Starting phenix.real_space_refine on Tue Sep 24 21:27:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/09_2024/6jt0_9883.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/09_2024/6jt0_9883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/09_2024/6jt0_9883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/09_2024/6jt0_9883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/09_2024/6jt0_9883.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt0_9883/09_2024/6jt0_9883.cif" } resolution = 4.0 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= 0.003 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 Fe 1 7.16 5 S 59 5.16 5 C 5529 2.51 5 N 1462 2.21 5 O 1551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8602 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4087 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 542, 4084 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 166 Conformer: "B" Number of residues, atoms: 542, 4084 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 166 bond proxies already assigned to first conformer: 4165 Chain: "B" Number of atoms: 4472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 576, 4468 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 576, 4468 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 16, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 4553 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU A 147 " occ=0.91 ... (3 atoms not shown) pdb=" CB GLU A 147 " occ=0.91 Time building chain proxies: 8.88, per 1000 atoms: 1.03 Number of scatterers: 8602 At special positions: 0 Unit cell: (148.39, 96.14, 74.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 59 16.00 O 1551 8.00 N 1462 7.00 C 5529 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: 2.15 Conformation dependent library (CDL) restraints added in 1.9 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 10 sheets defined 48.2% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 128 through 149 removed outlier: 3.588A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 158 through 174 removed outlier: 4.595A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 237 through 242 removed outlier: 4.090A pdb=" N HIS A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.845A pdb=" N TYR A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 323' Processing helix chain 'A' and resid 334 through 341 removed outlier: 4.043A pdb=" N MET A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.925A pdb=" N THR A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 419 removed outlier: 4.471A pdb=" N GLY A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 458 removed outlier: 3.941A pdb=" N GLY A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 removed outlier: 3.621A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.771A pdb=" N ILE A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 521 Processing helix chain 'A' and resid 544 through 561 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.970A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.912A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 30 removed outlier: 3.675A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Proline residue: B 19 - end of helix removed outlier: 3.931A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.927A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 81 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.521A pdb=" N ASP B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.757A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 354 removed outlier: 4.173A pdb=" N ASP B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 395 removed outlier: 4.209A pdb=" N TYR