Starting phenix.real_space_refine on Tue Sep 24 12:27:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/09_2024/7ocy_12816_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/09_2024/7ocy_12816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/09_2024/7ocy_12816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/09_2024/7ocy_12816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/09_2024/7ocy_12816_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocy_12816/09_2024/7ocy_12816_neut.cif" } resolution = 4.25 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= 0.001 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5051 2.51 5 N 1423 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7994 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 3613 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PTRANS': 13, 'TRANS': 543} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 715 Unresolved non-hydrogen angles: 909 Unresolved non-hydrogen dihedrals: 569 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 15, 'TYR:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 25, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 383 Chain: "B" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 3852 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 10, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 742 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 16, 'TYR:plan': 5, 'ASN:plan1': 16, 'HIS:plan': 7, 'PHE:plan': 9, 'GLU:plan': 27, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 414 Chain: "C" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 3, 'TRANS': 104} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 222 Time building chain proxies: 5.34, per 1000 atoms: 0.67 Number of scatterers: 7994 At special positions: 0 Unit cell: (76.96, 83.2, 165.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1488 8.00 N 1423 7.00 C 5051 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 66.5% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 11 through 46 removed outlier: 4.019A pdb=" N ILE A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 47 through 97 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 107 through 132 removed outlier: 4.268A pdb=" N ASP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 4.034A pdb=" N PHE A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 200 removed outlier: 3.732A pdb=" N ILE A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 208 through 258 removed outlier: 4.304A pdb=" N ASN A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 4.033A pdb=" N SER A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 311 removed outlier: 4.357A pdb=" N ALA A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 298 " --> pdb=" O MET A 294 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.987A pdb=" N ILE A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.530A pdb=" N LEU A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 432 through 444 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 468 through 483 removed outlier: 4.646A pdb=" N GLY A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.705A pdb=" N VAL A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 555 removed outlier: 4.040A pdb=" N ALA A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 563 removed outlier: 4.411A pdb=" N GLN A 559 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 560 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 removed outlier: 3.772A pdb=" N TYR B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 60 removed outlier: 3.857A pdb=" N PHE B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Proline residue: B 40 - end of helix removed outlier: 3.674A pdb=" N GLN B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 112 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.581A pdb=" N PHE B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 133 Processing helix chain 'B' and resid 133 through 167 removed outlier: 4.753A pdb=" N LEU B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN B 148 " --> pdb=" O GLN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 177 through 224 removed outlier: 6.567A pdb=" N ARG B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 