Starting phenix.real_space_refine on Sun Nov 17 05:39:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/11_2024/8j5r_35991.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/11_2024/8j5r_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/11_2024/8j5r_35991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/11_2024/8j5r_35991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/11_2024/8j5r_35991.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5r_35991/11_2024/8j5r_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.36, per 1000 atoms: 0.64 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: 3.76 Conformation dependent library (CDL) restraints added in 1.9 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: 1.50 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: 3.91 Time building geometry restraints manager: 4.02 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 34.580 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.520 ------------------------------------------------------------------------------- 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 : 0.007 0.075 13297 Z= 0.496 Angle : 0.961 11.137 18113 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 *********************** 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 : 1.505 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: 0.3132 time to fit residues: 61.3046 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 : 1.462 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 13297 Z= 0.293 Angle : 0.639 8.572 18113 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 *********************** 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 : 1.490 Fit side-chains REVERT: A 238 MET cc_start: 0.7368 (tpp) cc_final: 0.6841 (tpp) REVERT: C 204 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8013 (mp) REVERT: D 406 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7973 (tm-30) outliers start: 12 outliers final: 8 residues processed: 124 average time/residue: 0.2630 time to fit residues: 47.8714 Evaluate side-chains 118 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13297 Z= 0.172 Angle : 0.555 8.399 18113 Z= 0.284 Chirality : 0.041 0.190 2142 Planarity : 0.004 0.041 2347 Dihedral : 4.456 19.474 1890 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.10 % Allowed : 13.29 % Favored : 85.61 % 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 : -1.63 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 172 HIS 0.006 0.001 HIS D 558 PHE 0.013 0.001 PHE A 484 TYR 0.012 0.001 TYR B 66 ARG 0.005 0.001 ARG D 319 *********************** 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 137 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.480 Fit side-chains REVERT: D 406 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8042 (tm-30) outliers start: 15 outliers final: 9 residues processed: 133 average time/residue: 0.2777 time to fit residues: 53.5679 Evaluate side-chains 124 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 262 VAL 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 152 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13297 Z= 0.221 Angle : 0.544 8.402 18113 Z= 0.279 Chirality : 0.041 0.190 2142 Planarity : 0.004 0.042 2347 Dihedral : 4.330 18.006 1890 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.76 % Allowed : 14.76 % Favored : 83.48 % 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: 1.16 (0.19), residues: 817 sheet: -2.13 (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 0.013 0.001 PHE C 177 TYR 0.013 0.001 TYR C 108 ARG 0.005 0.000 ARG D 319 *********************** 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 143 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.530 Fit side-chains REVERT: A 238 MET cc_start: 0.7319 (tpp) cc_final: 0.7107 (tpp) REVERT: B 165 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8137 (mp10) REVERT: B 280 TRP cc_start: 0.9563 (OUTLIER) cc_final: 0.8647 (t60) REVERT: C 275 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8666 (tt) REVERT: D 246 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7339 (ptt-90) REVERT: D 406 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8049 (tm-30) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 0.2780 time to fit residues: 53.9442 Evaluate side-chains 129 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 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 136 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 0.0170 chunk 122 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13297 Z= 0.173 Angle : 0.522 8.228 18113 Z= 0.268 Chirality : 0.040 0.186 2142 Planarity : 0.004 0.043 2347 Dihedral : 4.173 18.703 1890 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.98 % Allowed : 15.93 % Favored : 82.09 % 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: -0.28 (0.21), residues: 1718 helix: 1.29 (0.19), residues: 819 sheet: -1.86 (0.39), residues: 176 loop : -1.47 (0.22), 