Starting phenix.real_space_refine on Thu Jul 31 01:49:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5r_35991/07_2025/8j5r_35991.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5r_35991/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j5r_35991/07_2025/8j5r_35991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5r_35991/07_2025/8j5r_35991.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5r_35991/07_2025/8j5r_35991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5r_35991/07_2025/8j5r_35991.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.051 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.57, per 1000 atoms: 0.66 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: 3.47 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.30 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: 4.34 Time building geometry restraints manager: 3.85 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: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.630 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.710 ------------------------------------------------------------------------------- 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 : 14.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (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 TRP 0.029 0.002 TRP B 280 HIS 0.006 0.001 HIS D 153 PHE 0.024 0.002 PHE A 484 TYR 0.015 0.002 TYR A 406 ARG 0.010 0.001 ARG D 268 Details of bonding type rmsd hydrogen bonds : bond 0.13658 ( 618) hydrogen bonds : angle 6.51292 ( 1791) metal coordination : bond 0.07168 ( 4) metal coordination : angle 6.84770 ( 12) covalent geometry : bond 0.00746 (13297) covalent geometry : angle 0.96126 (18113) *********************** 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 : 1.454 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: 0.3042 time to fit residues: 59.5458 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 : 1.634 ------------------------------------------------------------------------------- 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 143 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.105611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.087152 restraints weight = 23173.175| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.19 r_work: 0.2984 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13301 Z= 0.186 Angle : 0.671 12.185 18125 Z= 0.330 Chirality : 0.044 0.197 2142 Planarity : 0.005 0.040 2347 Dihedral : 4.908 28.403 1894 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.88 % Allowed : 9.84 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1718 helix: 0.70 (0.19), residues: 818 sheet: -2.40 (0.37), residues: 176 loop : -1.83 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 172 HIS 0.005 0.001 HIS D 558 PHE 0.021 0.002 PHE C 109 TYR 0.016 0.002 TYR A 156 ARG 0.007 0.001 ARG D 319 Details of bonding type rmsd hydrogen bonds : bond 0.05157 ( 618) hydrogen bonds : angle 4.91212 ( 1791) metal coordination : bond 0.01356 ( 4) metal coordination : angle 7.92121 ( 12) covalent geometry : bond 0.00443 (13297) covalent geometry : angle 0.63911 (18113) *********************** 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 128 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.538 Fit side-chains REVERT: A 238 MET cc_start: 0.7723 (tpp) cc_final: 0.7106 (tpp) REVERT: C 13 ARG cc_start: 0.8253 (ttt180) cc_final: 0.7553 (ttm110) REVERT: C 204 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8186 (mp) REVERT: D 406 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8371 (tm-30) outliers start: 12 outliers final: 8 residues processed: 124 average time/residue: 0.2680 time to fit residues: 49.1534 Evaluate side-chains 119 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 21 VAL 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 69 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 146 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089682 restraints weight = 23313.637| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.27 r_work: 0.3017 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1379 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= 0.118 Angle : 0.583 12.281 18125 Z= 0.286 Chirality : 0.041 0.189 2142 Planarity : 0.004 0.042 2347 Dihedral : 4.466 19.516 1890 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.17 % Allowed : 13.36 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1718 helix: 1.02 (0.19), residues: 821 sheet: -2.21 (0.38), residues: 178 loop : -1.64 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 172 HIS 0.005 0.001 HIS D 558 PHE 0.012 0.001 PHE A 484 TYR 0.012 0.001 TYR B 66 ARG 0.005 0.000 ARG D 319 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 618) hydrogen bonds : angle 4.53003 ( 1791) metal coordination : bond 0.00488 ( 4) metal coordination : angle 6.72565 ( 12) covalent geometry : bond 0.00266 (13297) covalent geometry : angle 0.55658 (18113) *********************** 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 139 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.487 Fit side-chains REVERT: A 238 MET cc_start: 0.7597 (tpp) cc_final: 0.7325 (tpp) REVERT: A 501 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8365 (pp) REVERT: B 90 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8555 (mt-10) REVERT: C 13 ARG cc_start: 0.8151 (ttt180) cc_final: 0.7447 (ttm110) REVERT: D 406 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8425 (tm-30) outliers start: 16 outliers final: 9 residues processed: 134 average time/residue: 0.2894 time to fit residues: 55.9491 Evaluate side-chains 125 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 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 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 100 optimal weight: 1.9990 chunk 68 optimal weight: 0.0050 chunk 108 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 590 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089279 