253 Processing helix chain 'B' and resid 253 through 280 Processing helix chain 'B' and resid 283 through 330 Proline residue: B 304 - end of helix removed outlier: 4.155A pdb=" N SER B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N MET B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 397 removed outlier: 4.430A pdb=" N MET B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 425 Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.941A pdb=" N GLN B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 488 through 504 removed outlier: 3.726A pdb=" N LYS B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 removed outlier: 4.194A pdb=" N GLY B 535 " --> pdb=" O GLU B 531 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 removed outlier: 3.568A pdb=" N LEU B 549 " --> pdb=" O LYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 574 Processing helix chain 'B' and resid 576 through 583 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 353 removed outlier: 5.941A pdb=" N LYS A 347 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER A 335 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 349 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL A 334 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU A 384 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 406 through 408 removed outlier: 6.764A pdb=" N MET A 358 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU A 535 " --> pdb=" O MET A 358 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY A 360 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU A 537 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL A 362 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 534 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU A 545 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 536 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA4, first strand: chain 'B' and resid 366 through 369 removed outlier: 4.749A pdb=" N VAL B 355 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL B 355 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU B 404 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 426 through 429 removed outlier: 5.931A pdb=" N LEU B 508 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE B 541 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 510 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET B 378 " --> pdb=" O ARG B 553 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE B 555 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA B 380 " --> pdb=" O ILE B 555 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU B 557 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 382 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU B 564 " --> pdb=" O VAL B 556 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 7 through 10 Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.997A pdb=" N VAL C 15 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C 98 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG C 33 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG C 38 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N MET C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2776 1.34 - 1.46: 1649 1.46 - 1.58: 3585 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 8074 Sorted by residual: bond pdb=" N THR B 2 " pdb=" CA THR B 2 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N GLN C 6 " pdb=" CA GLN C 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ASP A 2 " pdb=" CA ASP A 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" C GLU A 484 " pdb=" O GLU A 484 " ideal model delta sigma weight residual 1.233 1.241 -0.008 4.80e-03 4.34e+04 2.80e+00 bond pdb=" CA THR B 363 " pdb=" C THR B 363 " ideal model delta sigma weight residual 1.531 1.524 0.008 7.40e-03 1.83e+04 1.03e+00 ... (remaining 8069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 10483 1.24 - 2.49: 451 2.49 - 3.73: 59 3.73 - 4.97: 21 4.97 - 6.21: 5 Bond angle restraints: 11019 Sorted by residual: angle pdb=" N ILE A 561 " pdb=" CA ILE A 561 " pdb=" C ILE A 561 " ideal model delta sigma weight residual 111.90 107.47 4.43 8.10e-01 1.52e+00 2.98e+01 angle pdb=" N VAL C 48 " pdb=" CA VAL C 48 " pdb=" C