B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 378 " --> pdb=" O ASP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.603A pdb=" N HIS B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 461 removed outlier: 3.709A pdb=" N LYS B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 508 removed outlier: 4.028A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.986A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 193 removed outlier: 4.003A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.744A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 290 " --> pdb=" O PHE A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 482 removed outlier: 5.484A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 583 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 487 removed outlier: 7.599A pdb=" N MET A 573 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASN A 617 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 575 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 523 through 525 removed outlier: 3.741A pdb=" N TYR A 523 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.612A pdb=" N GLN B 178 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.672A pdb=" N ILE B 222 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS B 232 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS B 220 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.737A pdb=" N ASN B 419 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY B 526 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR B 421 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS B 524 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU B 423 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY B 522 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 529 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.737A pdb=" N ASN B 419 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY B 526 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR B 421 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS B 524 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU B 423 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY B 522 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE B 523 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 601 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 511 through 512 457 hydrogen bonds defined for protein. 1298 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: 2.59 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3085 1.38 - 1.55: 5579 1.55 - 1.71: 26 1.71 - 1.88: 90 1.88 - 2.05: 4 Bond restraints: 8784 Sorted by residual: bond pdb=" C ASP B 106 " pdb=" O ASP B 106 " ideal model delta sigma weight residual 1.237 1.266 -0.029 1.17e-02 7.31e+03 6.10e+00 bond pdb=" C ALA B 103 " pdb=" O ALA B 103 " ideal model delta sigma weight residual 1.237 1.263 -0.026 1.17e-02 7.31e+03 4.90e+00 bond pdb=" CA ALA B 103 " pdb=" C ALA B 103 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.30e-02 5.92e+03 4.74e+00 bond pdb=" CA GLU A 230 " pdb=" CB GLU A 230 " ideal model delta sigma weight residual 1.524 1.551 -0.026 1.22e-02 6.72e+03 4.62e+00 bond pdb=" CA THR B 110 " pdb=" C THR B 110 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.30e-02 5.92e+03 4.59e+00 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11684 2.05 - 4.09: 207 4.09 - 6.14: 33 6.14 - 8.18: 9 8.18 - 10.23: 2 Bond angle restraints: 11935 Sorted by residual: angle pdb=" C THR B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta sigma weight residual 120.56 130.79 -10.23 1.28e+00 6.10e-01 6.38e+01 angle pdb=" N VAL A 231 " pdb=" CA VAL A 231 " pdb=" C VAL A 231 " ideal model delta sigma weight residual 108.17 