Starting phenix.real_space_refine on Sun Nov 17 07:00:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/11_2024/8j5t_35993.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/11_2024/8j5t_35993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/11_2024/8j5t_35993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/11_2024/8j5t_35993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/11_2024/8j5t_35993.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5t_35993/11_2024/8j5t_35993.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.080 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 8378 2.51 5 N 2359 2.21 5 O 2443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13234 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3947 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 28, 'TRANS': 490} Chain: "B" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2475 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain: "C" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2185 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain: "D" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4555 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 35, 'TRANS': 572} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {' MG': 2, 'ATP': 2, 'SF4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10760 SG CYS D 292 57.075 44.527 16.961 1.00 73.85 S ATOM 10813 SG CYS D 299 62.442 47.997 16.652 1.00 84.80 S ATOM 10713 SG CYS D 286 58.566 48.547 21.699 1.00 77.21 S ATOM 10946 SG CYS D 317 56.814 50.799 15.887 1.00 80.19 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER A 195 " occ=0.47 ... (4 atoms not shown) pdb=" OG SER A 195 " occ=0.47 residue: pdb=" N GLY A 509 " occ=0.48 ... (2 atoms not shown) pdb=" O GLY A 509 " occ=0.48 residue: pdb=" N GLU A 510 " occ=0.48 ... (7 atoms not shown) pdb=" OE2 GLU A 510 " occ=0.48 residue: pdb=" N SER A 511 " occ=0.48 ... (4 atoms not shown) pdb=" OG SER A 511 " occ=0.48 Time building chain proxies: 7.88, per 1000 atoms: 0.60 Number of scatterers: 13234 At special positions: 0 Unit cell: (85.696, 89.856, 163.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 42 16.00 P 6 15.00 Mg 2 11.99 O 2443 8.00 N 2359 7.00 C 8378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 705 " pdb="FE2 SF4 D 705 " - pdb=" SG CYS D 299 " pdb="FE1 SF4 D 705 " - pdb=" SG CYS D 292 " pdb="FE4 SF4 D 705 " - pdb=" SG CYS D 317 " pdb="FE3 SF4 D 705 " - pdb=" SG CYS D 286 " Number of angles added : 12 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 49.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 171 through 182 removed outlier: 4.121A pdb=" N ILE A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 223 through 227 removed outlier: 4.204A pdb=" N PHE A 227 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 296 through 306 removed outlier: 4.680A pdb=" N LEU A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix removed outlier: 3.663A pdb=" N ASN A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 375 Processing helix chain 'A' and resid 407 through 417 removed outlier: 3.986A pdb=" N ALA A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 459 removed outlier: 3.812A pdb=" N THR A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 459 " --> pdb=" O HIS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 4.060A pdb=" N LEU A 501 " --> pdb=" O PRO A 497 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.805A pdb=" N ARG A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 529 " --> pdb=" O ILE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 Processing helix chain 'B' and resid 2 through 31 removed outlier: 4.191A pdb=" N LEU B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TYR B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.633A pdb=" N MET B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.665A pdb=" N LYS B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 74 removed outlier: 3.706A pdb=" N HIS B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 123 removed outlier: 5.274A pdb=" N VAL B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 141 Processing helix chain 'B' and resid 143 through 163 Processing helix chain 'B' and resid 182 through 192 Processing helix chain 'B' and resid 192 through 219 removed outlier: 3.899A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.708A pdb=" N GLY B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 4.275A pdb=" N ARG B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 4.127A pdb=" N LEU B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 removed outlier: 3.582A pdb=" N ILE B 271 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 288 removed outlier: 3.518A pdb=" N VAL B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 305 removed outlier: 3.702A pdb=" N VAL B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 319 Processing helix chain 'C' and resid 6 through 16 removed outlier: 3.563A pdb=" N LEU C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 38 removed outlier: 4.937A pdb=" N LEU