VAL C 48 " ideal model delta sigma weight residual 111.62 108.56 3.06 7.90e-01 1.60e+00 1.50e+01 angle pdb=" N ILE A 376 " pdb=" CA ILE A 376 " pdb=" C ILE A 376 " ideal model delta sigma weight residual 112.35 107.76 4.59 1.20e+00 6.94e-01 1.46e+01 angle pdb=" C ILE A 136 " pdb=" CA ILE A 136 " pdb=" CB ILE A 136 " ideal model delta sigma weight residual 114.00 109.50 4.50 1.31e+00 5.83e-01 1.18e+01 angle pdb=" N ARG B 558 " pdb=" CA ARG B 558 " pdb=" C ARG B 558 " ideal model delta sigma weight residual 110.80 104.59 6.21 2.13e+00 2.20e-01 8.51e+00 ... (remaining 11014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4463 17.53 - 35.05: 260 35.05 - 52.58: 43 52.58 - 70.11: 6 70.11 - 87.64: 6 Dihedral angle restraints: 4778 sinusoidal: 1208 harmonic: 3570 Sorted by residual: dihedral pdb=" CA ASN C 32 " pdb=" C ASN C 32 " pdb=" N ARG C 33 " pdb=" CA ARG C 33 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LEU B 557 " pdb=" C LEU B 557 " pdb=" N ARG B 558 " pdb=" CA ARG B 558 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLY A 270 " pdb=" C GLY A 270 " pdb=" N VAL A 271 " pdb=" CA VAL A 271 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 892 0.031 - 0.062: 338 0.062 - 0.093: 107 0.093 - 0.124: 45 0.124 - 0.156: 4 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA ILE B 541 " pdb=" N ILE B 541 " pdb=" C ILE B 541 " pdb=" CB ILE B 541 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA ILE A 519 " pdb=" N ILE A 519 " pdb=" C ILE A 519 " pdb=" CB ILE A 519 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA VAL B 356 " pdb=" N VAL B 356 " pdb=" C VAL B 356 " pdb=" CB VAL B 356 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1383 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 303 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO B 304 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 31 " 0.012 2.00e-02 2.50e+03 9.44e-03 2.23e+00 pdb=" CG TRP A 31 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 31 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 31 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 31 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 31 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 31 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 31 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 31 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 210 " -0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C MET B 210 " 0.024 2.00e-02 2.50e+03 pdb=" O MET B 210 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP B 211 " -0.008 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 77 2.56 - 3.15: 7525 3.15 - 3.73: 12918 3.73 - 4.32: 15305 4.32 - 4.90: 25084 Nonbonded interactions: 60909 Sorted by model distance: nonbonded pdb=" O GLU A 222 " pdb=" OG1 THR A 225 " model vdw 1.980 3.040 nonbonded pdb=" O VAL A 250 " pdb=" OG SER A 253 " model vdw 2.047 3.040 nonbonded pdb=" OE2 GLU A 89 " pdb=" NE ARG A 93 " model vdw 2.077 3.120 nonbonded pdb=" O LYS A 219 " pdb=" OE1 GLU A 223 " model vdw 2.158 3.040 nonbonded pdb=" NZ LYS A 94 " pdb=" O MET A 309 " model vdw 2.255 3.120 ... (remaining 60904 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=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: 0.010 Normalize map: mean=0, sd=1: 3.880 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.003 0.034 8074 Z= 0.203 Angle : 0.616 6.212 11019 Z= 0.391 Chirality : 0.039 0.156 1386 Planarity : 0.003 0.042 1450 Dihedral : 12.493 87.635 2462 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1231 helix: 0.68 (0.18), residues: 756 sheet: -0.97 (0.45), residues: 119 loop : -1.15 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 31 HIS 0.001 0.000 HIS A 179 PHE 0.015 0.001 PHE B 86 TYR 0.017 0.002 TYR B 12 ARG 0.002 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9616 (mm) cc_final: 0.9406 (mp) REVERT: A 118 ASP cc_start: 0.9208 (m-30) cc_final: 0.8883 (m-30) REVERT: A 196 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8312 (tm-30) REVERT: A 277 TYR cc_start: 0.8650 (m-80) cc_final: 0.8375 (m-80) REVERT: A 287 ILE cc_start: 0.9531 (tt) cc_final: 0.9298 (tt) REVERT: A 307 GLU cc_start: 0.9332 (pt0) cc_final: 0.8659 (pp20) REVERT: B 67 PHE