REVERT: C 163 LYS cc_start: 0.7142 (mmtt) cc_final: 0.6779 (mmtm) REVERT: C 172 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7500 (mppt) REVERT: C 177 ARG cc_start: 0.4167 (OUTLIER) cc_final: 0.1876 (ttp-170) REVERT: D 49 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8675 (pp20) REVERT: E 57 VAL cc_start: 0.8166 (t) cc_final: 0.7896 (p) REVERT: F 40 GLU cc_start: 0.8276 (mp0) cc_final: 0.8030 (mt-10) REVERT: F 79 GLU cc_start: 0.8689 (mp0) cc_final: 0.8473 (mp0) REVERT: G 12 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8234 (tt0) REVERT: H 99 ARG cc_start: 0.8713 (tpt170) cc_final: 0.7843 (tpm170) REVERT: H 142 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: H 164 MET cc_start: 0.9118 (mmm) cc_final: 0.8815 (mmm) REVERT: H 166 MET cc_start: 0.9008 (mmt) cc_final: 0.8593 (mmt) REVERT: J 11 MET cc_start: 0.8253 (tpp) cc_final: 0.7970 (tpp) REVERT: J 306 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8442 (mp) REVERT: K 157 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: K 203 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8886 (mp0) REVERT: K 266 LEU cc_start: 0.9499 (mp) cc_final: 0.9278 (tp) REVERT: K 301 ARG cc_start: 0.9030 (mtm-85) cc_final: 0.7856 (mtm180) REVERT: L 95 HIS cc_start: 0.9268 (OUTLIER) cc_final: 0.8057 (m-70) REVERT: L 157 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: P 92 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.7866 (mtp-110) REVERT: R 55 GLU cc_start: 0.8853 (tp30) cc_final: 0.8468 (tp30) REVERT: R 66 ASP cc_start: 0.8485 (p0) cc_final: 0.8221 (p0) REVERT: R 81 CYS cc_start: 0.8096 (m) cc_final: 0.7739 (t) REVERT: R 84 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.8248 (t70) REVERT: S 33 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8410 (mtt) REVERT: T 12 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8223 (tt0) REVERT: T 39 ARG cc_start: 0.8360 (tpp80) cc_final: 0.6722 (pmt170) REVERT: T 47 TYR cc_start: 0.9038 (t80) cc_final: 0.8649 (t80) REVERT: U 142 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7915 (tp30) REVERT: U 190 ASN cc_start: 0.8644 (t0) cc_final: 0.8436 (t0) REVERT: V 11 MET cc_start: 0.8623 (mmt) cc_final: 0.8336 (tpp) REVERT: V 68 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.8093 (t-90) REVERT: V 148 ASN cc_start: 0.8298 (t0) cc_final: 0.7896 (t160) REVERT: V 306 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8479 (mp) REVERT: V 366 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8165 (mtm) REVERT: W 157 GLN cc_start: 0.9154 (tp40) cc_final: 0.8884 (tm-30) REVERT: W 203 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8867 (mp0) REVERT: W 268 HIS cc_start: 0.8307 (OUTLIER) cc_final: 0.7939 (p-80) REVERT: Y 157 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: Y 368 MET cc_start: 0.8718 (mmm) cc_final: 0.8332 (tpp) REVERT: N 47 PHE cc_start: 0.8914 (m-10) cc_final: 0.7746 (t80) REVERT: N 50 VAL cc_start: 0.8682 (t) cc_final: 0.8481 (t) outliers start: 121 outliers final: 53 residues processed: 563 average time/residue: 0.6515 time to fit residues: 440.2802 Evaluate side-chains 507 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 435 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 16 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain J residue 278 TYR Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 438 MET Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 157 GLU Chi-restraints excluded: chain L residue 255 TRP Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain S residue 33 MET Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain U residue 298 LEU Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 68 HIS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain V residue 278 TYR Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 306 ILE Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain V residue 366 MET Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 69 SER Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain W residue 197 ILE Chi-restraints excluded: chain W residue 203 GLU Chi-restraints excluded: chain W residue 227 HIS Chi-restraints excluded: chain W residue 267 VAL Chi-restraints excluded: chain W residue 268 HIS Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 