Starting phenix.real_space_refine on Sat Oct 11 08:01:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5r_35991/10_2025/8j5r_35991.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5r_35991/10_2025/8j5r_35991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j5r_35991/10_2025/8j5r_35991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5r_35991/10_2025/8j5r_35991.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j5r_35991/10_2025/8j5r_35991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5r_35991/10_2025/8j5r_35991.map" } resolution = 3.28 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= 0.003 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8 atoms to isotropic. 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 4 7.16 5 S 42 5.16 5 C 8284 2.51 5 N 2322 2.21 5 O 2398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13050 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3938 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 28, 'TRANS': 490} Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2476 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain: "C" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2063 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain: "D" Number of atoms: 4565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4565 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 35, 'TRANS': 573} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10692 SG CYS D 299 26.965 45.541 153.891 1.00 45.63 S ATOM 10592 SG CYS D 286 27.544 48.860 148.613 1.00 40.82 S ATOM 10639 SG CYS D 292 32.360 48.886 153.417 1.00 41.28 S ATOM 10825 SG CYS D 317 26.763 51.504 154.587 1.00 43.60 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: 2.60, per 1000 atoms: 0.20 Number of scatterers: 13050 At special positions: 0 Unit cell: (93.184, 105.664, 172.224, 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 4 26.01 S 42 16.00 O 2398 8.00 N 2322 7.00 C 8284 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: 1.17 Conformation dependent library (CDL) restraints added in 624.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 701 " pdb="FE1 SF4 D 701 " - pdb=" SG CYS D 299 " pdb="FE2 SF4 D 701 " - pdb=" SG CYS D 286 " pdb="FE4 SF4 D 701 " - pdb=" SG CYS D 317 " pdb="FE3 SF4 D 701 " - pdb=" SG CYS D 292 " Number of angles added : 12 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3144 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 9 sheets defined 51.6% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 111 through 120 removed outlier: 4.293A pdb=" N ALA A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.988A pdb=" N ILE A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.911A pdb=" N MET A 226 " --> pdb=" O TRP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.567A pdb=" N ALA A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) 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 410 through 419 removed outlier: 3.550A pdb=" N GLY A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 459 removed outlier: 3.718A pdb=" N GLN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A 459 " --> pdb=" O HIS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 475 removed outlier: 4.089A pdb=" N GLY A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 474 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 475 " --> pdb=" O SER A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 470 through 475' Processing helix chain 'A' and resid 496 through 500 removed outlier: 4.044A pdb=" N SER A 499 " --> pdb=" O PHE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 526 removed outlier: 3.867A pdb=" N GLU A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 550 removed outlier: 4.341A pdb=" N ALA A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.771A pdb=" N ASN B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 61 through 74 Processing helix chain 'B' and resid 87 through 123 removed outlier: 4.220A pdb=" N GLY B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 142 removed outlier: 3.546A pdb=" N THR B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 163 Processing helix chain 'B' and resid 180 through 220 removed outlier: 5.131A pdb=" N LEU B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix removed outlier: 3.598A pdb=" N LEU B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.896A pdb=" N ILE B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 253 through 273 removed outlier: 3.605A pdb=" N ALA B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.550A pdb=" N THR B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 319 removed outlier: 3.662A pdb=" N VAL B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 removed outlier: 4.058A pdb=" N ARG B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.632A pdb=" N ARG C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 38 Processing helix chain 'C' and resid 39 through 42 Processing helix chain 'C' and resid 72 through 110 removed outlier: 3.540A pdb=" N GLN C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 128 through 141 Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 146 through 156 