cc_start: 0.9357 (t80) cc_final: 0.9142 (t80) REVERT: B 71 ILE cc_start: 0.9676 (mm) cc_final: 0.9471 (mm) REVERT: B 136 ASP cc_start: 0.9160 (m-30) cc_final: 0.8897 (m-30) REVERT: B 210 MET cc_start: 0.9661 (mtp) cc_final: 0.9297 (mtp) REVERT: B 225 LEU cc_start: 0.9082 (mt) cc_final: 0.8786 (mt) REVERT: B 327 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8572 (mt-10) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1584 time to fit residues: 35.6298 Evaluate side-chains 121 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8074 Z= 0.391 Angle : 0.717 8.929 11019 Z= 0.404 Chirality : 0.044 0.168 1386 Planarity : 0.004 0.042 1450 Dihedral : 4.568 22.454 1274 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.18 % Allowed : 9.98 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1231 helix: 0.56 (0.18), residues: 765 sheet: -0.78 (0.45), residues: 118 loop : -0.86 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 31 HIS 0.003 0.001 HIS A 227 PHE 0.024 0.002 PHE B 86 TYR 0.034 0.003 TYR B 88 ARG 0.004 0.001 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.9142 (tpt) cc_final: 0.8934 (tpp) REVERT: A 49 ASP cc_start: 0.8828 (p0) cc_final: 0.8628 (p0) REVERT: A 118 ASP cc_start: 0.9257 (m-30) cc_final: 0.8947 (m-30) REVERT: A 154 LEU cc_start: 0.9711 (mm) cc_final: 0.9475 (mt) REVERT: A 196 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8471 (tm-30) REVERT: A 223 GLU cc_start: 0.8900 (mp0) cc_final: 0.8591 (mp0) REVERT: A 287 ILE cc_start: 0.9484 (tt) cc_final: 0.9272 (tt) REVERT: A 304 ARG cc_start: 0.8994 (ttm110) cc_final: 0.8552 (ttm110) REVERT: B 35 LEU cc_start: 0.8938 (tp) cc_final: 0.8593 (tp) REVERT: B 58 MET cc_start: 0.9425 (mmp) cc_final: 0.9170 (mmm) REVERT: B 71 ILE cc_start: 0.9740 (mm) cc_final: 0.9496 (mm) REVERT: B 122 HIS cc_start: 0.8382 (m90) cc_final: 0.7929 (m90) REVERT: B 130 ARG cc_start: 0.8793 (tpp80) cc_final: 0.8516 (tpp80) REVERT: B 136 ASP cc_start: 0.9211 (m-30) cc_final: 0.8942 (m-30) REVERT: B 210 MET cc_start: 0.9655 (mtp) cc_final: 0.9223 (mtp) REVERT: B 225 LEU cc_start: 0.9045 (mt) cc_final: 0.8761 (mt) REVERT: B 293 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8946 (ttt) REVERT: B 324 ARG cc_start: 0.9468 (mtt90) cc_final: 0.8726 (mtt90) REVERT: B 327 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8583 (mt-10) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1596 time to fit residues: 31.9107 Evaluate side-chains 119 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 40.0000 chunk 98 optimal weight: 0.0980 chunk 37 optimal weight: 0.0270 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8074 Z= 0.180 Angle : 0.595 8.261 11019 Z= 0.320 Chirality : 0.042 0.205 1386 Planarity : 0.003 0.032 1450 Dihedral : 4.167 20.268 1274 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1231 helix: 1.07 (0.19), residues: 769 sheet: -0.56 (0.49), residues: 100 loop : -0.77 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 31 HIS 0.002 0.001 HIS A 179 PHE 0.022 0.002 PHE B 86 TYR 0.030 0.003 TYR B 88 ARG 0.003 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8844 (p0) cc_final: 0.8283 (p0) REVERT: A 96 GLN cc_start: 0.9238 (mp10) cc_final: 0.8974 (mm-40) REVERT: A 118 ASP cc_start: 0.9325 (m-30) cc_final: 0.9002 (m-30) REVERT: A 131 GLN cc_start: 0.8700 (tt0) cc_final: 0.8308 (tt0) REVERT: A 138 PHE cc_start: 0.8809 (t80) cc_final: 0.8604 (t80) REVERT: A 196 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8412 (tm-30) REVERT: A 223 GLU cc_start: 0.8841 (mp0) cc_final: 0.8508 (mp0) REVERT: A 304 ARG cc_start: 0.9099 (ttm110) cc_final: 0.8645 (ttm110) REVERT: B 35 LEU cc_start: 0.8883 (tp) cc_final: 0.8479 (tp) REVERT: B 58 MET cc_start: 0.9372 (mmp) cc_final: 0.9118 (mmm) REVERT: B 71 ILE cc_start: 0.9743 (mm) cc_final: 0.9481 (mm) REVERT: B 122 HIS cc_start: 0.8328 (m90) cc_final: 0.7833 (m90) REVERT: B 210 MET cc_start: 0.9617 (mtp) cc_final: 0.9209 (mtp) REVERT: B 225 LEU cc_start: 0.8943 (mt) cc_final: 0.8738 (mt) REVERT: B 324 ARG cc_start: 0.9471 (mtt90) cc_final: 0.8965 (mtt90) REVERT: B 327 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8504 (mt-10) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1634 time to fit residues: 38.7590 Evaluate side-chains 