Starting phenix.real_space_refine on Mon Mar 11 06:23:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irt_9722/03_2024/6irt_9722_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irt_9722/03_2024/6irt_9722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irt_9722/03_2024/6irt_9722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irt_9722/03_2024/6irt_9722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irt_9722/03_2024/6irt_9722_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6irt_9722/03_2024/6irt_9722_neut_updated.pdb" } resolution = 3.5 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= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 4815 2.51 5 N 1173 2.21 5 O 1331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 421": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7348 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Chain: "B" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3479 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'3PH': 2, 'AUU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.63, per 1000 atoms: 0.63 Number of scatterers: 7348 At special positions: 0 Unit cell: (82.916, 84.007, 124.374, 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) S 27 16.00 P 2 15.00 O 1331 8.00 N 1173 7.00 C 4815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.7 seconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 5 sheets defined 49.5% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 169 through 174 removed outlier: 4.150A pdb=" N VAL A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 174' Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 186 through 207 removed outlier: 3.616A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 231 through 234 No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 242 through 247 removed outlier: 4.142A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 255 removed outlier: 3.876A pdb=" N SER A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 Processing helix chain 'A' and resid 325 through 341 removed outlier: 4.203A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 357 through 369 removed outlier: 3.709A pdb=" N LEU A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.665A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.787A pdb=" N GLN A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.522A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.595A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 removed outlier: 3.784A pdb=" N HIS A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 539' Processing helix chain 'B' and resid 55 through 62 removed outlier: 3.656A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 82 through 109 removed outlier: 3.607A pdb=" N LEU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 93 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.569A pdb=" N VAL B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 140 through 157 removed outlier: 3.660A pdb=" N GLN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 186 removed outlier: 4.333A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 182 " --> pdb=" O CYS B 178 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.151A pdb=" N ARG B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 221 removed outlier: 3.544A pdb=" N LEU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 234 removed outlier: 4.399A pdb=" N GLU B 234 " --> pdb=" O PHE B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 231 through 234' Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.633A pdb=" N SER B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 268 removed outlier: 3.854A pdb=" N THR B 264 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 265 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU B 266 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET B 267 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 299 removed outlier: 3.725A pdb=" N ILE B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.730A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 No H-bonds generated for 'chain 'B' and resid 304 through 307' Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.708A pdb=" N HIS B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.598A pdb=" N LEU B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.675A pdb=" N PHE B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 420 removed outlier: 3.509A pdb=" N PHE B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 419 " --> pdb=" O MET B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 