C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 110 removed outlier: 3.620A pdb=" N LYS C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 127 Processing helix chain 'C' and resid 128 through 137 removed outlier: 3.946A pdb=" N LEU C 132 " --> pdb=" O PRO C 128 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 137 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 156 removed outlier: 3.819A pdb=" N ILE C 146 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 removed outlier: 3.712A pdb=" N SER C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.964A pdb=" N ARG C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 225 removed outlier: 3.553A pdb=" N ILE C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Proline residue: C 198 - end of helix removed outlier: 4.867A pdb=" N SER C 202 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 204 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 245 through 248 removed outlier: 4.573A pdb=" N THR C 248 " --> pdb=" O ALA C 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 245 through 248' Processing helix chain 'C' and resid 250 through 280 removed outlier: 4.159A pdb=" N PHE C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) Proline residue: C 257 - end of helix removed outlier: 3.548A pdb=" N GLY C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.784A pdb=" N MET D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 107 through 119 removed outlier: 4.452A pdb=" N HIS D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 149 through 150 No H-bonds generated for 'chain 'D' and resid 149 through 150' Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.794A pdb=" N VAL D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 203 removed outlier: 4.330A pdb=" N GLN D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.542A pdb=" N GLU D 220 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 removed outlier: 3.574A pdb=" N TYR D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.518A pdb=" N GLY D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 399 through 409 removed outlier: 3.571A pdb=" N LEU D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 409 " --> pdb=" O HIS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 456 through 463 Processing helix chain 'D' and resid 464 through 467 Processing helix chain 'D' and resid 473 through 486 removed outlier: 3.884A pdb=" N ASP D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.609A pdb=" N PHE D 500 " --> pdb=" O PRO D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 531 through 548 removed outlier: 3.627A pdb=" N GLY D 537 " --> pdb=" O SER D 533 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN D 548 " --> pdb=" O ASP D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 595 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 95 removed outlier: 6.300A pdb=" N THR A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL A 262 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 146 removed outlier: 4.044A pdb=" N SER A 143 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLN A 211 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG A 205 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 213 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 203 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR A 215 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 468 removed outlier: 6.080A pdb=" N ASP A 438 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 465 through 468 removed outlier: 6.080A pdb=" N ASP A 438 " --> pdb=" O GLN A 467 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER A 338 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN A 559 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR A 340 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 421 through 423 removed outlier: 3.659A pdb=" N SER A 423 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 426 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA9, first strand: chain 'D' and resid 21 through 31 removed outlier: 6.566A pdb=" N ALA D 23 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR D 13 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG D 25 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA D 11 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ILE D 27 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 92 through 94 removed outlier: 6.479A pdb=" N GLY D 92 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP D 179 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL D 94 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU D 176 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE D 211 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N CYS D 178 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL D 36 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU D 226 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA D 38 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET D 228 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL D 40 