157 GLU Chi-restraints excluded: chain Y residue 271 THR Chi-restraints excluded: chain Y residue 286 HIS Chi-restraints excluded: chain Y residue 360 CYS Chi-restraints excluded: chain Y residue 419 THR Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 383 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 GLN J 44 GLN ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** T 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.079011 restraints weight = 58092.783| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.36 r_work: 0.2908 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.415 32683 Z= 0.323 Angle : 0.735 19.752 44438 Z= 0.356 Chirality : 0.047 0.230 4867 Planarity : 0.005 0.048 5656 Dihedral : 6.890 89.444 4425 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.41 % Allowed : 20.55 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.14), residues: 3947 helix: 1.95 (0.11), residues: 2109 sheet: -0.23 (0.29), residues: 360 loop : -0.34 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 60 TYR 0.021 0.002 TYR J 224 PHE 0.029 0.002 PHE Y 341 TRP 0.017 0.002 TRP V 379 HIS 0.014 0.002 HIS J 196 Details of bonding type rmsd covalent geometry : bond 0.00773 (32666) covalent geometry : angle 0.73013 (44426) SS BOND : bond 0.01401 ( 3) SS BOND : angle 2.60574 ( 6) hydrogen bonds : bond 0.05005 ( 1856) hydrogen bonds : angle 4.57122 ( 5349) metal coordination : bond 0.01465 ( 8) metal coordination : angle 7.13595 ( 6) Misc. bond : bond 0.35557 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 436 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 74 ASN cc_start: 0.9063 (p0) cc_final: 0.8282 (t0) REVERT: C 143 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8027 (t) REVERT: C 154 ILE cc_start: 0.4250 (OUTLIER) cc_final: 0.3589 (tp) REVERT: C 168 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7752 (mtpt) REVERT: C 172 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7537 (mppt) REVERT: C 177 ARG cc_start: 0.4297 (OUTLIER) cc_final: 0.1930 (ttp-170) REVERT: C 203 ASP cc_start: 0.8843 (t0) cc_final: 0.8367 (p0) REVERT: D 49 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8619 (pp20) REVERT: E 57 VAL cc_start: 0.8196 (t) cc_final: 0.7961 (p) REVERT: F 17 ILE cc_start: 0.9191 (mm) cc_final: 0.8914 (mp) REVERT: F 54 ASN cc_start: 0.8695 (p0) cc_final: 0.8484 (p0) REVERT: F 79 GLU cc_start: 0.8691 (mp0) cc_final: 0.8439 (mp0) REVERT: G 12 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8229 (tt0) REVERT: H 99 ARG cc_start: 0.8714 (tpt170) cc_final: 0.7863 (tpm170) REVERT: H 164 MET cc_start: 0.9101 (mmm) cc_final: 0.8881 (mmm) REVERT: H 244 MET cc_start: 0.9286 (ttp) cc_final: 0.8355 (ttp) REVERT: J 11 MET cc_start: 0.8307 (tpp) cc_final: 0.8031 (tpp) REVERT: J 68 HIS cc_start: 0.8895 (OUTLIER) cc_final: 0.7875 (t-90) REVERT: J 146 ILE cc_start: 0.8745 (mm) cc_final: 0.8526 (mt) REVERT: J 273 TYR cc_start: 0.9681 (OUTLIER) cc_final: 0.9122 (p90) REVERT: J 306 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8467 (mp) REVERT: K 157 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: K 203 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8902 (mp0) REVERT: K 238 LEU cc_start: 0.8894 (pp) cc_final: 0.8391 (mt) REVERT: K 301 ARG cc_start: 0.9089 (mtm-85) cc_final: 0.8187 (mtm180) REVERT: L 95 HIS cc_start: 0.9299 (OUTLIER) cc_final: 0.8341 (m-70) REVERT: L 153 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7833 (p0) REVERT: L 286 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.8203 (t-90) REVERT: P 92 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8022 (mtp-110) REVERT: P 95 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: R 48 GLU cc_start: 0.8690 (pt0) cc_final: 0.8448 (pp20) REVERT: R 49 ARG cc_start: 0.9373 (ttm110) cc_final: 0.9149 (ttm-80) REVERT: R 55 GLU cc_start: 0.8889 (tp30) cc_final: 0.8516 (tp30) REVERT: R 66 ASP cc_start: 0.8505 (p0) cc_final: 0.8229 (p0) REVERT: R 81 CYS cc_start: 0.8286 (m) cc_final: 0.7938 (t) REVERT: S 33 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8480 (mtt) REVERT: T 12 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8169 (tt0) REVERT: T 39 ARG cc_start: 0.8449 (tpp80) cc_final: 0.6784 (pmt170) REVERT: T 47 TYR cc_start: 