452 removed outlier: 3.808A pdb=" N ALA B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 447 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 465 removed outlier: 4.028A pdb=" N ILE B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 475 Processing helix chain 'B' and resid 485 through 500 removed outlier: 3.950A pdb=" N PHE B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 225 through 227 Processing sheet with id= B, first strand: chain 'A' and resid 259 through 262 removed outlier: 6.775A pdb=" N ARG A 304 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU A 262 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE A 306 " --> pdb=" O LEU A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 345 through 348 removed outlier: 6.291A pdb=" N LEU A 376 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL A 348 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE A 378 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 400 " --> pdb=" O ALA A 379 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.700A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 556 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG A 626 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU A 596 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.968A pdb=" N GLN A 280 " --> pdb=" O LYS A 267 " (cutoff:3.500A) 228 hydrogen bonds defined for protein. 672 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: 1.92 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2069 1.33 - 1.45: 1333 1.45 - 1.57: 4077 1.57 - 1.69: 3 1.69 - 1.81: 42 Bond restraints: 7524 Sorted by residual: bond pdb=" C06 AUU B 603 " pdb=" C08 AUU B 603 " ideal model delta sigma weight residual 1.531 1.707 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" C04 AUU B 603 " pdb=" C09 AUU B 603 " ideal model delta sigma weight residual 1.535 1.362 0.173 2.00e-02 2.50e+03 7.53e+01 bond pdb=" C04 AUU B 603 " pdb=" C08 AUU B 603 " ideal model delta sigma weight residual 1.533 1.699 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C06 AUU B 603 " pdb=" C07 AUU B 603 " ideal model delta sigma weight residual 1.534 1.370 0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" C06 AUU B 603 " pdb=" C11 AUU B 603 " ideal model delta sigma weight residual 1.537 1.383 0.154 2.00e-02 2.50e+03 5.94e+01 ... (remaining 7519 not shown) Histogram of bond angle deviations from ideal: 89.17 - 98.87: 6 98.87 - 108.57: 561 108.57 - 118.27: 5332 118.27 - 127.98: 4248 127.98 - 137.68: 82 Bond angle restraints: 10229 Sorted by residual: angle pdb=" N HIS B 319 " pdb=" CA HIS B 319 " pdb=" C HIS B 319 " ideal model delta sigma weight residual 111.36 122.33 -10.97 1.09e+00 8.42e-01 1.01e+02 angle pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta sigma weight residual 119.84 128.89 -9.05 1.25e+00 6.40e-01 5.24e+01 angle pdb=" N LEU B 320 " pdb=" CA LEU B 320 " pdb=" C LEU B 320 " ideal model delta sigma weight residual 108.34 116.69 -8.35 1.31e+00 5.83e-01 4.07e+01 angle pdb=" C PHE B 161 " pdb=" N PRO B 162 " pdb=" CD PRO B 162 " ideal model delta sigma weight residual 120.60 109.75 10.85 2.20e+00 2.07e-01 2.43e+01 angle pdb=" CA LEU B 469 " pdb=" C LEU B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 120.81 116.58 4.23 8.60e-01 1.35e+00 2.42e+01 ... (remaining 10224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 4295 21.14 - 42.28: 211 42.28 - 63.42: 34 63.42 - 84.56: 12 84.56 - 105.70: 10 Dihedral angle restraints: 4562 sinusoidal: 1909 harmonic: 2653 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual -86.00 -157.02 71.02 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CA VAL B 322 " pdb=" C VAL B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLN A 323 " pdb=" C GLN A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual 180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 4559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 1194 0.277 - 0.553: 7 0.553 - 0.830: 0 0.830 - 1.106: 0 1.106 - 1.383: 2 Chirality restraints: 1203 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-01 2.50e+01 4.78e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 382 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.22e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.88 0.48 2.00e-01 2.50e+01 5.74e+00 ... (remaining 1200 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 366 " 0.102 2.00e-02 2.50e+03 2.65e-01 8.75e+02 pdb=" CG ASN A 366 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN A 366 " 0.153 2.00e-02 2.50e+03 pdb=" ND2 ASN A 366 " -0.471 