Processing helix chain 'C' and resid 161 through 174 removed outlier: 3.780A pdb=" N GLU C 174 " --> pdb=" O MET C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.802A pdb=" N ARG C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 196 through 225 removed outlier: 4.845A pdb=" N SER C 202 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.723A 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 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 251 through 278 Proline residue: C 257 - end of helix Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 107 through 120 removed outlier: 4.368A pdb=" N HIS D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 124 through 140 removed outlier: 3.844A pdb=" N ARG D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 removed outlier: 3.735A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) 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 removed outlier: 3.602A pdb=" N LEU D 155 " --> pdb=" O PRO D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 186 through 205 Processing helix chain 'D' and resid 214 through 222 removed outlier: 3.957A pdb=" N VAL D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 297 through 302 removed outlier: 3.692A pdb=" N THR D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 297 through 302' Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 327 through 333 Processing helix chain 'D' and resid 400 through 408 Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 437 Processing helix chain 'D' and resid 456 through 467 Proline residue: D 464 - end of helix Processing helix chain 'D' and resid 471 through 487 removed outlier: 4.080A pdb=" N HIS D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA D 477 " --> pdb=" O ASN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 495 removed outlier: 4.117A pdb=" N SER D 494 " --> pdb=" O GLY D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 502 through 514 removed outlier: 3.897A pdb=" N GLN D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 550 removed outlier: 4.095A pdb=" N GLY D 537 " --> pdb=" O SER D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 567 removed outlier: 3.720A pdb=" N HIS D 565 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 590 Processing helix chain 'D' and resid 593 through 602 removed outlier: 3.585A pdb=" N ARG D 597 " --> pdb=" O HIS D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.958A pdb=" N SER A 143 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLN A 211 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG A 205 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 213 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 203 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR A 215 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 265 removed outlier: 6.859A pdb=" N VAL A 273 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 333 Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 467 removed outlier: 8.311A pdb=" N ILE A 486 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG A 437 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLN A 488 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU A 439 " --> pdb=" O GLN A 488 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N GLY A 490 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE A 342 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A 344 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER A 554 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 31 removed outlier: 5.609A pdb=" N LEU D 10 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER D 28 " --> pdb=" O THR D 8 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR D 8 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG D 30 " --> pdb=" O GLU D 6 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU D 6 " --> pdb=" O ARG D 30 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU D 10 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG D 65 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL D 12 " --> pdb=" O GLN D 63 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN D 63 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.445A pdb=" N GLY D 92 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP D 179 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL D 94 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA D 225 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER D 236 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D 227 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N HIS D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 372 through 385 removed outlier: 5.819A pdb=" N VAL D 374 " --> pdb=" O ARG D 360 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ARG D 360 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA D 376 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR D 358 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP D 378 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL D 356 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE D 380 " --> pdb=" O HIS D 354 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU D 355 " --> pdb=" O SER D 415 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER D 415 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 420 " --> pdb=" O THR D 423 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 441 through 443 removed outlier: 7.088A pdb=" N LEU D 521 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL D 556 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU D 523 " --> pdb=" O VAL D 556 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 390 " --> pdb=" O TYR D 553 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL D 570 " --> pdb=" O GLN D 581 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN D 581 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 572 " --> pdb=" O VAL D 579 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.53 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: 5239 1.39 - 1.62: 7978 1.62 - 1.85: 68 1.85 - 2.08: 0 2.08 - 2.31: 12 Bond restraints: 13297 Sorted by residual: bond pdb=" C GLN D 111 " pdb=" O GLN D 111 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.19e-02 7.06e+03 4.00e+01 bond pdb=" C LEU D 483 " pdb=" O LEU D 483 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.17e-02 7.31e+03 2.73e+01 bond pdb=" CA SER A 499 " pdb=" CB SER A 499 " ideal model delta sigma weight residual 1.534 1.458 0.075 1.45e-02 4.76e+03 2.71e+01 bond pdb=" C VAL D 486 " pdb=" O VAL D 486 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.19e-02 7.06e+03 2.64e+01 bond pdb=" N GLU D 525 " pdb=" CA GLU D 525 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.10e-03 1.98e+04 1.87e+01 ... (remaining 13292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 17419 2.23 - 4.45: 577 4.45 - 6.68: 85 6.68 - 8.91: 23 8.91 - 11.14: 9 Bond angle restraints: 18113 Sorted by residual: angle pdb=" C THR A 291 " pdb=" CA THR A 291 " pdb=" CB THR A 291 " ideal model delta sigma weight residual 109.80 98.66 11.14 1.23e+00 6.61e-01 8.20e+01 angle pdb=" N LEU A 434 " pdb=" CA LEU A 434 " pdb=" C LEU A 434 " ideal model delta sigma weight residual 109.15 99.35 9.80 1.44e+00 4.82e-01 4.63e+01 angle pdb=" N ASN A 246 " pdb=" CA ASN A 246 " pdb=" C ASN A 246 " ideal model delta sigma weight residual 110.97 103.97 7.00 1.09e+00 8.42e-01 4.12e+01 angle pdb=" C THR A 502 " pdb=" CA THR A 502 " pdb=" CB THR A 502 " ideal model delta sigma weight residual 111.36 101.44 9.92 1.63e+00 3.76e-01 3.71e+01 angle pdb=" N THR A 291 " pdb=" CA THR A 291 " pdb=" C THR A 291 " ideal model delta sigma weight residual 110.64 119.54 -8.90 1.48e+00 4.57e-01 3.62e+01 ... (remaining 18108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6959 17.97 - 35.94: 792 35.94 - 53.91: 178 53.91 - 71.88: 15 71.88 - 89.85: 11 Dihedral angle restraints: 7955 sinusoidal: 3051 harmonic: 4904 Sorted by residual: dihedral pdb=" C ARG A 224 " pdb=" N ARG A 224 " pdb=" CA ARG A 224 " pdb=" CB ARG A 224 " ideal model delta harmonic sigma weight residual -122.60 -140.36 17.76 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" N ARG A 224 " pdb=" C ARG A 224 " pdb=" CA ARG A 224 " pdb=" CB ARG A 224 " ideal model delta harmonic sigma weight residual 122.80 137.70 -14.90 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" C GLU A 222 " pdb=" N GLU A 222 " pdb=" CA GLU A 222 " pdb=" CB GLU A 222 " ideal model delta harmonic sigma weight residual -122.60 -137.44 14.84 0 2.50e+00 1.60e-01 3.53e+01 ... (remaining 7952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2084 0.148 - 0.297: 44 0.297 - 0.445: 7 0.445 - 0.594: 4 0.594 - 0.742: 3 Chirality restraints: 2142 Sorted by residual: chirality pdb=" CA ARG A 224 " pdb=" N ARG A 224 " pdb=" C ARG A 224 " pdb=" CB ARG A 224 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA PRO A 302 " pdb=" N PRO A 302 " pdb=" C PRO A 302 " pdb=" CB PRO A 302 " both_signs ideal model delta sigma weight residual False 2.72 2.06 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA GLU A 222 " pdb=" N GLU A 222 " pdb=" C GLU A 222 " pdb=" CB GLU A 222 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.69e+00 ... (remaining 2139 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 296 " 0.023 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C ASP A 296 " -0.084 2.00e-02 2.50e+03 pdb=" O ASP A 296 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP A 297 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 466 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C LEU A 466 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU A 466 " 0.024 2.00e-02 2.50e+03 pdb=" N GLN A 467 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 157 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C THR A 157 " -0.061 2.00e-02 2.50e+03 pdb=" O THR A 157 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 158 " 0.021 2.00e-02 2.50e+03 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 457 2.70 - 3.25: 13271 3.25 - 3.80: 19617 3.80 - 4.35: 25182 4.35 - 4.90: 44013 Nonbonded interactions: 102540 Sorted by model distance: nonbonded pdb=" O ASN A 407 " pdb=" OD1 ASN A 407 " model vdw 2.145 3.040 nonbonded pdb=" N GLU D 432 " pdb=" OE1 GLU D 432 " model vdw 2.176 3.120 nonbonded pdb=" OD1 ASN A 277 " pdb=" N ARG A 279 " model vdw 2.225 3.120 nonbonded pdb=" O ASP A 266 " pdb=" N ALA A 269 " model vdw 2.227 3.120 nonbonded pdb=" O PHE B 145 " pdb=" ND2 ASN B 149 " model vdw 2.241 3.120 ... (remaining 102535 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.600 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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 : 0.008 0.120 13301 Z= 0.406 Angle : 0.977 16.001 18125 Z= 0.594 Chirality : 0.067 0.742 2142 Planarity : 0.006 0.107 2347 Dihedral : 15.638 89.855 4811 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.22 % Allowed : 1.32 % Favored : 98.46 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 1.16 % 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: -1.53 (0.20), residues: 1718 helix: 0.19 (0.18), residues: 821 sheet: -2.49 (0.37), residues: 179 loop : -2.00 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 268 TYR 0.015 0.002 TYR A 406 PHE 0.024 0.002 PHE A 484 TRP 0.029 0.002 TRP B 280 HIS 0.006 0.001 HIS D 153 Details of bonding type rmsd covalent geometry : bond 0.00746 (13297) covalent geometry : angle 0.96126 (18113) hydrogen bonds : bond 0.13658 ( 618) hydrogen bonds : angle 6.51292 ( 1791) metal coordination : bond 0.07168 ( 4) metal coordination : angle 6.84770 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.384 Fit side-chains REVERT: D 406 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7936 (tm-30) outliers start: 3 outliers final: 1 residues processed: 140 average time/residue: 0.1283 time to fit residues: 25.0190 Evaluate side-chains 110 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN D 81 ASN D 111 GLN D 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.089494 restraints weight = 23074.565| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.21 r_work: 0.3024 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13301 Z= 0.131 Angle : 0.643 12.359 18125 Z= 0.316 Chirality : 0.042 0.193 2142 Planarity : 0.005 0.043 2347 Dihedral : 4.781 27.451 1894 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.81 % Allowed : 8.66 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: -0.85 (0.20), residues: 1718 helix: 0.82 (0.19), residues: 818 sheet: -2.31 (0.38), residues: 175 loop : -1.73 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 30 TYR 0.018 0.001 TYR A 156 PHE 0.024 0.001 PHE C 109 TRP 0.017 0.001 TRP A 172 HIS 0.006 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00290 (13297) covalent geometry : angle 0.61417 (18113) hydrogen bonds : bond 0.04601 ( 618) hydrogen bonds : angle 4.81593 ( 1791) metal coordination : bond 0.00997 ( 4) metal coordination : angle 7.41143 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.509 Fit side-chains REVERT: A 238 MET cc_start: 0.7624 (tpp) cc_final: 0.7070 (tpp) REVERT: C 13 ARG cc_start: 0.8231 (ttt180) cc_final: 0.7529 (ttm110) REVERT: C 204 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8106 (mp) REVERT: D 406 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8395 (tm-30) outliers start: 11 outliers final: 7 residues processed: 131 average time/residue: 0.1123 time to fit residues: 21.3964 Evaluate side-chains 124 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 586 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 136 optimal weight: 0.0170 chunk 111 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 488 GLN B 11 ASN D 81 ASN D 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.090902 restraints weight = 23276.404| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.28 r_work: 0.3036 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13301 Z= 0.111 Angle : 0.567 11.993 18125 Z= 0.279 Chirality : 0.041 0.186 2142 Planarity : 0.004 0.038 2347 Dihedral : 4.338 18.921 1890 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.40 % Allowed : 12.11 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: -0.49 (0.21), residues: 1718 helix: 1.17 (0.19), residues: 815 sheet: -2.15 (0.38), residues: 179 loop : -1.58 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 319 TYR 0.013 0.001 TYR C 108 PHE 0.011 0.001 PHE C 109 TRP 0.012 0.001 TRP A 172 HIS 0.006 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00247 (13297) covalent geometry : angle 0.54353 (18113) hydrogen bonds : bond 0.04037 ( 618) hydrogen bonds : angle 4.44621 ( 1791) metal coordination : bond 0.00509 ( 4) metal coordination : angle 6.34438 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.507 Fit side-chains REVERT: A 238 MET cc_start: 0.7555 (tpp) cc_final: 0.7301 (tpp) REVERT: A 501 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8329 (pp) REVERT: A 578 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7401 (mp) REVERT: B 46 GLN cc_start: 0.7930 (tp40) cc_final: 0.7704 (tp40) REVERT: C 13 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7432 (ttm110) REVERT: D 406 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8451 (tm-30) outliers start: 19 outliers final: 12 residues processed: 142 average time/residue: 0.1107 time to fit residues: 22.6750 Evaluate side-chains 133 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 586 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 