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA D 225 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER D 236 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 227 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 369 through 384 removed outlier: 6.649A pdb=" N LEU D 361 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU D 373 " --> pdb=" O TYR D 359 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR D 359 " --> pdb=" O GLU D 373 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ARG D 375 " --> pdb=" O LYS D 357 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS D 357 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL D 377 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU D 355 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY D 379 " --> pdb=" O ARG D 353 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ARG D 353 " --> pdb=" O GLY D 379 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N SER D 381 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ARG D 351 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 441 through 443 removed outlier: 6.453A pdb=" N LEU D 574 " --> pdb=" O VAL D 578 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 5287 1.39 - 1.61: 8120 1.61 - 1.84: 68 1.84 - 2.06: 0 2.06 - 2.29: 12 Bond restraints: 13487 Sorted by residual: bond pdb=" C4 ATP D 703 " pdb=" C5 ATP D 703 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.57e+01 bond pdb=" C4 ATP D 701 " pdb=" C5 ATP D 701 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.36e+01 bond pdb=" C5 ATP D 701 " pdb=" C6 ATP D 701 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.30e+01 bond pdb=" C5 ATP D 703 " pdb=" C6 ATP D 703 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.99e+01 bond pdb=" C ALA A 450 " pdb=" O ALA A 450 " ideal model delta sigma weight residual 1.237 1.167 0.069 1.17e-02 7.31e+03 3.51e+01 ... (remaining 13482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 18161 3.50 - 7.01: 195 7.01 - 10.51: 22 10.51 - 14.02: 4 14.02 - 17.52: 2 Bond angle restraints: 18384 Sorted by residual: angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 122.35 17.52 1.00e+00 1.00e+00 3.07e+02 angle pdb=" PB ATP D 703 " pdb=" O3B ATP D 703 " pdb=" PG ATP D 703 " ideal model delta sigma weight residual 139.87 122.89 16.98 1.00e+00 1.00e+00 2.88e+02 angle pdb=" N VAL B 181 " pdb=" CA VAL B 181 " pdb=" C VAL B 181 " ideal model delta sigma weight residual 113.71 102.08 11.63 9.50e-01 1.11e+00 1.50e+02 angle pdb=" PA ATP D 703 " pdb=" O3A ATP D 703 " pdb=" PB ATP D 703 " ideal model delta sigma weight residual 136.83 125.12 11.71 1.00e+00 1.00e+00 1.37e+02 angle pdb=" PA ATP D 701 " pdb=" O3A ATP D 701 " pdb=" PB ATP D 701 " ideal model delta sigma weight residual 136.83 127.87 8.96 1.00e+00 1.00e+00 8.03e+01 ... (remaining 18379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7042 17.98 - 35.95: 839 35.95 - 53.93: 174 53.93 - 71.90: 31 71.90 - 89.87: 12 Dihedral angle restraints: 8098 sinusoidal: 3152 harmonic: 4946 Sorted by residual: dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N ASN A 407 " pdb=" CA ASN A 407 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLU D 594 " pdb=" C GLU D 594 " pdb=" N TYR D 595 " pdb=" CA TYR D 595 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C ARG A 447 " pdb=" N ARG A 447 " pdb=" CA ARG A 447 " pdb=" CB ARG A 447 " ideal model delta harmonic sigma weight residual -122.60 -110.95 -11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 8095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1826 0.071 - 0.141: 307 0.141 - 0.212: 25 0.212 - 0.283: 5 0.283 - 0.353: 3 Chirality restraints: 2166 Sorted by residual: chirality pdb=" CA ARG A 447 " pdb=" N ARG A 447 " pdb=" C ARG A 447 " pdb=" CB ARG A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA TRP B 182 " pdb=" N TRP B 182 " pdb=" C TRP B 182 " pdb=" CB TRP B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ALA A 443 " pdb=" N ALA A 443 " pdb=" C ALA A 443 " pdb=" CB ALA A 443 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 2163 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 123 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ARG B 123 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG B 123 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN B 124 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 38 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C MET B 38 " 0.055 2.00e-02 2.50e+03 pdb=" O MET B 38 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN B 39 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 151 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C LEU C 151 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU C 151 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 152 " 0.017 2.00e-02 2.50e+03 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 123 2.58 - 3.16: 11371 3.16 - 3.74: 19833 3.74 - 4.32: 29245 4.32 - 4.90: 48819 Nonbonded interactions: 109391 Sorted by model distance: nonbonded pdb=" OE1 GLN D 96 " pdb="MG MG D 704 " model vdw 2.004 2.170 nonbonded