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.296 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 382 " -0.123 2.00e-02 2.50e+03 2.00e-01 5.00e+02 pdb=" CG ASN A 382 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 382 " -0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN A 382 " 0.353 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 507 " -0.072 2.00e-02 2.50e+03 8.36e-02 8.74e+01 pdb=" CG ASN A 507 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 507 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 507 " 0.139 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.098 2.00e-02 2.50e+03 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1775 2.77 - 3.30: 6649 3.30 - 3.84: 11755 3.84 - 4.37: 13783 4.37 - 4.90: 22993 Nonbonded interactions: 56955 Sorted by model distance: nonbonded pdb=" OG1 THR A 460 " pdb=" OH TYR A 554 " model vdw 2.241 2.440 nonbonded pdb=" OG SER A 599 " pdb=" OE2 GLU A 621 " model vdw 2.284 2.440 nonbonded pdb=" O ASP A 516 " pdb=" OG SER A 522 " model vdw 2.284 2.440 nonbonded pdb=" O THR A 460 " pdb=" NH1 ARG A 556 " model vdw 2.291 2.520 nonbonded pdb=" O GLY B 107 " pdb=" OG SER B 111 " model vdw 2.300 2.440 ... (remaining 56950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.830 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.360 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.012 0.176 7524 Z= 0.729 Angle : 1.234 10.971 10229 Z= 0.644 Chirality : 0.088 1.383 1203 Planarity : 0.008 0.063 1255 Dihedral : 14.319 105.703 2855 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.22 % Favored : 90.02 % Rotamer: Outliers : 3.01 % Allowed : 6.54 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -5.53 (0.19), residues: 922 helix: -4.19 (0.12), residues: 470 sheet: -1.95 (0.65), residues: 49 loop : -3.07 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP B 417 HIS 0.009 0.004 HIS A 620 PHE 0.024 0.003 PHE A 552 TYR 0.036 0.004 TYR A 454 ARG 0.012 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 226 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7076 (mm-30) REVERT: B 146 TYR cc_start: 0.8686 (t80) cc_final: 0.8121 (t80) REVERT: B 195 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7737 (ptt180) REVERT: B 218 GLN cc_start: 0.8445 (tp40) cc_final: 0.8213 (tp40) REVERT: B 315 PHE cc_start: 0.8297 (t80) cc_final: 0.8064 (t80) REVERT: B 419 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7342 (mmp-170) REVERT: B 440 ILE cc_start: 0.9232 (mt) cc_final: 0.9008 (mt) REVERT: B 466 LEU cc_start: 0.8515 (mp) cc_final: 0.8275 (tp) REVERT: B 478 TRP cc_start: 0.6616 (t-100) cc_final: 0.6280 (t-100) REVERT: B 501 GLN cc_start: 0.8096 (tt0) cc_final: 0.7827 (tm-30) outliers start: 23 outliers final: 5 residues processed: 234 average time/residue: 0.2136 time to fit residues: 65.0059 Evaluate side-chains 139 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 131 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 221 HIS A 232 GLN A 268 ASN A 388 GLN A 483 GLN A 561 ASN B 186 ASN B 293 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7524 Z= 0.216 Angle : 0.797 12.230 10229 Z= 0.380 Chirality : 0.049 0.612 1203 Planarity : 0.006 0.045 1255 Dihedral : 12.719 89.734 1274 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.59 % Favored : 92.08 % Rotamer: Outliers : 3.53 % Allowed : 13.87 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -4.03 (0.23), residues: 922 helix: -2.59 (0.18), residues: 471 sheet: -1.81 (0.66), residues: 55 loop : -2.78 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 134 HIS 0.004 0.001 HIS B 420 PHE 0.021 0.002 PHE B 95 TYR 0.014 0.002 TYR B 318 ARG 0.010 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.7879 (ttp) cc_final: 0.7516 (mmp) REVERT: A 534 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6920 (mm-30) REVERT: B 120 MET cc_start: 0.9146 (tpp) cc_final: 0.8771 (tpp) REVERT: B 146 TYR cc_start: 0.8640 (t80) cc_final: 0.8088 (t80) REVERT: B 195 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7742 (ptt180) REVERT: B 254 TYR cc_start: 0.8714 (m-80) cc_final: 0.8280 (m-80) REVERT: B 265 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 272 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6729 (mmp-170) REVERT: B 352 VAL cc_start: 0.9325 (t) cc_final: 0.9002 (t) REVERT: B 466 LEU cc_start: 0.8695 (mp) cc_final: 0.8325 (tp) REVERT: B 478 TRP cc_start: 0.6522 (t-100) cc_final: 0.6194 (t-100) REVERT: B 499 LEU cc_start: 0.9123 (tt) cc_final: 0.8895 (tt) REVERT: B 501 GLN cc_start: 0.8308 (tt0) cc_final: 0.7949 (tm-30) outliers