115.21 -7.04 1.46e+00 4.69e-01 2.33e+01 angle pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C LEU B 108 " pdb=" N ALA B 109 " pdb=" CA ALA B 109 " ideal model delta sigma weight residual 120.28 125.10 -4.82 1.34e+00 5.57e-01 1.29e+01 angle pdb=" N TYR B 395 " pdb=" CA TYR B 395 " pdb=" C TYR B 395 " ideal model delta sigma weight residual 110.06 115.00 -4.94 1.43e+00 4.89e-01 1.19e+01 ... (remaining 11930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4896 17.53 - 35.05: 289 35.05 - 52.58: 48 52.58 - 70.10: 12 70.10 - 87.63: 7 Dihedral angle restraints: 5252 sinusoidal: 1996 harmonic: 3256 Sorted by residual: dihedral pdb=" CA LEU A 398 " pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP B 262 " pdb=" C ASP B 262 " pdb=" N ILE B 263 " pdb=" CA ILE B 263 " ideal model delta harmonic sigma weight residual -180.00 -155.07 -24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA HIS A 655 " pdb=" C HIS A 655 " pdb=" N PHE A 656 " pdb=" CA PHE A 656 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1037 0.044 - 0.088: 264 0.088 - 0.132: 82 0.132 - 0.176: 6 0.176 - 0.220: 1 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CG LEU B 9 " pdb=" CB LEU B 9 " pdb=" CD1 LEU B 9 " pdb=" CD2 LEU B 9 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PRO B 210 " pdb=" N PRO B 210 " pdb=" C PRO B 210 " pdb=" CB PRO B 210 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA VAL B 564 " pdb=" N VAL B 564 " pdb=" C VAL B 564 " pdb=" CB VAL B 564 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1387 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 250 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO A 251 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 112 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 113 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 328 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 329 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " 0.020 5.00e-02 4.00e+02 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1258 2.76 - 3.29: 8396 3.29 - 3.83: 13964 3.83 - 4.36: 15931 4.36 - 4.90: 27305 Nonbonded interactions: 66854 Sorted by model distance: nonbonded pdb=" NH2 ARG A 410 " pdb=" OD1 ASN B 100 " model vdw 2.225 3.120 nonbonded pdb=" O THR B 392 " pdb=" OG SER B 396 " model vdw 2.267 3.040 nonbonded pdb=" O SER A 581 " pdb=" ND2 ASN A 600 " model vdw 2.295 3.120 nonbonded pdb=" O LEU A 74 " pdb=" OG SER A 77 " model vdw 2.309 3.040 nonbonded pdb=" ND1 HIS B 524 " pdb=" OG SER B 565 " model vdw 2.335 3.120 ... (remaining 66849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 1.150 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 27.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.004 0.100 8784 Z= 0.231 Angle : 0.710 10.228 11935 Z= 0.391 Chirality : 0.043 0.220 1390 Planarity : 0.004 0.057 1515 Dihedral : 12.208 87.630 3144 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.73 % Favored : 93.91 % Rotamer: Outliers : 4.73 % Allowed : 6.59 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -2.84 (0.22), residues: 1101 helix: -1.01 (0.20), residues: 505 sheet: -2.10 (0.31), residues: 211 loop : -2.74 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 602 HIS 0.004 0.001 HIS B 176 PHE 0.023 0.002 PHE A 458 TYR 0.016 0.002 TYR B 339 ARG 0.003 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 178 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9551 (pp) cc_final: 0.9186 (tt) REVERT: A 256 SER cc_start: 0.8985 (t) cc_final: 0.8331 (p) REVERT: A 309 MET cc_start: 0.8928 (ttm) cc_final: 0.8504 (tmm) REVERT: A 341 MET cc_start: 0.9062 (mmt) cc_final: 0.8707 (mmm) REVERT: A 384 SER cc_start: 0.9182 (m) cc_final: 0.8978 (p) REVERT: A 503 