pdb=" O3G ATP D 701 " pdb="MG MG D 702 " model vdw 2.061 2.170 nonbonded pdb=" OG SER D 48 " pdb="MG MG D 704 " model vdw 2.066 2.170 nonbonded pdb=" O1G ATP D 703 " pdb="MG MG D 704 " model vdw 2.124 2.170 nonbonded pdb=" O PHE B 254 " pdb=" N GLY B 257 " model vdw 2.208 3.120 ... (remaining 109386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.720 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.007 0.109 13487 Z= 0.480 Angle : 0.962 17.519 18384 Z= 0.617 Chirality : 0.054 0.353 2166 Planarity : 0.007 0.106 2370 Dihedral : 16.081 89.875 4926 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.65 % Allowed : 1.38 % Favored : 97.96 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.19), residues: 1732 helix: -1.22 (0.17), residues: 807 sheet: -1.53 (0.41), residues: 165 loop : -1.93 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 339 HIS 0.013 0.001 HIS C 62 PHE 0.018 0.002 PHE A 440 TYR 0.017 0.002 TYR A 441 ARG 0.013 0.001 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 1.556 Fit side-chains REVERT: A 442 ASP cc_start: 0.7813 (t0) cc_final: 0.7335 (t70) REVERT: B 7 ARG cc_start: 0.7583 (ttt180) cc_final: 0.7353 (ttm170) REVERT: D 63 GLN cc_start: 0.8003 (tt0) cc_final: 0.7523 (tm-30) REVERT: D 65 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7545 (ttp80) REVERT: D 360 ARG cc_start: 0.7514 (ttp80) cc_final: 0.6983 (ptp-110) REVERT: D 409 GLU cc_start: 0.7723 (pp20) cc_final: 0.7412 (pp20) outliers start: 9 outliers final: 5 residues processed: 165 average time/residue: 1.2258 time to fit residues: 222.2542 Evaluate side-chains 127 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.0670 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 39 GLN B 190 GLN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13487 Z= 0.221 Angle : 0.641 10.852 18384 Z= 0.331 Chirality : 0.044 0.159 2166 Planarity : 0.005 0.059 2370 Dihedral : 8.518 107.958 1985 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.89 % Allowed : 10.25 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.19), residues: 1732 helix: -0.40 (0.18), residues: 811 sheet: -1.64 (0.39), residues: 172 loop : -1.66 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 119 HIS 0.008 0.001 HIS C 62 PHE 0.010 0.001 PHE D 151 TYR 0.013 0.001 TYR A 156 ARG 0.007 0.001 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.544 Fit side-chains REVERT: A 442 ASP cc_start: 0.7543 (t0) cc_final: 0.7013 (t70) REVERT: B 95 ILE cc_start: 0.8450 (pt) cc_final: 0.8247 (mt) REVERT: D 63 GLN cc_start: 0.7926 (tt0) cc_final: 0.7533 (tm-30) REVERT: D 65 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7459 (ttp80) REVERT: D 248 MET cc_start: 0.7527 (tpt) cc_final: 0.6567 (tpt) REVERT: D 360 ARG cc_start: 0.7360 (ttp80) cc_final: 0.6953 (ptt180) REVERT: D 409 GLU cc_start: 0.7685 (pp20) cc_final: 0.7413 (pp20) outliers start: 26 outliers final: 8 residues processed: 157 average time/residue: 1.1609 time to fit residues: 202.3713 Evaluate side-chains 132 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 583 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 211 GLN C 211 ASN D 441 GLN D 476 HIS ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13487 Z= 0.335 Angle : 0.646 10.106 18384 Z= 0.332 Chirality : 0.045 0.161 2166 Planarity : 0.005 0.058 2370 Dihedral : 7.832 74.884 1980 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.62 % Allowed : 14.91 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1732 helix: -0.08 (0.18), residues: 806 sheet: -1.48 (0.39), residues: 178 loop : -1.74 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 339 HIS 0.006 0.001 HIS C 62 PHE 0.015 0.002 PHE B 272 TYR 0.014 0.001 TYR A 156 ARG 0.004 0.000 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.713 Fit side-chains REVERT: C 16 LEU cc_start: 0.8482 (pp) cc_final: 0.8191 (mt) REVERT: D 63 GLN cc_start: 0.7950 (tt0) cc_final: 0.7528 (tm-30) REVERT: D 99 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7176 (tmt) REVERT: D 269 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8205 (pp) REVERT: D 360 ARG cc_start: 0.7407 (ttp80) cc_final: 0.7039 (ptt180) REVERT: D 409 GLU cc_start: 0.7679 (pp20) cc_final: 0.7379 (pp20) outliers start: 36 outliers final: 15 residues processed: 153 average time/residue: 1.1820 time to fit residues: 201.0174 Evaluate side-chains 137 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN B 39 GLN B 68 ASN B 191 HIS C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13487 Z= 0.170 Angle : 0.578 9.606 18384 Z= 0.294 Chirality : 0.041 0.142 2166 Planarity : 0.004 0.056 2370 Dihedral : 7.312 70.308 1980 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.33 % Allowed : 16.73 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1732 helix: 0.25 (0.19), residues: 810 sheet: -1.26 (0.40), residues: 186 loop : -1.50 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 119 HIS 0.004 0.001 HIS C 62 PHE 0.010 0.001 PHE A 484 TYR 0.013 0.001 TYR A 156 ARG 0.009 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.826 Fit side-chains REVERT: C 147 