0.9111 (t80) cc_final: 0.8681 (t80) REVERT: U 142 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: U 190 ASN cc_start: 0.8761 (t0) cc_final: 0.8545 (t0) REVERT: U 244 MET cc_start: 0.9399 (ttp) cc_final: 0.8285 (ttp) REVERT: V 11 MET cc_start: 0.8665 (mmt) cc_final: 0.8371 (tpp) REVERT: V 68 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.8055 (t-90) REVERT: V 102 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9101 (tt) REVERT: V 148 ASN cc_start: 0.8498 (t0) cc_final: 0.8120 (t160) REVERT: V 306 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8484 (mp) REVERT: V 366 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8273 (mtm) REVERT: W 157 GLN cc_start: 0.9167 (tp40) cc_final: 0.8902 (tm-30) REVERT: W 203 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8895 (mp0) REVERT: W 384 MET cc_start: 0.8868 (mtt) cc_final: 0.8663 (mtt) REVERT: Y 157 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: Y 163 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8491 (mtmp) REVERT: Y 368 MET cc_start: 0.8789 (mmm) cc_final: 0.8478 (tpp) REVERT: N 13 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7430 (p90) REVERT: N 47 PHE cc_start: 0.8965 (m-10) cc_final: 0.7750 (t80) outliers start: 149 outliers final: 68 residues processed: 543 average time/residue: 0.6543 time to fit residues: 426.8027 Evaluate side-chains 509 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 416 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 16 ASN Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 68 HIS Chi-restraints excluded: chain J residue 273 TYR Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 416 ILE Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 153 ASN Chi-restraints excluded: chain L residue 255 TRP Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 286 HIS Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 271 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain S residue 33 MET Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 216 THR Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain U residue 298 LEU Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 68 HIS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 201 HIS Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain V residue 278 TYR Chi-restraints excluded: chain V residue 306 ILE Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain V residue 366 MET Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 69 SER Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain W residue 197 ILE Chi-restraints excluded: chain W residue 203 GLU Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 85 LYS Chi-restraints excluded: chain Y residue 116 MET Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 157 GLU Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 271 THR Chi-restraints excluded: chain Y residue 286 HIS Chi-restraints excluded: chain Y residue 419 THR Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 132 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 358 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 346 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 GLN ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** T 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 GLN ** V 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 452 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082304 restraints weight = 57106.968| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.34 r_work: 0.2958 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.339 32683 Z= 0.168 Angle : 0.656 16.347 44438 Z= 0.319 Chirality : 0.042 0.206 4867 Planarity : 0.004 0.047 5656 Dihedral : 6.714 87.869 4425 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.61 % Allowed : 21.68 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.14), residues: 3947 helix: 2.10 (0.11), residues: 2115 sheet: -0.24 (0.28), residues: 357 loop : -0.30 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 47 TYR 0.019 0.001 TYR V 224 PHE 0.027 0.001 PHE Y 341 TRP 0.019 0.001 TRP J 141 HIS 0.009 0.001 HIS L 286 Details of bonding type rmsd covalent geometry : bond 0.00398 (32666) covalent geometry : angle 0.65191 (44426) SS BOND : bond 0.01133 ( 3) SS BOND : angle 2.50090 ( 6) hydrogen bonds : bond 0.04383 ( 1856) hydrogen bonds : angle 4.41822 ( 5349) metal coordination : bond 0.00892 ( 8) metal coordination : angle 6.25127 ( 6) Misc. bond : bond 0.26781 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7894 Ramachandran restraints generated. 