restraints weight = 23181.304| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.29 r_work: 0.3003 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 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 = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13301 Z= 0.137 Angle : 0.565 11.697 18125 Z= 0.277 Chirality : 0.041 0.189 2142 Planarity : 0.004 0.042 2347 Dihedral : 4.323 18.069 1890 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.84 % Allowed : 14.54 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1718 helix: 1.15 (0.19), residues: 817 sheet: -2.12 (0.38), residues: 179 loop : -1.53 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.005 0.001 HIS D 558 PHE 0.014 0.001 PHE A 484 TYR 0.016 0.001 TYR B 66 ARG 0.005 0.000 ARG D 319 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 618) hydrogen bonds : angle 4.41172 ( 1791) metal coordination : bond 0.00727 ( 4) metal coordination : angle 6.66537 ( 12) covalent geometry : bond 0.00324 (13297) covalent geometry : angle 0.53900 (18113) *********************** 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 146 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.356 Fit side-chains REVERT: A 238 MET cc_start: 0.7672 (tpp) cc_final: 0.7390 (tpp) REVERT: A 501 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8380 (pp) REVERT: B 46 GLN cc_start: 0.8050 (tp40) cc_final: 0.7846 (tp40) REVERT: B 165 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: B 280 TRP cc_start: 0.9631 (OUTLIER) cc_final: 0.8728 (t60) REVERT: C 13 ARG cc_start: 0.8104 (ttt180) cc_final: 0.7416 (ttm110) REVERT: C 275 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8681 (tt) REVERT: D 246 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.7146 (ptt-90) REVERT: D 406 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8436 (tm-30) outliers start: 25 outliers final: 14 residues processed: 138 average time/residue: 0.2699 time to fit residues: 53.3756 Evaluate side-chains 132 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 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 C residue 16 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 246 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 94 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 162 optimal weight: 0.0870 chunk 3 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 590 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085711 restraints weight = 23004.545| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.26 r_work: 0.2950 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 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 = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13301 Z= 0.122 Angle : 0.551 11.327 18125 Z= 0.271 Chirality : 0.040 0.187 2142 Planarity : 0.004 0.043 2347 Dihedral : 4.195 18.573 1890 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.20 % Allowed : 15.57 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1718 helix: 1.27 (0.19), residues: 818 sheet: -1.89 (0.39), residues: 176 loop : -1.47 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.005 0.001 HIS D 558 PHE 0.013 0.001 PHE A 484 TYR 0.017 0.001 TYR B 66 ARG 0.005 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 618) hydrogen bonds : angle 4.28987 ( 1791) metal coordination : bond 0.00592 ( 4) metal coordination : angle 6.35585 ( 12) covalent geometry : bond 0.00281 (13297) covalent geometry : angle 0.52609 (18113) *********************** 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 153 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 1.428 Fit side-chains REVERT: A 238 MET cc_start: 0.7542 (tpp) cc_final: 0.7256 (tpp) REVERT: A 265 LEU cc_start: 0.9172 (pt) cc_final: 0.8906 (pt) REVERT: A 501 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8234 (pp) REVERT: B 46 GLN cc_start: 0.8096 (tp40) cc_final: 0.7799 (tp40) REVERT: B 165 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8413 (mp10) REVERT: B 280 TRP cc_start: 0.9596 (OUTLIER) cc_final: 0.8746 (t60) REVERT: C 13 ARG cc_start: 0.7990 (ttt180) cc_final: 0.7283 (ttm110) REVERT: C 115 ARG cc_start: 0.5187 (tmt170) cc_final: 0.4812 (tmt170) REVERT: C 275 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8570 (tt) REVERT: D 22 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8718 (t) REVERT: D 406 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8359 (tm-30) outliers start: 30 outliers final: 17 residues processed: 144 average time/residue: 0.2536 time to fit residues: 53.4023 Evaluate side-chains 138 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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 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 C residue 170 MET 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 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 239 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 19 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.084251 restraints weight = 23541.666| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.29 r_work: 0.2922 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13301 Z= 0.162 Angle : 0.573 10.900 18125 Z= 0.280 Chirality : 0.041 0.192 2142 Planarity : 0.004 0.043 2347 Dihedral : 4.227 18.516 1890 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.42 % Allowed : 16.52 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1718 helix: 1.25 (0.19), residues: 815 sheet: -1.89 (0.39), residues: 176 loop : -1.45 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.005 0.001 HIS D 558 PHE 0.016 0.001 PHE A 484 TYR 0.017 0.001 TYR B 66 ARG 0.004 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 618) hydrogen bonds : angle 4.31092 ( 1791) metal coordination : bond 0.00883 ( 4) metal coordination : angle 6.83239 ( 12) covalent geometry : bond 0.00389 (13297) covalent geometry : angle 0.54552 (18113) *********************** 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 153 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.533 