109 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 40 optimal weight: 0.0270 chunk 72 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 92 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN C 82 GLN D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088070 restraints weight = 23108.547| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.26 r_work: 0.2992 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13301 Z= 0.099 Angle : 0.534 11.989 18125 Z= 0.262 Chirality : 0.040 0.182 2142 Planarity : 0.004 0.041 2347 Dihedral : 4.095 18.497 1890 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.25 % Allowed : 14.39 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: -0.22 (0.21), residues: 1718 helix: 1.37 (0.19), residues: 816 sheet: -1.96 (0.38), residues: 180 loop : -1.42 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 85 TYR 0.016 0.001 TYR B 66 PHE 0.010 0.001 PHE C 177 TRP 0.009 0.001 TRP A 339 HIS 0.007 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00217 (13297) covalent geometry : angle 0.51202 (18113) hydrogen bonds : bond 0.03652 ( 618) hydrogen bonds : angle 4.26028 ( 1791) metal coordination : bond 0.00399 ( 4) metal coordination : angle 5.88692 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.307 Fit side-chains REVERT: A 238 MET cc_start: 0.7519 (tpp) cc_final: 0.7033 (tpp) REVERT: A 501 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8238 (pp) REVERT: C 13 ARG cc_start: 0.8007 (ttt180) cc_final: 0.7297 (ttm110) REVERT: C 275 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8536 (tt) REVERT: D 406 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8434 (tm-30) outliers start: 17 outliers final: 11 residues processed: 146 average time/residue: 0.1211 time to fit residues: 25.4866 Evaluate side-chains 140 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 586 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 135 optimal weight: 5.9990 chunk 8 optimal weight: 0.0770 chunk 111 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.088506 restraints weight = 23238.178| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.32 r_work: 0.2995 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13301 Z= 0.098 Angle : 0.522 11.371 18125 Z= 0.256 Chirality : 0.040 0.183 2142 Planarity : 0.004 0.042 2347 Dihedral : 3.961 18.707 1890 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.91 % Allowed : 15.20 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: -0.03 (0.21), residues: 1718 helix: 1.52 (0.19), residues: 815 sheet: -1.82 (0.39), residues: 181 loop : -1.33 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 85 TYR 0.016 0.001 TYR B 66 PHE 0.012 0.001 PHE A 484 TRP 0.008 0.001 TRP A 339 HIS 0.006 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00218 (13297) covalent geometry : angle 0.50268 (18113) hydrogen bonds : bond 0.03551 ( 618) hydrogen bonds : angle 4.15471 ( 1791) metal coordination : bond 0.00419 ( 4) metal coordination : angle 5.52121 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.533 Fit side-chains REVERT: A 76 ASP cc_start: 0.8671 (t70) cc_final: 0.8377 (t70) REVERT: A 238 MET cc_start: 0.7540 (tpp) cc_final: 0.7283 (tpp) REVERT: A 265 LEU cc_start: 0.9205 (pt) cc_final: 0.8942 (pt) REVERT: A 501 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8267 (pp) REVERT: B 165 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8415 (mp10) REVERT: B 280 TRP cc_start: 0.9582 (OUTLIER) cc_final: 0.8778 (t60) REVERT: C 36 TYR cc_start: 0.8278 (m-80) cc_final: 0.8033 (m-80) REVERT: C 275 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8570 (tt) REVERT: D 22 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8647 (t) REVERT: D 406 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8389 (tm-30) REVERT: D 580 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8993 (mt-10) outliers start: 26 outliers final: 11 residues processed: 157 average time/residue: 0.1115 time to fit residues: 25.6974 Evaluate side-chains 142 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 580 GLU Chi-restraints excluded: chain D residue 586 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN C 82 GLN D 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.104260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.085061 restraints weight = 23143.461| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.26 r_work: 0.2947 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13301 Z= 0.161 Angle : 0.564 10.790 18125 Z= 0.274 Chirality : 0.041 0.194 2142 Planarity : 0.004 0.041 2347 Dihedral : 4.078 18.133 1890 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.50 % Allowed : 15.35 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: -0.09 (0.21), residues: 1718 helix: 1.40 (0.19), residues: 818 sheet: -1.67 (0.40), residues: 174 loop : -1.35 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 319 TYR 0.018 0.001 TYR B 66 PHE 0.016 0.001 PHE A 484 TRP 0.008 0.001 TRP A 339 HIS 0.004 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00387 (13297) covalent geometry : angle 0.53697 (18113) hydrogen bonds : bond 0.04279 ( 618) hydrogen bonds : angle 4.22970 ( 