ILE cc_start: 0.9734 (mm) cc_final: 0.9468 (tt) REVERT: A 520 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8777 (tt) REVERT: A 557 MET cc_start: 0.9490 (mmt) cc_final: 0.9003 (tmm) REVERT: B 65 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9073 (tp30) REVERT: B 69 MET cc_start: 0.9468 (mtm) cc_final: 0.9091 (ptm) REVERT: B 162 ILE cc_start: 0.9430 (pt) cc_final: 0.8938 (mm) REVERT: B 164 MET cc_start: 0.9129 (ttm) cc_final: 0.8891 (ttm) REVERT: B 243 LEU cc_start: 0.8978 (tt) cc_final: 0.8581 (pp) REVERT: B 338 LEU cc_start: 0.9191 (mt) cc_final: 0.8910 (mt) REVERT: B 373 THR cc_start: 0.9292 (m) cc_final: 0.9035 (p) REVERT: B 388 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8615 (tppt) REVERT: B 423 LEU cc_start: 0.9667 (tt) cc_final: 0.9438 (tp) REVERT: B 424 PHE cc_start: 0.9273 (m-80) cc_final: 0.8741 (m-10) REVERT: B 478 LYS cc_start: 0.9289 (mttm) cc_final: 0.8762 (mmtm) REVERT: B 499 LEU cc_start: 0.9494 (tp) cc_final: 0.9061 (tp) REVERT: B 503 MET cc_start: 0.9462 (mtp) cc_final: 0.9098 (mtm) REVERT: B 505 GLU cc_start: 0.9620 (OUTLIER) cc_final: 0.9385 (mt-10) REVERT: B 537 MET cc_start: 0.8906 (mmm) cc_final: 0.8503 (tmm) REVERT: B 541 CYS cc_start: 0.9380 (m) cc_final: 0.8863 (m) REVERT: B 572 LEU cc_start: 0.9692 (mm) cc_final: 0.9441 (mm) REVERT: B 573 MET cc_start: 0.9467 (mmp) cc_final: 0.9226 (mmp) outliers start: 43 outliers final: 11 residues processed: 211 average time/residue: 0.1874 time to fit residues: 56.3319 Evaluate side-chains 116 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 505 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS B 367 GLN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN B 563 ASN B 581 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8784 Z= 0.206 Angle : 0.779 14.874 11935 Z= 0.369 Chirality : 0.045 0.195 1390 Planarity : 0.005 0.094 1515 Dihedral : 7.609 86.399 1231 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.09 % Favored : 95.64 % Rotamer: Outliers : 3.52 % Allowed : 14.84 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.62 (0.24), residues: 1101 helix: 0.00 (0.21), residues: 520 sheet: -1.29 (0.32), residues: 217 loop : -2.41 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.005 0.001 HIS B 498 PHE 0.030 0.002 PHE A 646 TYR 0.026 0.002 TYR B 569 ARG 0.007 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9475 (pp) cc_final: 0.9136 (tt) REVERT: A 236 MET cc_start: 0.8420 (mmm) cc_final: 0.8087 (mmm) REVERT: A 256 SER cc_start: 0.9023 (t) cc_final: 0.8570 (p) REVERT: A 309 MET cc_start: 0.8741 (ttm) cc_final: 0.8447 (tmm) REVERT: A 344 MET cc_start: 0.9227 (mtm) cc_final: 0.8961 (tpp) REVERT: A 384 SER cc_start: 0.9103 (m) cc_final: 0.8863 (p) REVERT: A 503 ILE cc_start: 0.9736 (mm) cc_final: 0.9526 (tt) REVERT: A 520 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8765 (tt) REVERT: A 556 MET cc_start: 0.9743 (ttm) cc_final: 0.9210 (mpp) REVERT: A 557 MET cc_start: 0.9663 (mmt) cc_final: 0.9237 (tpp) REVERT: A 573 MET cc_start: 0.9427 (mmm) cc_final: 0.8695 (mmm) REVERT: A 578 HIS cc_start: 0.8515 (t70) cc_final: 0.8313 (t70) REVERT: B 1 MET cc_start: 0.9289 (tpp) cc_final: 0.8732 (tpp) REVERT: B 11 LEU cc_start: 0.9521 (tp) cc_final: 0.9257 (tp) REVERT: B 66 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9241 (pt) REVERT: B 69 MET cc_start: 0.9548 (mtm) cc_final: 0.9134 (ptm) REVERT: B 320 LEU cc_start: 0.9478 (tp) cc_final: 0.9082 (tt) REVERT: B 373 THR cc_start: 0.9339 (m) cc_final: 0.9084 (p) REVERT: B 444 MET cc_start: 0.9328 (tmm) cc_final: 0.8981 (tpt) REVERT: B 478 LYS cc_start: 0.9329 (mttm) cc_final: 0.8866 (mmtm) REVERT: B 503 MET cc_start: 0.9398 (mtp) cc_final: 0.9119 (mtm) REVERT: B 505 GLU cc_start: 