130 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 0.3980 chunk 117 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 98 optimal weight: 0.0470 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8074 Z= 0.168 Angle : 0.562 7.907 11019 Z= 0.306 Chirality : 0.040 0.139 1386 Planarity : 0.003 0.034 1450 Dihedral : 3.981 18.528 1274 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), residues: 1231 helix: 1.16 (0.19), residues: 769 sheet: -0.43 (0.48), residues: 100 loop : -0.69 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 31 HIS 0.002 0.001 HIS A 179 PHE 0.024 0.001 PHE B 67 TYR 0.018 0.002 TYR A 277 ARG 0.005 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.9219 (m-80) cc_final: 0.8994 (m-80) REVERT: A 118 ASP cc_start: 0.9318 (m-30) cc_final: 0.9054 (m-30) REVERT: A 131 GLN cc_start: 0.8691 (tt0) cc_final: 0.8297 (tt0) REVERT: A 138 PHE cc_start: 0.8833 (t80) cc_final: 0.8623 (t80) REVERT: A 196 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8392 (tm-30) REVERT: A 223 GLU cc_start: 0.8794 (mp0) cc_final: 0.8410 (mp0) REVERT: A 275 MET cc_start: 0.9315 (ppp) cc_final: 0.9097 (ppp) REVERT: A 282 MET cc_start: 0.8753 (tmm) cc_final: 0.8487 (tmm) REVERT: A 294 MET cc_start: 0.8669 (tmm) cc_final: 0.8417 (tmm) REVERT: A 304 ARG cc_start: 0.9039 (ttm110) cc_final: 0.8560 (ttm110) REVERT: B 35 LEU cc_start: 0.8969 (tp) cc_final: 0.8586 (tp) REVERT: B 58 MET cc_start: 0.9429 (mmp) cc_final: 0.9156 (mmm) REVERT: B 67 PHE cc_start: 0.9276 (t80) cc_final: 0.8835 (t80) REVERT: B 71 ILE cc_start: 0.9750 (mm) cc_final: 0.9501 (mm) REVERT: B 122 HIS cc_start: 0.8260 (m90) cc_final: 0.7758 (m90) REVERT: B 130 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8210 (tpp80) REVERT: B 136 ASP cc_start: 0.9147 (m-30) cc_final: 0.8913 (m-30) REVERT: B 162 MET cc_start: 0.8504 (ttm) cc_final: 0.8293 (ttm) REVERT: B 210 MET cc_start: 0.9623 (mtp) cc_final: 0.9270 (mtp) REVERT: B 257 MET cc_start: 0.9255 (mmm) cc_final: 0.8809 (tmm) REVERT: B 293 MET cc_start: 0.8968 (ttt) cc_final: 0.8211 (tmm) REVERT: B 306 MET cc_start: 0.8439 (mtm) cc_final: 0.8132 (mtt) REVERT: B 324 ARG cc_start: 0.9446 (mtt90) cc_final: 0.8762 (mtt90) REVERT: B 327 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8537 (mt-10) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1614 time to fit residues: 37.0644 Evaluate side-chains 134 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8074 Z= 0.175 Angle : 0.586 8.693 11019 Z= 0.312 Chirality : 0.041 0.151 1386 Planarity : 0.003 0.032 1450 Dihedral : 3.855 18.768 1274 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1231 helix: 1.23 (0.19), residues: 770 sheet: -0.35 (0.47), residues: 105 loop : -0.67 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 31 HIS 0.002 0.001 HIS A 179 PHE 0.021 0.001 PHE B 86 TYR 0.035 0.002 TYR B 78 ARG 0.006 0.000 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9146 (tpt) cc_final: 0.8859 (tpp) REVERT: A 75 PHE cc_start: 0.9199 (m-80) cc_final: 0.8912 (m-10) REVERT: A 96 GLN cc_start: 0.9259 (mm-40) cc_final: 0.9030 (mm-40) REVERT: A 118 ASP cc_start: 0.9308 (m-30) cc_final: 0.8900 (m-30) REVERT: A 131 GLN cc_start: 0.8731 (tt0) cc_final: 0.8315 (tt0) REVERT: A 196 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8362 (tm-30) REVERT: A 282 MET cc_start: 0.8788 (tmm) cc_final: 0.8463 (tmm) REVERT: A 304 ARG cc_start: 0.9054 (ttm110) cc_final: 0.8625 (ttm110) REVERT: B 35 LEU cc_start: 0.8920 (tp) cc_final: 0.8691 (tp) REVERT: B 58 MET cc_start: 0.9404 (mmp) cc_final: 0.9168 (mmm) REVERT: B 67 PHE cc_start: 0.9301 (t80) cc_final: 0.8790 (t80) REVERT: B 71 ILE cc_start: 0.9775 (mm) cc_final: 0.9522 (mm) REVERT: B 122 HIS cc_start: 0.8249 (m90) cc_final: 0.7733 (m90) REVERT: B 293 MET cc_start: 0.8894 (ttt) cc_final: 0.8106 (tmm) REVERT: B 302 TYR cc_start: 0.8941 (m-10) cc_final: 0.8693 (m-10) REVERT: B 324 ARG cc_start: 0.9452 (mtt90) cc_final: 0.8981 (mtt90) REVERT: B 327 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8527 (mt-10) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1632 time to fit residues: 35.5671 Evaluate side-chains 126 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 7.9990 chunk 23 optimal weight: 0.0570 chunk 69 