1791) metal coordination : bond 0.00889 ( 4) metal coordination : angle 6.68222 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.403 Fit side-chains REVERT: A 238 MET cc_start: 0.7664 (tpp) cc_final: 0.7371 (tpp) REVERT: A 265 LEU cc_start: 0.9213 (pt) cc_final: 0.8929 (pt) REVERT: A 501 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8237 (pp) REVERT: B 165 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: B 280 TRP cc_start: 0.9598 (OUTLIER) cc_final: 0.8779 (t60) REVERT: D 22 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8740 (t) REVERT: D 406 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8391 (tm-30) outliers start: 34 outliers final: 19 residues processed: 146 average time/residue: 0.1150 time to fit residues: 24.1941 Evaluate side-chains 142 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 586 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 93 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN C 82 GLN D 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.086850 restraints weight = 23123.635| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.29 r_work: 0.2968 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13301 Z= 0.110 Angle : 0.531 11.116 18125 Z= 0.259 Chirality : 0.040 0.187 2142 Planarity : 0.004 0.039 2347 Dihedral : 3.974 18.984 1890 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.13 % Allowed : 16.52 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.03 (0.21), residues: 1718 helix: 1.50 (0.19), residues: 819 sheet: -1.59 (0.40), residues: 176 loop : -1.29 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 148 TYR 0.012 0.001 TYR B 66 PHE 0.013 0.001 PHE A 484 TRP 0.009 0.001 TRP A 339 HIS 0.006 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00252 (13297) covalent geometry : angle 0.50757 (18113) hydrogen bonds : bond 0.03796 ( 618) hydrogen bonds : angle 4.14199 ( 1791) metal coordination : bond 0.00498 ( 4) metal coordination : angle 6.03075 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.492 Fit side-chains REVERT: A 76 ASP cc_start: 0.8719 (t70) cc_final: 0.8330 (t70) REVERT: A 238 MET cc_start: 0.7562 (tpp) cc_final: 0.7278 (tpp) REVERT: A 265 LEU cc_start: 0.9190 (pt) cc_final: 0.8903 (pt) REVERT: A 501 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8308 (pp) REVERT: B 165 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8425 (mp10) REVERT: B 280 TRP cc_start: 0.9582 (OUTLIER) cc_final: 0.8761 (t60) REVERT: C 115 ARG cc_start: 0.5174 (tmt170) cc_final: 0.4611 (tmt170) REVERT: D 22 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8658 (t) REVERT: D 246 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.6979 (ptt-90) REVERT: D 406 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8323 (tm-30) outliers start: 29 outliers final: 21 residues processed: 145 average time/residue: 0.1123 time to fit residues: 23.5940 Evaluate side-chains 143 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 586 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.086316 restraints weight = 23006.028| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.28 r_work: 0.2959 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13301 Z= 0.124 Angle : 0.540 10.774 18125 Z= 0.262 Chirality : 0.040 0.190 2142 Planarity : 0.004 0.040 2347 Dihedral : 3.962 17.936 1890 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.98 % Allowed : 17.11 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.07 (0.21), residues: 1718 helix: 1.54 (0.19), residues: 817 sheet: -1.56 (0.40), residues: 176 loop : -1.29 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 148 TYR 0.019 0.001 TYR B 66 PHE 0.014 0.001 PHE A 484 TRP 0.009 0.001 TRP A 339 HIS 0.004 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00294 (13297) covalent geometry : angle 0.51662 (18113) hydrogen bonds : bond 0.03918 ( 618) hydrogen bonds : angle 4.13346 ( 1791) metal coordination : bond 0.00649 ( 4) metal coordination : angle 6.08156 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.356 Fit side-chains REVERT: A 76 ASP cc_start: 0.8751 (t70) cc_final: 0.8343 (t70) REVERT: A 238 MET cc_start: 0.7560 (tpp) cc_final: 0.7272 (tpp) REVERT: A 265 LEU cc_start: 0.9198 (pt) cc_final: 0.8915 (pt) REVERT: A 501 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8286 (pp) REVERT: B 165 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8438 (mp10) REVERT: B 280 TRP cc_start: 0.9573 (OUTLIER) cc_final: 0.8745 (t60) REVERT: C 115 ARG cc_start: 0.5173 (tmt170) cc_final: 0.4630 (tmt170) REVERT: D 22 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8713 (t) REVERT: D 246 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.6959 (ptt-90) REVERT: D 406 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8306 (tm-30) REVERT: D 590 ASN cc_start: 0.7966 (t0) cc_final: 0.7762 (t0) outliers start: 27 outliers final: 20 residues processed: 138 average time/residue: 0.1121 time to fit residues: 22.5196 Evaluate side-chains 143 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 168 optimal weight: 0.0470 chunk 68 optimal weight: 9.9990 chunk 140 optimal weight: 0.0470 chunk 137 optimal weight: 0.0270 