0.9587 (OUTLIER) cc_final: 0.9368 (mt-10) REVERT: B 541 CYS cc_start: 0.9299 (m) cc_final: 0.8877 (m) REVERT: B 572 LEU cc_start: 0.9700 (mm) cc_final: 0.9378 (mm) REVERT: B 573 MET cc_start: 0.9485 (mmp) cc_final: 0.9233 (mmp) outliers start: 32 outliers final: 16 residues processed: 135 average time/residue: 0.1769 time to fit residues: 34.4121 Evaluate side-chains 109 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8784 Z= 0.198 Angle : 0.744 13.209 11935 Z= 0.349 Chirality : 0.044 0.190 1390 Planarity : 0.004 0.060 1515 Dihedral : 7.074 79.526 1228 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 2.86 % Allowed : 16.15 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.93 (0.24), residues: 1101 helix: 0.62 (0.22), residues: 512 sheet: -1.07 (0.33), residues: 219 loop : -2.00 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 22 HIS 0.003 0.001 HIS B 498 PHE 0.028 0.002 PHE A 141 TYR 0.016 0.001 TYR A 399 ARG 0.005 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9491 (pp) cc_final: 0.9149 (tt) REVERT: A 236 MET cc_start: 0.8487 (mmm) cc_final: 0.8145 (mmm) REVERT: A 256 SER cc_start: 0.9119 (t) cc_final: 0.8600 (p) REVERT: A 309 MET cc_start: 0.8703 (ttm) cc_final: 0.8400 (tmm) REVERT: A 344 MET cc_start: 0.8960 (mtm) cc_final: 0.8725 (tpp) REVERT: A 384 SER cc_start: 0.9117 (m) cc_final: 0.8862 (p) REVERT: A 520 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8733 (tt) REVERT: A 556 MET cc_start: 0.9744 (ttm) cc_final: 0.9208 (mtt) REVERT: A 557 MET cc_start: 0.9688 (mmt) cc_final: 0.9229 (tpp) REVERT: A 573 MET cc_start: 0.9429 (mmm) cc_final: 0.8815 (mmm) REVERT: B 1 MET cc_start: 0.9310 (tpp) cc_final: 0.8746 (tpp) REVERT: B 11 LEU cc_start: 0.9531 (tp) cc_final: 0.9213 (tp) REVERT: B 69 MET cc_start: 0.9507 (mtm) cc_final: 0.9233 (ptm) REVERT: B 320 LEU cc_start: 0.9512 (tp) cc_final: 0.9173 (tt) REVERT: B 373 THR cc_start: 0.9354 (m) cc_final: 0.9114 (p) REVERT: B 444 MET cc_start: 0.9330 (tmm) cc_final: 0.9062 (tpt) REVERT: B 503 MET cc_start: 0.9395 (mtp) cc_final: 0.8997 (mtt) REVERT: B 541 CYS cc_start: 0.9306 (m) cc_final: 0.8919 (m) REVERT: B 572 LEU cc_start: 0.9698 (mm) cc_final: 0.9492 (mm) REVERT: B 573 MET cc_start: 0.9574 (mmp) cc_final: 0.9301 (mmp) REVERT: B 592 MET cc_start: 0.8133 (mmm) cc_final: 0.7698 (mmm) outliers start: 26 outliers final: 21 residues processed: 122 average time/residue: 0.1637 time to fit residues: 29.6573 Evaluate side-chains 111 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.0970 chunk 96 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8784 Z= 0.182 Angle : 0.720 12.690 11935 Z= 0.336 Chirality : 0.043 0.182 1390 Planarity : 0.004 0.048 1515 Dihedral : 6.427 76.850 1225 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 2.64 % Allowed : 17.36 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.36 (0.25), residues: 1101 helix: 1.10 (0.23), residues: 513 sheet: -0.78 (0.34), residues: 219 loop : -1.77 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 22 HIS 0.004 0.001 HIS A 578 PHE 0.027 0.002 PHE A 141 TYR 0.015 0.001 TYR A 399 ARG 0.004 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9499 (pp) cc_final: 0.9171 (tt) REVERT: A 236 MET cc_start: 0.8473 (mmm) cc_final: 0.8125 (mmm) REVERT: A 256 SER cc_start: 0.9186 (t) cc_final: 0.8728 (p) REVERT: A 384 SER cc_start: 0.9094 (m) cc_final: 0.8844 (p) REVERT: A 399 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8520 (m-10) REVERT: A 482 MET cc_start: 0.8636 (tpp) cc_final: 0.8379 (tpp) REVERT: A 520 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8724 (tt) REVERT: A 556 MET cc_start: 0.9736 (ttm) cc_final: 0.9161 (mtt) REVERT: A 557 MET cc_start: 0.9691 (mmt) cc_final: 0.9268 (tpp) REVERT: A 573 MET cc_start: 0.9281 (mmm) cc_final: 0.8779 (mmm) REVERT: B 1 MET cc_start: 0.9223 (tpp) cc_final: 0.8799 (tpp) REVERT: B 11 LEU cc_start: 0.9540 (tp) cc_final: 0.9172 (tp) REVERT: B 69 MET cc_start: 0.9534 (mtm) cc_final: 0.9205 (ptm) REVERT: B 373 THR cc_start: 0.9353 (m) cc_final: 0.9119 (p) REVERT: B 503 MET cc_start: 0.9453 (mtp) cc_final: 0.9209 (mtm) REVERT: B 541 CYS cc_start: 0.9280 (m) cc_final: 0.8812 (m) REVERT: B 573 MET cc_start: 0.9608 (mmp) cc_final: 0.9264 (mmp) REVERT: B 592 MET cc_start: 0.7978 (mmm) cc_final: 0.7445 (mmm) outliers start: 24 outliers final: 17 residues processed: 118 average time/residue: 0.1672 time to fit residues: 29.2576 Evaluate side-chains 106 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 399 TYR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 0.0970 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8784 Z= 0.233 Angle : 0.729 12.266 11935 Z= 0.341 Chirality : 0.043 0.184 1390 Planarity : 0.004 0.046 1515 Dihedral : 6.235 73.635 1223 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.27 % Favored : 95.55 % Rotamer: Outliers : 3.41 % Allowed : 17.47 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1101 helix: 1.36 (0.23), residues: 515 sheet: -0.76 (0.34), residues: 221 loop : -1.61 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 22 HIS 0.003 0.001 HIS A 578 PHE 0.026 0.002 PHE B 75 TYR 0.017 0.001 TYR A 399 ARG 0.003 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9507 (pp) cc_final: 0.9175 (tt) REVERT: A 236 MET cc_start: 0.8602 (mmm) cc_final: 0.8326 (mmm) REVERT: A 256 SER cc_start: 0.9258 (t) cc_final: 0.8778 (p) REVERT: A 301 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: A 482 MET cc_start: 0.8756 (tpp) cc_final: 0.8489 (tpp) REVERT: A 520 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8790 (tt) REVERT: A 557 MET cc_start: 0.9679 (mmt) cc_final: 0.9257 (tpp) REVERT: A 573 MET cc_start: 0.9249 (mmm) cc_final: 0.8833 (mmm) REVERT: B 1 MET cc_start: 0.9266 (tpp) cc_final: 0.8738 (tpp) REVERT: B 11 LEU cc_start: 0.9560 (tp) cc_final: 0.9197 (tp) REVERT: B 373 THR cc_start: 0.9392 (m) cc_final: 0.9149 (p) REVERT: B 503 MET cc_start: 0.9421 (mtp) cc_final: 0.9112 (mtt) REVERT: B 541 CYS cc_start: 0.9315 (m) cc_final: 0.8859 (m) REVERT: B 573 MET cc_start: 0.9607 (mmp) cc_final: 0.9303 (mmp) REVERT: B 592 MET cc_start: 0.7942 (mmm) cc_final: 0.7460 (mmm) outliers start: 31 outliers final: 19 residues processed: 112 average time/residue: 0.1753 time to fit residues: 29.0038 Evaluate side-chains 107 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.0470 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 HIS ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.181 Angle : 0.735 12.061 11935 Z= 0.338 Chirality : 0.044 0.328 1390 Planarity : 0.004 0.041 1515 Dihedral : 5.899 70.508 1221 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.45 % Favored : 96.36 % Rotamer: Outliers : 2.86 % Allowed : 18.13 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.10 (0.26), residues: 1101 helix: 1.46 (0.23), residues: 515 sheet: -0.57 (0.34), residues: 223 loop : -1.52 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 22 HIS 0.006 0.001 HIS B 583 PHE 0.025 0.002 PHE A 141 TYR 0.020 0.001 TYR A 399 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9504 (pp) cc_final: 0.9182 (tt) REVERT: A 236 MET cc_start: 0.8613 (mmm) cc_final: 0.8317 (mmm) REVERT: A 256 SER cc_start: 0.9277 (t) cc_final: 0.8856 (p) REVERT: A 301 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7902 (m-80) REVERT: A 341 MET cc_start: 0.9305 (tpp) cc_final: 0.8666 (tpp) REVERT: A 384 SER cc_start: 0.9116 (m) cc_final: 0.8829 (p) REVERT: A 520 