Fit side-chains REVERT: A 238 MET cc_start: 0.7587 (tpp) cc_final: 0.7263 (tpp) REVERT: A 265 LEU cc_start: 0.9184 (pt) cc_final: 0.8904 (pt) REVERT: A 501 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8244 (pp) REVERT: B 165 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8428 (mp10) REVERT: B 280 TRP cc_start: 0.9604 (OUTLIER) cc_final: 0.8778 (t60) REVERT: C 13 ARG cc_start: 0.7951 (ttt180) cc_final: 0.7161 (tpp80) REVERT: C 275 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8584 (tt) REVERT: D 22 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8738 (t) REVERT: D 406 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8336 (tm-30) outliers start: 33 outliers final: 19 residues processed: 144 average time/residue: 0.2640 time to fit residues: 55.2233 Evaluate side-chains 141 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 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 C residue 16 LEU Chi-restraints excluded: chain C residue 170 MET 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 137 ASP Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 239 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085727 restraints weight = 23243.909| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.29 r_work: 0.2947 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13301 Z= 0.118 Angle : 0.544 10.988 18125 Z= 0.267 Chirality : 0.040 0.187 2142 Planarity : 0.004 0.042 2347 Dihedral : 4.103 19.009 1890 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.28 % Allowed : 16.96 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1718 helix: 1.36 (0.19), residues: 817 sheet: -1.76 (0.39), residues: 176 loop : -1.39 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.006 0.001 HIS D 558 PHE 0.015 0.001 PHE A 484 TYR 0.018 0.001 TYR B 66 ARG 0.003 0.000 ARG D 353 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 618) hydrogen bonds : angle 4.22088 ( 1791) metal coordination : bond 0.00577 ( 4) metal coordination : angle 6.20865 ( 12) covalent geometry : bond 0.00275 (13297) covalent geometry : angle 0.52052 (18113) *********************** 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 147 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.567 Fit side-chains REVERT: A 76 ASP cc_start: 0.8782 (t70) cc_final: 0.8405 (t70) REVERT: A 238 MET cc_start: 0.7586 (tpp) cc_final: 0.7297 (tpp) REVERT: A 265 LEU cc_start: 0.9140 (pt) cc_final: 0.8869 (pt) REVERT: A 501 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8255 (pp) REVERT: B 165 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8416 (mp10) REVERT: B 280 TRP cc_start: 0.9585 (OUTLIER) cc_final: 0.8790 (t60) REVERT: C 115 ARG cc_start: 0.5205 (tmt170) cc_final: 0.4788 (tmt170) REVERT: C 275 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8575 (tt) REVERT: D 22 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8666 (t) REVERT: D 406 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8295 (tm-30) outliers start: 31 outliers final: 22 residues processed: 139 average time/residue: 0.2525 time to fit residues: 51.7780 Evaluate side-chains 141 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 C residue 16 LEU Chi-restraints excluded: chain C residue 170 MET 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 137 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 307 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 97 optimal weight: 0.9980 chunk 121 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.086339 restraints weight = 22957.704| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.25 r_work: 0.2957 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13301 Z= 0.112 Angle : 0.535 10.765 18125 Z= 0.262 Chirality : 0.040 0.190 2142 Planarity : 0.004 0.043 2347 Dihedral : 3.991 18.160 1890 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.35 % Allowed : 17.33 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1718 helix: 1.47 (0.19), residues: 819 sheet: -1.69 (0.40), residues: 176 loop : -1.31 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 339 HIS 0.005 0.001 HIS D 558 PHE 0.013 0.001 PHE C 177 TYR 0.018 0.001 TYR B 66 ARG 0.004 0.000 ARG D 353 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 618) hydrogen bonds : angle 4.15495 ( 1791) metal coordination : bond 0.00540 ( 4) metal coordination : angle 5.81967 ( 12) covalent geometry : bond 0.00258 (13297) covalent geometry : angle 0.51333 (18113) *********************** 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 153 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.514 Fit side-chains REVERT: A 76 ASP cc_start: 0.8758 (t70) cc_final: 0.8364 (t70) REVERT: A 238 MET cc_start: 0.7524 (tpp) cc_final: 0.7241 (tpp) REVERT: A 265 LEU cc_start: 0.9147 (pt) cc_final: 0.8878 (pt) REVERT: A 501 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8287 (pp) REVERT: B 165 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8421 (mp10) REVERT: B 280 TRP cc_start: 0.9576 (OUTLIER) cc_final: 0.8785 (t60) REVERT: C 115 ARG cc_start: 0.5212 (tmt170) cc_final: 0.4794 (tmt170) REVERT: C 275 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8564 (tt) REVERT: D 22 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8660 (t) REVERT: D 406 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8285 (tm-30) REVERT: D 590 ASN cc_start: 0.7923 (t0) cc_final: 0.7712 (t0) outliers start: 32 outliers final: 23 residues processed: 145 average time/residue: 0.2631 time to fit residues: 55.7910 Evaluate side-chains 145 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 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 C residue 170 MET 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 103 THR Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 307 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 155 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN D 81 ASN D 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.087218 