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 0.012 0.001 PHE A 484 TYR 0.018 0.001 TYR B 66 ARG 0.005 0.000 ARG A 148 *********************** 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 152 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.510 Fit side-chains REVERT: A 238 MET cc_start: 0.7303 (tpp) cc_final: 0.7075 (tpp) REVERT: A 265 LEU cc_start: 0.9033 (pt) cc_final: 0.8765 (pt) REVERT: B 165 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: B 280 TRP cc_start: 0.9553 (OUTLIER) cc_final: 0.8651 (t60) REVERT: C 115 ARG cc_start: 0.5079 (tmt170) cc_final: 0.4790 (tmt170) REVERT: C 275 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8632 (tt) REVERT: D 194 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8341 (tp) outliers start: 27 outliers final: 13 residues processed: 144 average time/residue: 0.2549 time to fit residues: 54.2613 Evaluate side-chains 135 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 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 194 LEU 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 55 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 0.0170 chunk 54 optimal weight: 0.0070 chunk 86 optimal weight: 2.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- 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 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13297 Z= 0.133 Angle : 0.511 8.000 18113 Z= 0.261 Chirality : 0.040 0.271 2142 Planarity : 0.004 0.042 2347 Dihedral : 3.969 18.849 1890 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.06 % Allowed : 16.52 % Favored : 81.42 % 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: -0.03 (0.21), residues: 1718 helix: 1.49 (0.19), residues: 816 sheet: -1.67 (0.40), residues: 176 loop : -1.36 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 339 HIS 0.007 0.001 HIS D 558 PHE 0.011 0.001 PHE A 484 TYR 0.016 0.001 TYR B 66 ARG 0.004 0.000 ARG A 148 *********************** 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 166 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.667 Fit side-chains REVERT: A 76 ASP cc_start: 0.8348 (t70) cc_final: 0.8116 (t70) REVERT: A 265 LEU cc_start: 0.9025 (pt) cc_final: 0.8746 (pt) REVERT: B 165 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: B 280 TRP cc_start: 0.9519 (OUTLIER) cc_final: 0.8633 (t60) REVERT: C 275 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8599 (tt) outliers start: 28 outliers final: 16 residues processed: 160 average time/residue: 0.2504 time to fit residues: 59.3010 Evaluate side-chains 146 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 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 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 18 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13297 Z= 0.182 Angle : 0.518 8.283 18113 Z= 0.263 Chirality : 0.041 0.246 2142 Planarity : 0.004 0.043 2347 Dihedral : 3.940 18.361 1890 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.76 % Allowed : 17.40 % Favored : 80.84 % 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: 0.03 (0.21), residues: 1718 helix: 1.51 (0.19), residues: 819 sheet: -1.61 (0.40), residues: 176 loop : -1.30 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.005 0.001 HIS D 558 PHE 0.013 0.001 PHE C 177 TYR 0.017 0.001 TYR B 66 ARG 0.003 0.000 ARG A 148 *********************** 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 150 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.502 Fit side-chains REVERT: A 76 ASP cc_start: 0.8378 (t70) cc_final: 0.8119 (t70) REVERT: A 238 MET cc_start: 0.7085 (tpp) cc_final: 0.6707 (tpp) REVERT: A 265 LEU cc_start: 0.9060 (pt) cc_final: 0.8782 (pt) REVERT: B 165 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: B 280 TRP cc_start: 0.9539 (OUTLIER) cc_final: 0.8700 (t60) REVERT: C 115 ARG cc_start: 0.5113 (tmt170) cc_final: 0.4613 (tmt170) outliers start: 24 outliers final: 17 residues processed: 143 average time/residue: 0.2608 time to fit residues: 55.0080 Evaluate side-chains 139 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 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 D residue 21 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13297 Z= 0.251 Angle : 0.542 8.557 18113 Z= 0.277 Chirality : 0.042 0.243 2142 Planarity : 0.004 0.041 2347 Dihedral : 4.080 18.076 1890 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.76 % Allowed : 17.84 % Favored : 80.40 % 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: -0.03 (0.21), residues: 1718 helix: 1.45 (0.19), residues: 816 sheet: -1.60 (0.40), residues: 176 loop : -1.33 (0.22), residues: 726 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 C 177 TYR 0.017 0.001 TYR B 66 ARG 0.004 0.000 ARG D 353 *********************** 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 142 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.435 Fit side-chains REVERT: A 76 ASP cc_start: 0.8453 (t70) cc_final: 0.8174 (t70) REVERT: A 265 LEU cc_start: 0.9067 (pt) cc_final: 0.8793 (pt) REVERT: B 165 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: B 280 TRP cc_start: 0.9559 (OUTLIER) cc_final: 0.8640 (t60) REVERT: C 115 ARG cc_start: 0.5183 (tmt170) cc_final: 0.4659 (tmt170) REVERT: D 246 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.7307 (ptt-90) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.2934 time to fit residues: 57.7203 Evaluate side-chains 135 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 466 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 D residue 21 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.7980 chunk 143 optimal weight: 0.0000 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13297 Z= 0.180 Angle : 0.522 8.365 18113 Z= 0.267 Chirality : 0.041 0.234 2142 Planarity : 0.004 0.042 2347 Dihedral : 3.991 18.683 1890 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.91 % Allowed : 18.36 % Favored : 79.74 % 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: 0.07 (0.21), residues: 1718 helix: 1.54 (0.19), residues: 817 sheet: -1.53 (0.40), residues: 176 loop : -1.29 (0.23), residues: 725 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 0.030 0.001 TYR B 66 ARG 0.007 0.000 ARG A 148 *********************** 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 144 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.472 Fit side-chains REVERT: A 76 ASP cc_start: 0.8391 (t70) cc_final: 0.8120 (t70) REVERT: A 238 MET cc_start: 0.7039 (tpp) cc_final: 0.6764 (tpp) REVERT: A 265 LEU cc_start: 0.9005 (pt) cc_final: 0.8741 (pt) REVERT: B 165 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: B 280 TRP cc_start: 0.9536 (OUTLIER) cc_final: 0.8611 (t60) REVERT: C 115 ARG cc_start: 0.5124 (tmt170) cc_final: 0.4600 (tmt170) REVERT: D 246 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.6901 (ptt-90) outliers start: 26 outliers final: 20 residues processed: 138 average time/residue: 0.2717 time to fit residues: 54.2379 Evaluate side-chains 140 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 466 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 D residue 21 VAL 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 239 VAL Chi-restraints excluded: chain D residue 246 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 112 optimal weight: 0.0020 chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 0.2980 chunk 143 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13297 Z= 0.153 Angle : 0.509 8.283 18113 Z= 0.259 Chirality : 0.040 0.234 2142 Planarity : 0.004 0.042 2347 Dihedral : 3.882 18.315 1890 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.91 % Allowed : 18.21 % Favored : 79.88 % 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: -1.46 (0.41), residues: 176 loop : -1.25 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.005 0.001 HIS D 558 PHE 0.012 0.001 PHE C 177 TYR 0.024 0.001 TYR B 66 ARG 0.007 0.000 ARG A 148 ********************** 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 150 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.548 Fit side-chains REVERT: A 76 ASP cc_start: 0.8344 (t70) cc_final: 0.8059 (t70) REVERT: A 238 MET cc_start: 0.7035 (tpp) cc_final: 0.6777 (tpp) REVERT: A 265 LEU cc_start: 0.9053 (pt) cc_final: 0.8789 (pt) REVERT: B 165 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8129 (mp10) REVERT: B 280 TRP cc_start: 0.9512 (OUTLIER) cc_final: 0.8705 (t60) REVERT: C 115 ARG cc_start: 0.5125 (tmt170) cc_final: 0.4791 (tmt170) REVERT: D 246 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.6794 (ptt-90) REVERT: D 590 ASN cc_start: 0.7424 (t0) cc_final: 0.6928 (p0) outliers start: 26 outliers final: 21 residues processed: 143 average time/residue: 0.2674 time to fit residues: 55.3619 Evaluate side-chains 142 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 466 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 D residue 21 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 246 ARG 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 41 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 56 optimal weight: 0.0060 chunk 138 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.089329 restraints weight = 22711.422| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.25 r_work: 0.2999 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13297 Z= 0.141 Angle : 0.501 8.107 18113 Z= 0.254 Chirality : 0.040 0.229 2142 Planarity : 0.003 0.042 2347 Dihedral : 3.778 18.618 1890 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.69 % Allowed : 18.43 % Favored : 79.88 % 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: 0.32 (0.21), residues: 1718 helix: 1.76 (0.19), residues: 816 sheet: -1.36 (0.41), residues: 176 loop : -1.19 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 339 HIS 0.005 0.000 HIS D 558 PHE 0.011 0.001 PHE C 177 TYR 0.019 0.001 TYR B 66 ARG 0.008 0.000 ARG D 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2728.14 seconds wall clock time: 50 minutes 13.81 seconds (3013.81 seconds total)