3947 Oldfield, 0 Emsley, 3947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 448 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.9066 (p0) cc_final: 0.8270 (t0) REVERT: C 143 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.7992 (t) REVERT: C 154 ILE cc_start: 0.4354 (OUTLIER) cc_final: 0.3706 (tp) REVERT: C 172 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7487 (mppt) REVERT: C 177 ARG cc_start: 0.4134 (OUTLIER) cc_final: 0.1840 (ttp-170) REVERT: C 203 ASP cc_start: 0.8852 (t0) cc_final: 0.8361 (p0) REVERT: D 49 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8632 (pp20) REVERT: E 57 VAL cc_start: 0.8133 (t) cc_final: 0.7839 (p) REVERT: F 17 ILE cc_start: 0.9184 (mm) cc_final: 0.8899 (mp) REVERT: F 79 GLU cc_start: 0.8709 (mp0) cc_final: 0.8477 (mp0) REVERT: G 12 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8210 (tt0) REVERT: H 99 ARG cc_start: 0.8673 (tpt170) cc_final: 0.7822 (tpm170) REVERT: H 164 MET cc_start: 0.9137 (mmm) cc_final: 0.8848 (mmm) REVERT: J 11 MET cc_start: 0.8259 (tpp) cc_final: 0.7799 (tpt) REVERT: J 68 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.7840 (t-90) REVERT: J 146 ILE cc_start: 0.8712 (mm) cc_final: 0.8487 (mt) REVERT: J 273 TYR cc_start: 0.9659 (OUTLIER) cc_final: 0.9165 (p90) REVERT: J 306 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8431 (mp) REVERT: K 113 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8544 (p) REVERT: K 157 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: K 203 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8876 (mp0) REVERT: K 238 LEU cc_start: 0.8865 (pp) cc_final: 0.8343 (mt) REVERT: L 95 HIS cc_start: 0.9271 (OUTLIER) cc_final: 0.9060 (m-70) REVERT: L 153 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7813 (p0) REVERT: L 286 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8208 (t-90) REVERT: P 92 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.7947 (mtp-110) REVERT: P 154 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6915 (tp) REVERT: P 231 PHE cc_start: 0.7762 (m-10) cc_final: 0.7418 (m-10) REVERT: R 48 GLU cc_start: 0.8681 (pt0) cc_final: 0.8461 (pp20) REVERT: R 49 ARG cc_start: 0.9360 (ttm110) cc_final: 0.9122 (ttm-80) REVERT: R 55 GLU cc_start: 0.8886 (tp30) cc_final: 0.8610 (tp30) REVERT: R 81 CYS cc_start: 0.8136 (m) cc_final: 0.7753 (t) REVERT: R 84 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.8228 (t70) REVERT: T 12 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8240 (tt0) REVERT: T 39 ARG cc_start: 0.8372 (tpp80) cc_final: 0.6709 (pmt170) REVERT: T 47 TYR cc_start: 0.9037 (t80) cc_final: 0.8591 (t80) REVERT: U 142 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7930 (tp30) REVERT: V 11 MET cc_start: 0.8561 (mmt) cc_final: 0.8260 (tpp) REVERT: V 68 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.7960 (t-90) REVERT: V 102 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9030 (tt) REVERT: V 148 ASN cc_start: 0.8389 (t0) cc_final: 0.7980 (t160) REVERT: V 306 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8453 (mp) REVERT: V 366 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8194 (mtm) REVERT: W 157 GLN cc_start: 0.9136 (tp40) cc_final: 0.8859 (tm-30) REVERT: W 203 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8823 (mp0) REVERT: W 268 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7996 (p-80) REVERT: Y 157 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: Y 163 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8409 (mtmp) REVERT: Y 368 MET cc_start: 0.8721 (mmm) cc_final: 0.7990 (tpt) REVERT: N 47 PHE cc_start: 0.8935 (m-10) cc_final: 0.7718 (t80) outliers start: 122 outliers final: 63 residues processed: 539 average time/residue: 0.6573 time to fit residues: 424.5930 Evaluate side-chains 515 residues out of total 3394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 427 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 262 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 