restraints weight = 23064.996| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.28 r_work: 0.2974 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 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 = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2064 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= 0.104 Angle : 0.528 10.516 18125 Z= 0.259 Chirality : 0.040 0.186 2142 Planarity : 0.004 0.043 2347 Dihedral : 3.924 18.941 1890 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.28 % Allowed : 17.77 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1718 helix: 1.57 (0.19), residues: 817 sheet: -1.59 (0.40), residues: 176 loop : -1.30 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.005 0.001 HIS D 558 PHE 0.014 0.001 PHE A 484 TYR 0.019 0.001 TYR B 66 ARG 0.008 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 618) hydrogen bonds : angle 4.10893 ( 1791) metal coordination : bond 0.00464 ( 4) metal coordination : angle 5.54684 ( 12) covalent geometry : bond 0.00237 (13297) covalent geometry : angle 0.50847 (18113) *********************** 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 160 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.402 Fit side-chains REVERT: A 76 ASP cc_start: 0.8722 (t70) cc_final: 0.8321 (t70) REVERT: A 238 MET cc_start: 0.7441 (tpp) cc_final: 0.7169 (tpp) REVERT: A 265 LEU cc_start: 0.9151 (pt) cc_final: 0.8877 (pt) REVERT: A 501 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8226 (pp) REVERT: B 165 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8411 (mp10) REVERT: B 280 TRP cc_start: 0.9575 (OUTLIER) cc_final: 0.8813 (t60) REVERT: C 115 ARG cc_start: 0.5226 (tmt170) cc_final: 0.4808 (tmt170) REVERT: C 275 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8567 (tt) REVERT: D 22 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8642 (t) REVERT: D 406 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8304 (tm-30) outliers start: 31 outliers final: 23 residues processed: 151 average time/residue: 0.2429 time to fit residues: 55.1974 Evaluate side-chains 148 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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 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 C residue 170 MET 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 103 THR Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 307 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 32 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.108916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.090685 restraints weight = 23129.126| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.12 r_work: 0.2995 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13301 Z= 0.103 Angle : 0.525 10.258 18125 Z= 0.257 Chirality : 0.040 0.185 2142 Planarity : 0.004 0.043 2347 Dihedral : 3.844 17.917 1890 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.98 % Allowed : 18.43 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1718 helix: 1.66 (0.19), residues: 817 sheet: -1.51 (0.41), residues: 176 loop : -1.23 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.005 0.001 HIS D 558 PHE 0.013 0.001 PHE A 484 TYR 0.018 0.001 TYR B 66 ARG 0.007 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 618) hydrogen bonds : angle 4.07178 ( 1791) metal coordination : bond 0.00433 ( 4) metal coordination : angle 5.34920 ( 12) covalent geometry : bond 0.00235 (13297) covalent geometry : angle 0.50654 (18113) ********************** 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 154 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.353 Fit side-chains REVERT: A 76 ASP cc_start: 0.8700 (t70) cc_final: 0.8257 (t70) REVERT: A 238 MET cc_start: 0.7390 (tpp) cc_final: 0.7128 (tpp) REVERT: A 265 LEU cc_start: 0.9153 (pt) cc_final: 0.8886 (pt) REVERT: A 501 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8137 (pp) REVERT: B 165 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8435 (mp10) REVERT: B 280 TRP cc_start: 0.9542 (OUTLIER) cc_final: 0.8726 (t60) REVERT: C 115 ARG cc_start: 0.5000 (tmt170) cc_final: 0.4597 (tmt170) REVERT: D 22 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8616 (t) REVERT: D 406 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8284 (tm-30) outliers start: 27 outliers final: 23 residues processed: 146 average time/residue: 0.2515 time to fit residues: 53.9893 Evaluate side-chains 147 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 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 C residue 170 MET 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 103 THR Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 356 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 161 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.085283 restraints weight = 23340.362| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.29 r_work: 0.2941 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 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 = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2052 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= 0.155 Angle : 0.559 10.021 18125 Z= 0.274 Chirality : 0.041 0.190 2142 Planarity : 0.004 0.043 2347 Dihedral : 3.961 18.366 1890 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.13 % Allowed : 18.58 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1718 helix: 1.56 (0.19), residues: 819 sheet: -1.48 (0.41), residues: 176 loop : -1.23 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.004 0.001 HIS D 558 PHE 0.016 0.001 PHE A 484 TYR 0.019 0.001 TYR B 66 ARG 0.006 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 618) hydrogen bonds : angle 4.14735 ( 1791) metal coordination : bond 0.00747 ( 4) metal coordination : angle 6.26647 ( 12) covalent geometry : bond 0.00371 (13297) covalent geometry : angle 0.53566 (18113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7740.33 seconds wall clock time: 135 minutes 36.82 seconds (8136.82 seconds total)