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 0.0010 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 overall best weight: 0.6908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8074 Z= 0.167 Angle : 0.570 9.118 11019 Z= 0.302 Chirality : 0.040 0.164 1386 Planarity : 0.003 0.032 1450 Dihedral : 3.764 17.589 1274 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.18 % Allowed : 2.54 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.24), residues: 1231 helix: 1.28 (0.19), residues: 770 sheet: -0.17 (0.47), residues: 105 loop : -0.64 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 172 HIS 0.002 0.001 HIS A 179 PHE 0.021 0.001 PHE B 86 TYR 0.038 0.002 TYR B 297 ARG 0.008 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.9209 (m-80) cc_final: 0.8927 (m-10) REVERT: A 96 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8945 (mm-40) REVERT: A 118 ASP cc_start: 0.9324 (m-30) cc_final: 0.8863 (m-30) REVERT: A 131 GLN cc_start: 0.8683 (tt0) cc_final: 0.8293 (tt0) REVERT: A 195 LYS cc_start: 0.9552 (tppp) cc_final: 0.9310 (tppt) REVERT: A 196 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8349 (tm-30) REVERT: A 275 MET cc_start: 0.9334 (ppp) cc_final: 0.9071 (ppp) REVERT: A 282 MET cc_start: 0.8804 (tmm) cc_final: 0.8421 (tmm) REVERT: A 304 ARG cc_start: 0.9032 (ttm110) cc_final: 0.8598 (ttm110) REVERT: B 35 LEU cc_start: 0.8893 (tp) cc_final: 0.8674 (tp) REVERT: B 58 MET cc_start: 0.9383 (mmp) cc_final: 0.9148 (mmm) REVERT: B 71 ILE cc_start: 0.9778 (mm) cc_final: 0.9531 (mm) REVERT: B 110 LYS cc_start: 0.9130 (tppt) cc_final: 0.8927 (tppt) REVERT: B 122 HIS cc_start: 0.8231 (m90) cc_final: 0.7719 (m90) REVERT: B 130 ARG cc_start: 0.8380 (tpp80) cc_final: 0.7950 (tpp80) REVERT: B 136 ASP cc_start: 0.9105 (m-30) cc_final: 0.8884 (m-30) REVERT: B 139 GLN cc_start: 0.9313 (tp40) cc_final: 0.9106 (tp40) REVERT: B 210 MET cc_start: 0.9597 (mtp) cc_final: 0.9311 (mtp) REVERT: B 257 MET cc_start: 0.9170 (mmm) cc_final: 0.8799 (tmm) REVERT: B 297 TYR cc_start: 0.8944 (m-80) cc_final: 0.8665 (m-80) REVERT: B 306 MET cc_start: 0.8512 (mtm) cc_final: 0.8160 (mtt) REVERT: B 324 ARG cc_start: 0.9433 (mtt90) cc_final: 0.8938 (mtp85) REVERT: B 327 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8528 (mt-10) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1584 time to fit residues: 35.7271 Evaluate side-chains 136 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.0670 chunk 99 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 117 optimal weight: 0.0770 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8074 Z= 0.157 Angle : 0.551 7.751 11019 Z= 0.295 Chirality : 0.041 0.267 1386 Planarity : 0.003 0.035 1450 Dihedral : 3.706 18.903 1274 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1231 helix: 1.36 (0.19), residues: 770 sheet: 0.01 (0.47), residues: 104 loop : -0.59 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 172 HIS 0.002 0.001 HIS A 179 PHE 0.027 0.001 PHE B 67 TYR 0.023 0.002 TYR B 297 ARG 0.006 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.9236 (m-80) cc_final: 0.8924 (m-10) REVERT: A 81 GLN cc_start: 0.9352 (pp30) cc_final: 0.8916 (pp30) REVERT: A 96 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8905 (mm-40) REVERT: A 118 ASP cc_start: 0.9310 (m-30) cc_final: 0.8838 (m-30) REVERT: A 131 GLN cc_start: 0.8681 (tt0) cc_final: 0.8232 (tt0) REVERT: A 133 LEU cc_start: 0.9150 (mm) cc_final: 0.8648 (mm) REVERT: A 138 PHE cc_start: 0.8672 (t80) cc_final: 0.8411 (t80) REVERT: A 196 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8103 (tm-30) REVERT: A 223 GLU cc_start: 0.8747 (mp0) cc_final: 0.8382 (mp0) REVERT: A 275 MET cc_start: 0.9294 (ppp) cc_final: 0.9092 (ppp) REVERT: A 282 MET cc_start: 0.8817 (tmm) cc_final: 0.8375 (tmm) REVERT: A 304 ARG cc_start: 0.9042 (ttm110) cc_final: 0.8620 (ttm110) REVERT: B 35 LEU cc_start: 0.8920 (tp) cc_final: 0.8587 (tp) REVERT: B 58 MET cc_start: 0.9372 (mmp) cc_final: 0.9133 (mmm) REVERT: B 110 LYS cc_start: 0.9128 (tppt) cc_final: 0.8913 (tppt) REVERT: B 122 HIS cc_start: 0.8229 (m90) cc_final: 0.7726 (m90) REVERT: B 136 ASP cc_start: 0.9110 (m-30) cc_final: 0.8894 (m-30) REVERT: B 139 GLN cc_start: 0.9305 (tp40) cc_final: 0.9087 (tp40) REVERT: B 210 MET cc_start: 0.9556 (mtp) cc_final: 0.9181 (mtm) REVERT: B 225 LEU cc_start: 0.9053 (mt) cc_final: 0.8840 (mt) REVERT: B 261 MET cc_start: 0.9449 (tpp) cc_final: 0.8996 (tpt) REVERT: B 306 MET cc_start: 0.8499 (mtm) cc_final: 0.8140 (mtt) REVERT: B 327 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8532 (mt-10) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1834 time to fit residues: 43.2087 Evaluate side-chains 136 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 30.0000 chunk 23 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8074 Z= 0.192 Angle : 0.573 7.499 11019 Z= 0.311 Chirality : 0.042 0.223 1386 Planarity : 0.003 0.034 1450 Dihedral : 3.712 19.022 1274 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.18 % Allowed : 2.18 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1231 helix: 1.31 (0.19), residues: 772 sheet: 0.16 (0.48), residues: 104 loop : -0.61 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 31 HIS 0.002 0.001 HIS A 179 PHE 0.066 0.002 PHE B 67 TYR 0.032 0.002 TYR B 302 ARG 0.006 0.001 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.9253 (m-80) cc_final: 0.9001 (m-80) REVERT: A 96 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8762 (mm-40) REVERT: A 118 ASP cc_start: 0.9329 (m-30) cc_final: 0.8832 (m-30) REVERT: A 131 GLN cc_start: 0.8677 (tt0) cc_final: 0.8334 (tt0) REVERT: A 138 PHE cc_start: 0.8703 (t80) cc_final: 0.8482 (t80) REVERT: A 170 MET cc_start: 0.8298 (ppp) cc_final: 0.8009 (ppp) REVERT: A 196 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8115 (tm-30) REVERT: A 223 GLU cc_start: 0.8803 (mp0) cc_final: 0.8465 (mp0) REVERT: A 282 MET cc_start: 0.8816 (tmm) cc_final: 0.8363 (tmm) REVERT: A 286 ILE cc_start: 0.9383 (pt) cc_final: 0.9176 (pt) REVERT: A 304 ARG cc_start: 0.9061 (ttm110) cc_final: 0.8626 (ttm110) REVERT: B 35 LEU cc_start: 0.8947 (tp) cc_final: 0.8616 (tp) REVERT: B 58 MET cc_start: 0.9372 (mmp) cc_final: 0.9139 (mmm) REVERT: B 122 HIS cc_start: 0.8243 (m90) cc_final: 0.7718 (m90) REVERT: B 136 ASP cc_start: 0.9095 (m-30) cc_final: 0.8867 (m-30) REVERT: B 139 GLN cc_start: 0.9321 (tp40) cc_final: 0.9095 (tp40) REVERT: B 210 MET cc_start: 0.9576 (mtp) cc_final: 0.9370 (mtp) REVERT: B 225 LEU cc_start: 0.9037 (mt) cc_final: 0.8817 (mt) REVERT: B 257 MET cc_start: 0.9147 (mmm) cc_final: 0.8781 (tmm) REVERT: B 293 MET cc_start: 0.9049 (ttt) cc_final: 0.8121 (tmm) REVERT: B 297 TYR cc_start: 0.8994 (m-80) cc_final: 0.8402 (m-80) REVERT: B 324 ARG cc_start: 0.9353 (mtt90) cc_final: 0.8865 (mtp85) REVERT: B 327 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8547 (mt-10) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1524 time to fit residues: 35.2685 Evaluate side-chains 129 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 30.0000 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 30.0000 chunk 99 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8074 Z= 0.185 Angle : 0.587 11.322 11019 Z= 0.316 Chirality : 0.042 0.215 1386 Planarity : 0.003 0.035 1450 Dihedral : 3.666 18.756 1274 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1231 helix: 1.32 (0.19), residues: 768 sheet: 0.26 (0.48), residues: 104 loop : -0.66 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 31 HIS 0.002 0.001 HIS A 179 PHE 0.035 0.001 PHE B 67 TYR 0.027 0.002 TYR B 302 ARG 0.005 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.9237 (m-80) cc_final: 0.8982 (m-80) REVERT: A 81 GLN cc_start: 0.9346 (pp30) cc_final: 0.8839 (pp30) REVERT: A 96 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8749 (mm-40) REVERT: A 118 ASP cc_start: 0.9335 (m-30) cc_final: 0.8877 (m-30) REVERT: A 131 GLN cc_start: 0.8636 (tt0) cc_final: 0.8305 (tt0) REVERT: A 138 PHE cc_start: 0.8674 (t80) cc_final: 0.8473 (t80) REVERT: A 196 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8087 (tm-30) REVERT: A 282 MET cc_start: 0.8820 (tmm) cc_final: 0.8338 (tmm) REVERT: A 286 ILE cc_start: 0.9389 (pt) cc_final: 0.9175 (pt) REVERT: A 304 ARG cc_start: 0.9078 (ttm110) cc_final: 0.8636 (ttm110) REVERT: B 35 LEU cc_start: 0.9036 (tp) cc_final: 0.8669 (tp) REVERT: B 58 MET cc_start: 0.9374 (mmp) cc_final: 0.9135 (mmm) REVERT: B 67 PHE cc_start: 0.9383 (t80) cc_final: 0.9126 (t80) REVERT: B 122 HIS cc_start: 0.8242 (m90) cc_final: 0.7691 (m90) REVERT: B 136 ASP cc_start: 0.9084 (m-30) cc_final: 0.8841 (m-30) REVERT: B 139 GLN cc_start: 0.9320 (tp40) cc_final: 0.9079 (tp40) REVERT: B 197 ASP cc_start: 0.9141 (m-30) cc_final: 0.8751 (m-30) REVERT: B 206 LEU cc_start: 0.9695 (tp) cc_final: 0.9494 (tp) REVERT: B 210 MET cc_start: 0.9587 (mtp) cc_final: 0.9180 (mtm) REVERT: B 225 LEU cc_start: 0.9008 (mt) cc_final: 0.8797 (mt) REVERT: B 261 MET cc_start: 0.9451 (tpp) cc_final: 0.9029 (tpt) REVERT: B 297 TYR cc_start: 0.8965 (m-80) cc_final: 0.8645 (m-80) REVERT: B 324 ARG cc_start: 0.9344 (mtt90) cc_final: 0.8929 (mtp85) REVERT: B 327 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8584 (mt-10) REVERT: B 330 ASP cc_start: 0.8997 (m-30) cc_final: 0.8716 (p0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1448 time to fit residues: 34.9162 Evaluate side-chains 135 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 80 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8074 Z= 0.169 Angle : 0.586 11.057 11019 Z= 0.312 Chirality : 0.041 0.189 1386 Planarity : 0.003 0.038 1450 Dihedral : 3.631 18.017 1274 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.18 % Allowed : 0.36 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.24), residues: 1231 helix: 1.25 (0.19), residues: 772 sheet: 0.29 (0.48), residues: 104 loop : -0.61 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 31 HIS 0.002 0.001 HIS A 179 PHE 0.023 0.001 PHE B 67 TYR 0.027 0.002 TYR A 277 ARG 0.005 0.001 ARG A 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.9229 (m-80) cc_final: 0.8971 (m-10) REVERT: A 81 GLN cc_start: 0.9331 (pp30) cc_final: 0.8818 (pp30) REVERT: A 96 GLN cc_start: 0.9245 (mm-40) cc_final: 0.8744 (mm-40) REVERT: A 118 ASP cc_start: 0.9328 (m-30) cc_final: 0.8882 (m-30) REVERT: A 131 GLN cc_start: 0.8697 (tt0) cc_final: 0.8373 (tt0) REVERT: A 170 MET cc_start: 0.8145 (ppp) cc_final: 0.7880 (ppp) REVERT: A 196 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8008 (tm-30) REVERT: A 282 MET cc_start: 0.8804 (tmm) cc_final: 0.8310 (tmm) REVERT: A 286 ILE cc_start: 0.9389 (pt) cc_final: 0.9156 (pt) REVERT: A 304 ARG cc_start: 0.9094 (ttm110) cc_final: 0.8704 (ttm110) REVERT: B 35 LEU cc_start: 0.9014 (tp) cc_final: 0.8643 (tp) REVERT: B 58 MET cc_start: 0.9368 (mmp) cc_final: 0.9131 (mmm) REVERT: B 67 PHE cc_start: 0.9427 (t80) cc_final: 0.9220 (t80) REVERT: B 122 HIS cc_start: 0.8238 (m90) cc_final: 0.7693 (m90) REVERT: B 136 ASP cc_start: 0.9072 (m-30) cc_final: 0.8840 (m-30) REVERT: B 139 GLN cc_start: 0.9311 (tp40) cc_final: 0.9066 (tp40) REVERT: B 197 ASP cc_start: 0.9126 (m-30) cc_final: 0.8734 (m-30) REVERT: B 210 MET cc_start: 0.9563 (mtp) cc_final: 0.9329 (mtp) REVERT: B 225 LEU cc_start: 0.8970 (mt) cc_final: 0.8758 (mt) REVERT: B 261 MET cc_start: 0.9434 (tpp) cc_final: 0.8980 (tpt) REVERT: B 297 TYR cc_start: 0.8925 (m-80) cc_final: 0.8692 (m-80) REVERT: B 324 ARG cc_start: 0.9342 (mtt90) cc_final: 0.8924 (mtp85) REVERT: B 327 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8555 (mt-10) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1490 time to fit residues: 35.5102 Evaluate side-chains 136 residues out of total 1061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 0.0010 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.073861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.060118 restraints weight = 37326.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.061818 restraints weight = 23237.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.063075 restraints weight = 16220.922| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8074 Z= 0.194 Angle : 0.605 11.285 11019 Z= 0.322 Chirality : 0.042 0.187 1386 Planarity : 0.003 0.039 1450 Dihedral : 3.630 17.507 1274 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1231 helix: 1.26 (0.19), residues: 772 sheet: 0.30 (0.48), residues: 104 loop : -0.57 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 31 HIS 0.003 0.001 HIS A 179 PHE 0.026 0.002 PHE B 67 TYR 0.018 0.002 TYR A 277 ARG 0.003 0.000 ARG A 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1621.10 seconds wall clock time: 29 minutes 45.06 seconds (1785.06 seconds total)