68 HIS Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 273 TYR Chi-restraints excluded: chain J residue 295 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 157 GLN Chi-restraints excluded: chain K residue 192 CYS Chi-restraints excluded: chain K residue 203 GLU Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 277 VAL Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain L residue 153 ASN Chi-restraints excluded: chain L residue 255 TRP Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 286 HIS Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 154 ILE Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain P residue 271 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain S residue 75 ILE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 216 THR Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain U residue 298 LEU Chi-restraints excluded: chain U residue 313 VAL Chi-restraints excluded: chain V residue 27 ILE Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 68 HIS Chi-restraints excluded: chain V residue 102 LEU Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain V residue 278 TYR Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 306 ILE Chi-restraints excluded: chain V residue 338 ILE Chi-restraints excluded: chain V residue 366 MET Chi-restraints excluded: chain V residue 379 TRP Chi-restraints excluded: chain W residue 69 SER Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 173 VAL Chi-restraints excluded: chain W residue 197 ILE Chi-restraints excluded: chain W residue 203 GLU Chi-restraints excluded: chain W residue 267 VAL Chi-restraints excluded: chain W residue 268 HIS Chi-restraints excluded: chain W residue 416 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 157 GLU Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 179 MET Chi-restraints excluded: chain Y residue 271 THR Chi-restraints excluded: chain Y residue 286 HIS Chi-restraints excluded: chain Y residue 419 THR Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.8053 > 50: distance: 18 - 171: 16.583 distance: 21 - 183: 9.836 distance: 36 - 186: 10.142 distance: 39 - 196: 24.573 distance: 68 - 194: 31.971 distance: 71 - 191: 11.803 distance: 79 - 179: 5.522 distance: 82 - 176: 20.254 distance: 132 - 136: 7.635 distance: 136 - 137: 10.350 distance: 137 - 138: 11.420 distance: 137 - 140: 8.355 distance: 138 - 139: 15.997 distance: 138 - 145: 8.540 distance: 140 - 141: 25.611 distance: 141 - 142: 22.327 distance: 142 - 143: 4.633 distance: 143 - 144: 11.875 distance: 145 - 146: 8.585 distance: 146 - 147: 7.036 distance: 146 - 149: 12.501 distance: 147 - 148: 22.960 distance: 147 - 150: 16.107 distance: 150 - 151: 29.839 distance: 150 - 156: 15.460 distance: 151 - 152: 11.411 distance: 151 - 154: 6.137 distance: 152 - 153: 23.362 distance: 152 - 157: 18.586 distance: 154 - 155: 12.640 distance: 155 - 156: 19.360 distance: 157 - 158: 20.026 distance: 158 - 159: 16.523 distance: 158 - 161: 6.891 distance: 159 - 160: 15.155 distance: 159 - 168: 6.872 distance: 161 - 162: 9.254 distance: 162 - 163: 32.195 distance: 163 - 164: 9.461 distance: 164 - 165: 12.045 distance: 165 - 166: 16.698 distance: 165 - 167: 12.312 distance: 168 - 169: 22.337 distance: 169 - 170: 27.886 distance: 169 - 172: 17.610 distance: 170 - 171: 9.993 distance: 170 - 176: 37.615 distance: 172 - 173: 11.050 distance: 173 - 174: 18.884 distance: 174 - 175: 7.916 distance: 176 - 177: 16.732 distance: 177 - 178: 8.796 distance: 177 - 180: 9.994 distance: 178 - 179: 19.642 distance: 178 - 183: 17.824 distance: 180 - 181: 25.188 distance: 180 - 182: 19.767 distance: 183 - 184: 5.947 distance: 184 - 185: 20.499 distance: 184 - 187: 17.099 distance: 185 - 186: 21.303 distance: 185 - 191: 21.327 distance: 187 - 188: 14.867 distance: 188 - 189: 10.149 distance: 188 - 190: 6.467 distance: 191 - 192: 14.183 distance: 192 - 193: 15.078 distance: 192 - 195: 37.267 distance: 193 - 194: 6.190 distance: 193 - 196: 26.991 distance: 196 - 197: 11.673 distance: 197 - 198: 15.557 distance: 197 - 200: 37.682 distance: 198 - 199: 14.962 distance: 198 - 201: 15.616 distance: 201 - 202: 5.564 distance: 202 - 203: 9.138 distance: 202 - 205: 9.459 distance: 203 - 204: 6.822 distance: 203 - 206: 9.256