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6566 (mmp) REVERT: D 63 GLN cc_start: 0.7932 (tt0) cc_final: 0.7547 (tm-30) REVERT: D 65 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7333 (ttp80) REVERT: D 360 ARG cc_start: 0.7334 (ttp80) cc_final: 0.6959 (ptt180) REVERT: D 409 GLU cc_start: 0.7646 (pp20) cc_final: 0.7424 (pp20) REVERT: D 452 ASP cc_start: 0.8135 (p0) cc_final: 0.7840 (p0) outliers start: 32 outliers final: 12 residues processed: 166 average time/residue: 1.0751 time to fit residues: 198.5620 Evaluate side-chains 138 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 583 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13487 Z= 0.344 Angle : 0.627 9.660 18384 Z= 0.320 Chirality : 0.045 0.153 2166 Planarity : 0.005 0.057 2370 Dihedral : 7.332 75.008 1980 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.13 % Allowed : 17.53 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1732 helix: 0.21 (0.18), residues: 810 sheet: -1.32 (0.40), residues: 179 loop : -1.60 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.013 0.002 PHE B 272 TYR 0.014 0.001 TYR A 156 ARG 0.009 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 1.847 Fit side-chains REVERT: A 297 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7477 (t0) REVERT: D 63 GLN cc_start: 0.7961 (tt0) cc_final: 0.7614 (tm-30) REVERT: D 65 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7351 (ttp80) REVERT: D 269 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8187 (pp) REVERT: D 360 ARG cc_start: 0.7393 (ttp80) cc_final: 0.7033 (ptt180) REVERT: D 409 GLU cc_start: 0.7714 (pp20) cc_final: 0.7472 (pp20) REVERT: D 415 SER cc_start: 0.8410 (t) cc_final: 0.8137 (t) outliers start: 43 outliers final: 17 residues processed: 161 average time/residue: 1.1778 time to fit residues: 211.0674 Evaluate side-chains 144 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 386 GLN Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 583 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 68 ASN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13487 Z= 0.215 Angle : 0.581 9.257 18384 Z= 0.296 Chirality : 0.042 0.145 2166 Planarity : 0.004 0.055 2370 Dihedral : 7.179 75.260 1980 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.05 % Allowed : 18.33 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.20), residues: 1732 helix: 0.33 (0.19), residues: 812 sheet: -1.22 (0.39), residues: 193 loop : -1.51 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS C 62 PHE 0.011 0.001 PHE A 484 TYR 0.012 0.001 TYR A 156 ARG 0.011 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.436 Fit side-chains REVERT: A 297 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7442 (t0) REVERT: D 63 GLN cc_start: 0.7940 (tt0) cc_final: 0.7506 (tm-30) REVERT: D 65 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7253 (ttp80) REVERT: D 99 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7228 (tmt) REVERT: D 235 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: D 360 ARG cc_start: 0.7358 (ttp80) cc_final: 0.7000 (ptt180) REVERT: D 409 GLU cc_start: 0.7661 (pp20) cc_final: 0.7430 (pp20) REVERT: D 415 SER cc_start: 0.8393 (t) cc_final: 0.8115 (t) REVERT: D 545 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8595 (tt) outliers start: 42 outliers final: 20 residues processed: 165 average time/residue: 1.1498 time to fit residues: 211.4307 Evaluate side-chains 152 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 GLN Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 587 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 68 ASN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13487 Z= 0.185 Angle : 0.567 9.238 18384 Z= 0.287 Chirality : 0.042 0.161 2166 Planarity : 0.004 0.055 2370 Dihedral : 6.990 74.282 1980 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.62 % Allowed : 19.27 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1732 helix: 0.52 (0.19), residues: 812 sheet: -1.18 (0.39), residues: 192 loop : -1.45 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS B 241 PHE 0.010 0.001 PHE B 223 TYR 0.013 0.001 TYR A 156 ARG 0.011 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.641 Fit side-chains REVERT: A 297 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7434 (t0) REVERT: D 63 GLN cc_start: 0.7930 (tt0) cc_final: 0.7523 (tm-30) REVERT: D 65 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7206 (ttp80) REVERT: D 99 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7202 (tmt) REVERT: D 360 ARG cc_start: 0.7344 (ttp80) cc_final: 0.6911 (ptt180) REVERT: D 409 GLU cc_start: 0.7663 (pp20) cc_final: 0.7421 (pp20) REVERT: D 415 SER cc_start: 0.8336 (t) cc_final: 0.8064 (t) REVERT: D 452 ASP cc_start: 0.8167 (p0) cc_final: 0.7855 (p0) REVERT: D 472 LYS cc_start: 0.8388 (ptpp) cc_final: 0.8181 (tttt) REVERT: D 545 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8598 (tt) outliers start: 36 outliers final: 19 residues processed: 173 average time/residue: 1.0646 time to fit residues: 206.1057 Evaluate side-chains 156 