start: 27 outliers final: 13 residues processed: 190 average time/residue: 0.1674 time to fit residues: 44.2931 Evaluate side-chains 158 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 0.0050 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 81 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7524 Z= 0.173 Angle : 0.696 10.066 10229 Z= 0.332 Chirality : 0.045 0.455 1203 Planarity : 0.004 0.037 1255 Dihedral : 10.747 88.588 1267 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.48 % Favored : 92.08 % Rotamer: Outliers : 3.14 % Allowed : 17.28 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.25), residues: 922 helix: -1.42 (0.22), residues: 473 sheet: -1.38 (0.65), residues: 56 loop : -2.57 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 134 HIS 0.003 0.001 HIS B 367 PHE 0.021 0.001 PHE B 95 TYR 0.021 0.001 TYR A 405 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8479 (ptmt) cc_final: 0.8271 (ptmm) REVERT: A 197 MET cc_start: 0.7881 (ttp) cc_final: 0.7529 (mmp) REVERT: B 120 MET cc_start: 0.9162 (tpp) cc_final: 0.8956 (tpp) REVERT: B 146 TYR cc_start: 0.8642 (t80) cc_final: 0.8176 (t80) REVERT: B 195 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7610 (ptt180) REVERT: B 254 TYR cc_start: 0.8662 (m-80) cc_final: 0.8247 (m-80) REVERT: B 272 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6834 (mmp-170) REVERT: B 318 TYR cc_start: 0.7031 (t80) cc_final: 0.6821 (t80) REVERT: B 466 LEU cc_start: 0.8700 (mp) cc_final: 0.8358 (tp) REVERT: B 501 GLN cc_start: 0.8253 (tt0) cc_final: 0.8004 (tm-30) outliers start: 24 outliers final: 12 residues processed: 162 average time/residue: 0.1615 time to fit residues: 36.8674 Evaluate side-chains 152 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 427 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 9 optimal weight: 0.0670 chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.0470 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 0.0670 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7524 Z= 0.147 Angle : 0.671 9.949 10229 Z= 0.313 Chirality : 0.044 0.435 1203 Planarity : 0.004 0.040 1255 Dihedral : 9.362 89.566 1264 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.83 % Favored : 92.84 % Rotamer: Outliers : 3.80 % Allowed : 17.28 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.26), residues: 922 helix: -0.71 (0.23), residues: 474 sheet: -1.08 (0.65), residues: 56 loop : -2.43 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 405 HIS 0.003 0.000 HIS B 367 PHE 0.023 0.001 PHE B 95 TYR 0.014 0.001 TYR A 405 ARG 0.002 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8487 (ptmt) cc_final: 0.8271 (ptmm) REVERT: A 197 MET cc_start: 0.7826 (ttp) cc_final: 0.7375 (mmp) REVERT: B 120 MET cc_start: 0.9174 (tpp) cc_final: 0.8866 (tpp) REVERT: B 146 TYR cc_start: 0.8676 (t80) cc_final: 0.8244 (t80) REVERT: B 195 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7603 (ptt180) REVERT: B 254 TYR cc_start: 0.8615 (m-80) cc_final: 0.8266 (m-80) REVERT: B 265 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7339 (tm-30) REVERT: B 272 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6712 (mmp-170) REVERT: B 356 GLU cc_start: 0.7507 (mp0) cc_final: 0.7255 (mp0) REVERT: B 466 LEU cc_start: 0.8793 (mp) cc_final: 0.8445 (tp) outliers start: 29 outliers final: 17 residues processed: 160 average time/residue: 0.1523 time to fit residues: 34.8763 Evaluate side-chains 151 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 78 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7524 Z= 0.202 Angle : 0.668 9.876 10229 Z= 0.319 Chirality : 0.044 0.411 1203 Planarity : 0.004 0.039 1255 Dihedral : 8.960 87.345 1262 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.48 % Favored : 92.08 % Rotamer: Outliers : 3.93 % Allowed : 17.67 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.75 (0.27), residues: 922 helix: -0.27 (0.24), residues: 466 sheet: -0.56 (0.68), residues: 50 loop : -2.33 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 405 HIS 0.004 0.001 HIS B 367 PHE 0.025 0.001 PHE B 95 TYR 0.013 0.001 TYR A 405 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8334 (ptmm) REVERT: A 197 MET cc_start: 0.7914 (ttp) cc_final: 0.7445 (mmp) REVERT: B 120 MET cc_start: 0.9171 (tpp) cc_final: 0.8965 (mmm) REVERT: B 146 TYR cc_start: 0.8707 (t80) cc_final: 0.8290 (t80) REVERT: B 195 ARG cc_start: 0.7927 (mtm110) cc_final: 0.7625 (ptt180) REVERT: B 248 TYR cc_start: 0.8377 (m-10) cc_final: 0.8167 (m-10) REVERT: B 254 TYR cc_start: 0.8717 (m-80) cc_final: 0.8280 (m-80) REVERT: B 272 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6797 (mmp-170) REVERT: B 356 GLU cc_start: 0.7671 (mp0) cc_final: 0.7365 (mp0) REVERT: B 365 MET cc_start: 0.8715 (mmm) cc_final: 0.8330 (mtp) REVERT: B 466 LEU cc_start: 0.8800 (mp) cc_final: 0.8461 (tp) REVERT: B 501 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7937 (tm-30) outliers start: 30 outliers final: 22 residues processed: 148 average time/residue: 0.1607 time to fit residues: 33.8304 Evaluate side-chains 151 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 0.0570 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7524 Z= 0.161 Angle : 0.646 9.542 10229 Z= 0.305 Chirality : 0.044 0.411 1203 Planarity : 0.004 0.040 1255 Dihedral : 8.451 87.163 1262 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.38 % Favored : 92.19 % Rotamer: Outliers : 3.40 % Allowed : 18.59 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.46 (0.27), residues: 922 helix: 0.01 (0.24), residues: 471 sheet: -0.33 (0.69), residues: 50 loop : -2.28 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 405 HIS 0.002 0.001 HIS B 319 PHE 0.025 0.001 PHE B 95 TYR 0.012 0.001 TYR A 405 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8328 (ptmm) REVERT: A 197 MET cc_start: 0.7903 (ttp) cc_final: 0.7532 (mmp) REVERT: B 120 MET cc_start: 0.9166 (tpp) cc_final: 0.8934 (mmm) REVERT: B 146 TYR cc_start: 0.8686 (t80) cc_final: 0.8300 (t80) REVERT: B 195 ARG cc_start: 0.7922 (mtm110) cc_final: 0.7606 (ptt180) REVERT: B 254 TYR cc_start: 0.8710 (m-80) cc_final: 0.8304 (m-80) REVERT: B 272 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6741 (mmp-170) REVERT: B 352 VAL cc_start: 0.9184 (t) cc_final: 0.8147 (p) REVERT: B 466 LEU cc_start: 0.8759 (mp) cc_final: 0.8423 (tp) REVERT: B 501 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7659 (tm-30) outliers start: 26 outliers final: 19 residues processed: 151 average time/residue: 0.1638 time to fit residues: 35.1006 Evaluate side-chains 149 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7524 Z= 0.184 Angle : 0.655 9.460 10229 Z= 0.309 Chirality : 0.044 0.403 1203 Planarity : 0.004 0.041 1255 Dihedral : 8.225 86.516 1262 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.27 % Favored : 92.30 % Rotamer: Outliers : 3.93 % Allowed : 19.24 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.27 (0.27), residues: 922 helix: 0.16 (0.24), residues: 474 sheet: -0.05 (0.71), residues: 50 loop : -2.23 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 405 HIS 0.003 0.001 HIS B 319 PHE 0.025 0.001 PHE B 95 TYR 0.012 0.001 TYR B 119 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8349 (ptmm) REVERT: A 197 MET cc_start: 0.7872 (ttp) cc_final: 0.7537 (mmp) REVERT: A 388 GLN cc_start: 0.7773 (tt0) cc_final: 0.7515 (tt0) REVERT: B 120 MET cc_start: 0.9170 (tpp) cc_final: 0.8914 (mmm) REVERT: B 146 TYR cc_start: 0.8714 (t80) cc_final: 0.8341 (t80) REVERT: B 195 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7678 (ptt180) REVERT: B 254 TYR cc_start: 0.8718 (m-80) cc_final: 0.8254 (m-80) REVERT: B 272 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6884 (mmp-170) REVERT: B 320 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7613 (pp) REVERT: B 438 PHE cc_start: 0.8200 (t80) cc_final: 0.7893 (t80) REVERT: B 466 LEU cc_start: 0.8734 (mp) cc_final: 0.8404 (tp) REVERT: B 501 GLN cc_start: 0.8600 (tm-30) cc_final: 0.7801 (tm-30) outliers start: 30 outliers final: 23 residues processed: 151 average time/residue: 0.1610 time to fit residues: 34.4165 Evaluate side-chains 155 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 0.0370 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7524 Z= 0.156 Angle : 0.662 9.253 10229 Z= 0.310 Chirality : 0.044 0.408 1203 Planarity : 0.004 0.042 1255 Dihedral : 7.972 87.066 1262 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.94 % Favored : 92.62 % Rotamer: Outliers : 3.66 % Allowed : 20.03 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.10 (0.28), residues: 922 helix: 0.30 (0.24), residues: 475 sheet: -0.03 (0.69), residues: 50 loop : -2.15 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 405 HIS 0.001 0.000 HIS B 367 PHE 0.023 0.001 PHE B 95 TYR 0.013 0.001 TYR B 472 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8331 (ptmm) REVERT: A 197 MET cc_start: 0.7881 (ttp) cc_final: 0.7479 (mmp) REVERT: B 105 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8675 (tp30) REVERT: B 146 TYR cc_start: 0.8691 (t80) cc_final: 0.8354 (t80) REVERT: B 195 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7632 (ptt180) REVERT: B 254 TYR cc_start: 0.8688 (m-80) cc_final: 0.8275 (m-80) REVERT: B 272 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6836 (mmp-170) REVERT: B 365 MET cc_start: 0.8630 (mmm) cc_final: 0.8417 (mtp) REVERT: B 466 LEU cc_start: 0.8690 (mp) cc_final: 0.8374 (tp) REVERT: B 501 GLN cc_start: 0.8630 (tm-30) cc_final: 0.7813 (tm-30) outliers start: 28 outliers final: 23 residues processed: 152 average time/residue: 0.1703 time to fit residues: 37.0753 Evaluate side-chains 157 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7524 Z= 0.160 Angle : 0.666 9.369 10229 Z= 0.310 Chirality : 0.044 0.411 1203 Planarity : 0.004 0.042 1255 Dihedral : 7.770 87.279 1262 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.16 % Favored : 92.41 % Rotamer: Outliers : 3.80 % Allowed : 20.16 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.00 (0.28), residues: 922 helix: 0.41 (0.25), residues: 475 sheet: 0.08 (0.69), residues: 50 loop : -2.14 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 405 HIS 0.002 0.000 HIS B 319 PHE 0.025 0.001 PHE B 216 TYR 0.014 0.001 TYR B 472 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8336 (ptmm) REVERT: A 197 MET cc_start: 0.7878 (ttp) cc_final: 0.7499 (mmp) REVERT: A 534 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6816 (mm-30) REVERT: B 105 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8690 (tp30) REVERT: B 146 TYR cc_start: 0.8704 (t80) cc_final: 0.8380 (t80) REVERT: B 195 ARG cc_start: 0.7977 (mtm110) cc_final: 0.7636 (ptt180) REVERT: B 254 TYR cc_start: 0.8694 (m-80) cc_final: 0.8325 (m-80) REVERT: B 272 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6819 (mmp-170) REVERT: B 438 PHE cc_start: 0.8262 (t80) cc_final: 0.7918 (t80) REVERT: B 453 LYS cc_start: 0.8738 (tppt) cc_final: 0.8289 (mmmt) REVERT: B 466 LEU cc_start: 0.8630 (mp) cc_final: 0.8342 (tp) REVERT: B 501 GLN cc_start: 0.8688 (tm-30) cc_final: 0.7813 (tm-30) outliers start: 29 outliers final: 22 residues processed: 156 average time/residue: 0.1515 time to fit residues: 33.7297 Evaluate side-chains 156 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7524 Z= 0.175 Angle : 0.689 11.664 10229 Z= 0.318 Chirality : 0.044 0.410 1203 Planarity : 0.004 0.042 1255 Dihedral : 7.707 87.253 1262 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.94 % Favored : 92.62 % Rotamer: Outliers : 3.40 % Allowed : 20.29 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.28), residues: 922 helix: 0.49 (0.25), residues: 476 sheet: 0.31 (0.69), residues: 49 loop : -2.11 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 405 HIS 0.002 0.001 HIS B 319 PHE 0.024 0.001 PHE B 95 TYR 0.018 0.001 TYR B 472 ARG 0.003 0.000 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.7796 (ttp) cc_final: 0.7477 (mmp) REVERT: A 534 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6853 (mm-30) REVERT: B 146 TYR cc_start: 0.8720 (t80) cc_final: 0.8389 (t80) REVERT: B 195 ARG cc_start: 0.8027 (mtm110) cc_final: 0.7709 (ptt180) REVERT: B 254 TYR cc_start: 0.8711 (m-80) cc_final: 0.8327 (m-80) REVERT: B 438 PHE cc_start: 0.8214 (t80) cc_final: 0.7890 (t80) REVERT: B 453 LYS cc_start: 0.8718 (tppt) cc_final: 0.8302 (mmmt) REVERT: B 466 LEU cc_start: 0.8725 (mp) cc_final: 0.8430 (tp) REVERT: B 501 GLN cc_start: 0.8706 (tm-30) cc_final: 0.7803 (tm-30) outliers start: 26 outliers final: 22 residues processed: 146 average time/residue: 0.1626 time to fit residues: 33.5820 Evaluate side-chains 152 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.123880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096163 restraints weight = 13087.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.099986 restraints weight = 6685.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102442 restraints weight = 4595.471| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7524 Z= 0.254 Angle : 0.719 12.036 10229 Z= 0.335 Chirality : 0.046 0.395 1203 Planarity : 0.004 0.044 1255 Dihedral : 7.873 85.638 1262 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.03 % Favored : 91.54 % Rotamer: Outliers : 3.66 % Allowed : 20.16 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.99 (0.28), residues: 922 helix: 0.44 (0.24), residues: 486 sheet: 0.19 (0.68), residues: 49 loop : -2.24 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 405 HIS 0.004 0.001 HIS B 319 PHE 0.026 0.002 PHE B 95 TYR 0.023 0.002 TYR B 472 ARG 0.005 0.001 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.54 seconds wall clock time: 32 minutes 16.23 seconds (1936.23 seconds total)