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN D 81 ASN D 581 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089253 restraints weight = 22935.548| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.25 r_work: 0.3016 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13301 Z= 0.092 Angle : 0.512 10.698 18125 Z= 0.251 Chirality : 0.039 0.182 2142 Planarity : 0.003 0.040 2347 Dihedral : 3.790 19.471 1890 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.98 % Allowed : 17.47 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.27 (0.21), residues: 1718 helix: 1.74 (0.19), residues: 816 sheet: -1.43 (0.41), residues: 176 loop : -1.23 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 148 TYR 0.016 0.001 TYR B 66 PHE 0.011 0.001 PHE A 484 TRP 0.009 0.001 TRP A 339 HIS 0.006 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00202 (13297) covalent geometry : angle 0.49595 (18113) hydrogen bonds : bond 0.03297 ( 618) hydrogen bonds : angle 4.01808 ( 1791) metal coordination : bond 0.00335 ( 4) metal coordination : angle 4.97650 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.373 Fit side-chains REVERT: A 76 ASP cc_start: 0.8673 (t70) cc_final: 0.8253 (t70) REVERT: A 238 MET cc_start: 0.7488 (tpp) cc_final: 0.7029 (tpp) REVERT: A 265 LEU cc_start: 0.9181 (pt) cc_final: 0.8904 (pt) REVERT: A 501 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8180 (pp) REVERT: B 165 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8404 (mp10) REVERT: B 280 TRP cc_start: 0.9550 (OUTLIER) cc_final: 0.8742 (t60) REVERT: C 36 TYR cc_start: 0.8207 (m-80) cc_final: 0.7981 (m-80) REVERT: C 115 ARG cc_start: 0.5174 (tmt170) cc_final: 0.4704 (tmt170) REVERT: D 22 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8603 (t) outliers start: 27 outliers final: 18 residues processed: 152 average time/residue: 0.1051 time to fit residues: 23.7976 Evaluate side-chains 141 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 475 PHE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 586 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 129 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087690 restraints weight = 23137.783| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.29 r_work: 0.2983 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13301 Z= 0.115 Angle : 0.528 10.299 18125 Z= 0.259 Chirality : 0.040 0.187 2142 Planarity : 0.004 0.041 2347 Dihedral : 3.793 17.718 1890 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.62 % Allowed : 18.21 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.30 (0.21), residues: 1718 helix: 1.76 (0.19), residues: 815 sheet: -1.37 (0.41), residues: 176 loop : -1.22 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 148 TYR 0.019 0.001 TYR B 66 PHE 0.013 0.001 PHE C 177 TRP 0.006 0.001 TRP A 339 HIS 0.004 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00269 (13297) covalent geometry : angle 0.51004 (18113) hydrogen bonds : bond 0.03621 ( 618) hydrogen bonds : angle 4.02287 ( 1791) metal coordination : bond 0.00554 ( 4) metal coordination : angle 5.39870 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.496 Fit side-chains REVERT: A 76 ASP cc_start: 0.8698 (t70) cc_final: 0.8270 (t70) REVERT: A 238 MET cc_start: 0.7497 (tpp) cc_final: 0.7230 (tpp) REVERT: A 265 LEU cc_start: 0.9213 (pt) cc_final: 0.8944 (pt) REVERT: A 501 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8207 (pp) REVERT: B 165 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8431 (mp10) REVERT: B 280 TRP cc_start: 0.9565 (OUTLIER) cc_final: 0.8778 (t60) REVERT: C 115 ARG cc_start: 0.5133 (tmt170) cc_final: 0.4586 (tmt170) REVERT: D 22 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8652 (t) REVERT: D 590 ASN cc_start: 0.7863 (t0) cc_final: 0.7131 (p0) outliers start: 22 outliers final: 16 residues processed: 135 average time/residue: 0.1104 time to fit residues: 21.9328 Evaluate side-chains 137 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 586 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 0.0980 chunk 105 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.088735 restraints weight = 22963.251| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.26 r_work: 0.2996 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13301 Z= 0.101 Angle : 0.517 10.437 18125 Z= 0.253 Chirality : 0.040 0.184 2142 Planarity : 0.004 0.040 2347 Dihedral : 3.755 19.083 1890 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.62 % Allowed : 18.36 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.36 (0.21), residues: 1718 helix: 1.80 (0.19), residues: 816 sheet: -1.31 (0.41), residues: 176 loop : -1.19 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 148 TYR 0.018 0.001 TYR B 66 PHE 0.012 0.001 PHE C 177 TRP 0.007 0.001 TRP A 339 HIS 0.005 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00229 (13297) covalent geometry : angle 0.49878 (18113) hydrogen bonds : bond 0.03465 ( 618) hydrogen bonds : angle 3.98400 ( 1791) metal coordination : bond 0.00412 ( 4) metal coordination : angle 5.30941 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.53 seconds wall clock time: 58 minutes 2.58 seconds (3482.58 seconds total)