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 587 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13487 Z= 0.329 Angle : 0.638 10.543 18384 Z= 0.324 Chirality : 0.045 0.188 2166 Planarity : 0.005 0.055 2370 Dihedral : 7.166 78.643 1980 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.91 % Allowed : 19.13 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1732 helix: 0.37 (0.18), residues: 815 sheet: -1.22 (0.40), residues: 177 loop : -1.48 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.003 0.001 HIS C 62 PHE 0.013 0.001 PHE B 223 TYR 0.014 0.001 TYR A 156 ARG 0.009 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.535 Fit side-chains REVERT: D 63 GLN cc_start: 0.7959 (tt0) cc_final: 0.7577 (tm-30) REVERT: D 99 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7285 (tmt) REVERT: D 235 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: D 360 ARG cc_start: 0.7395 (ttp80) cc_final: 0.7053 (ptt180) REVERT: D 409 GLU cc_start: 0.7701 (pp20) cc_final: 0.7457 (pp20) REVERT: D 415 SER cc_start: 0.8406 (t) cc_final: 0.8116 (t) REVERT: D 545 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8628 (tt) outliers start: 40 outliers final: 24 residues processed: 164 average time/residue: 1.0947 time to fit residues: 200.9641 Evaluate side-chains 157 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 583 ASP Chi-restraints excluded: chain D residue 587 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 153 optimal weight: 0.4980 chunk 92 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 39 GLN B 68 ASN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13487 Z= 0.188 Angle : 0.591 10.170 18384 Z= 0.300 Chirality : 0.042 0.172 2166 Planarity : 0.004 0.056 2370 Dihedral : 7.033 76.944 1980 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.04 % Allowed : 20.44 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1732 helix: 0.53 (0.19), residues: 814 sheet: -1.17 (0.39), residues: 192 loop : -1.43 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.003 0.001 HIS C 62 PHE 0.010 0.001 PHE B 223 TYR 0.013 0.001 TYR A 156 ARG 0.009 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.592 Fit side-chains REVERT: A 297 ASP cc_start: 0.7732 (t70) cc_final: 0.7513 (t0) REVERT: D 63 GLN cc_start: 0.7932 (tt0) cc_final: 0.7517 (tm-30) REVERT: D 360 ARG cc_start: 0.7333 (ttp80) cc_final: 0.7000 (ptt180) REVERT: D 409 GLU cc_start: 0.7668 (pp20) cc_final: 0.7430 (pp20) REVERT: D 415 SER cc_start: 0.8390 (t) cc_final: 0.8115 (t) REVERT: D 472 LYS cc_start: 0.8379 (ptpp) cc_final: 0.8056 (ttpp) REVERT: D 545 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8612 (tt) outliers start: 28 outliers final: 21 residues processed: 158 average time/residue: 1.1190 time to fit residues: 196.4658 Evaluate side-chains 150 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 590 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 39 GLN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13487 Z= 0.182 Angle : 0.588 10.175 18384 Z= 0.298 Chirality : 0.042 0.153 2166 Planarity : 0.004 0.057 2370 Dihedral : 6.919 75.041 1980 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.82 % Allowed : 21.16 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1732 helix: 0.61 (0.19), residues: 816 sheet: -1.16 (0.39), residues: 192 loop : -1.33 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS B 241 PHE 0.010 0.001 PHE B 223 TYR 0.013 0.001 TYR A 156 ARG 0.013 0.000 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.545 Fit side-chains REVERT: D 63 GLN cc_start: 0.7950 (tt0) cc_final: 0.7552 (tm-30) REVERT: D 360 ARG cc_start: 0.7350 (ttp80) cc_final: 0.6925 (ptt180) REVERT: D 415 SER cc_start: 0.8350 (t) cc_final: 0.8069 (t) REVERT: D 472 LYS cc_start: 0.8364 (ptpp) cc_final: 0.8057 (ttpp) REVERT: D 545 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8618 (tt) outliers start: 25 outliers final: 23 residues processed: 156 average time/residue: 1.1067 time to fit residues: 192.2160 Evaluate side-chains 149 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 590 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.3980 chunk 41 optimal weight: 0.2980 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN B 39 GLN B 68 ASN C 211 ASN ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.090029 restraints weight = 20365.488| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.09 r_work: 0.2958 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13487 Z= 0.194 Angle : 0.597 10.042 18384 Z= 0.302 Chirality : 0.042 0.161 2166 Planarity : 0.004 0.057 2370 Dihedral : 6.892 74.076 1980 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.04 % Allowed : 21.24 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1732 helix: 0.67 (0.19), residues: 816 sheet: -1.13 (0.39), residues: 192 loop : -1.31 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS B 241 PHE 0.010 0.001 PHE B 223 TYR 0.013 0.001 TYR A 156 ARG 0.012 0.000 ARG B 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4251.11 seconds wall clock time: 77 minutes 8.46 seconds (4628.46 seconds total)