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8614 (tt) REVERT: A 556 MET cc_start: 0.9723 (ttm) cc_final: 0.9102 (tpt) REVERT: A 557 MET cc_start: 0.9675 (mmt) cc_final: 0.9242 (tpp) REVERT: A 573 MET cc_start: 0.9257 (mmm) cc_final: 0.8832 (mmm) REVERT: B 1 MET cc_start: 0.9248 (tpp) cc_final: 0.8719 (tpp) REVERT: B 11 LEU cc_start: 0.9575 (tp) cc_final: 0.9192 (tp) REVERT: B 340 LEU cc_start: 0.8509 (tt) cc_final: 0.8167 (tt) REVERT: B 373 THR cc_start: 0.9386 (m) cc_final: 0.9140 (p) REVERT: B 444 MET cc_start: 0.9291 (tmm) cc_final: 0.8960 (tpp) REVERT: B 478 LYS cc_start: 0.9341 (mttm) cc_final: 0.8791 (mmtm) REVERT: B 503 MET cc_start: 0.9438 (mtp) cc_final: 0.9186 (mtm) REVERT: B 541 CYS cc_start: 0.9258 (m) cc_final: 0.8809 (m) REVERT: B 573 MET cc_start: 0.9594 (mmp) cc_final: 0.9284 (mmp) REVERT: B 592 MET cc_start: 0.7905 (mmm) cc_final: 0.7369 (mmm) outliers start: 26 outliers final: 18 residues processed: 116 average time/residue: 0.1729 time to fit residues: 29.5732 Evaluate side-chains 109 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 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 134 HIS B 524 HIS B 563 ASN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.194 Angle : 0.736 12.505 11935 Z= 0.336 Chirality : 0.044 0.317 1390 Planarity : 0.004 0.040 1515 Dihedral : 5.797 68.442 1221 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 2.97 % Allowed : 18.35 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.21 (0.26), residues: 1101 helix: 1.52 (0.23), residues: 515 sheet: -0.43 (0.35), residues: 209 loop : -1.43 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 602 HIS 0.006 0.001 HIS B 583 PHE 0.025 0.001 PHE A 141 TYR 0.020 0.001 TYR A 399 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9492 (pp) cc_final: 0.9182 (tt) REVERT: A 236 MET cc_start: 0.8643 (mmm) cc_final: 0.8346 (mmm) REVERT: A 256 SER cc_start: 0.9293 (t) cc_final: 0.8871 (p) REVERT: A 301 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: A 341 MET cc_start: 0.9231 (tpp) cc_final: 0.8554 (tpp) REVERT: A 384 SER cc_start: 0.9108 (m) cc_final: 0.8805 (p) REVERT: A 557 MET cc_start: 0.9662 (mmt) cc_final: 0.9240 (tpp) REVERT: A 573 MET cc_start: 0.9219 (mmm) cc_final: 0.8901 (mmm) REVERT: B 1 MET cc_start: 0.9257 (tpp) cc_final: 0.8756 (tpp) REVERT: B 11 LEU cc_start: 0.9584 (tp) cc_final: 0.9249 (tp) REVERT: B 164 MET cc_start: 0.8717 (ttm) cc_final: 0.8442 (ttm) REVERT: B 340 LEU cc_start: 0.8516 (tt) cc_final: 0.8185 (tt) REVERT: B 373 THR cc_start: 0.9389 (m) cc_final: 0.9135 (p) REVERT: B 444 MET cc_start: 0.9334 (tmm) cc_final: 0.9048 (tpt) REVERT: B 478 LYS cc_start: 0.9382 (mttm) cc_final: 0.8811 (mmtm) REVERT: B 503 MET cc_start: 0.9427 (mtp) cc_final: 0.9187 (mtm) REVERT: B 541 CYS cc_start: 0.9225 (m) cc_final: 0.8787 (m) REVERT: B 573 MET cc_start: 0.9597 (mmp) cc_final: 0.9257 (mmp) REVERT: B 592 MET cc_start: 0.7741 (mmm) cc_final: 0.7341 (mmm) outliers start: 27 outliers final: 21 residues processed: 114 average time/residue: 0.1760 time to fit residues: 29.2210 Evaluate side-chains 112 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 0.0010 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 HIS ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8784 Z= 0.169 Angle : 0.736 13.370 11935 Z= 0.332 Chirality : 0.043 0.183 1390 Planarity : 0.004 0.039 1515 Dihedral : 5.438 66.841 1219 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 2.42 % Allowed : 19.12 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.29 (0.26), residues: 1101 helix: 1.51 (0.23), residues: 517 sheet: -0.28 (0.37), residues: 206 loop : -1.36 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 602 HIS 0.003 0.001 HIS B 583 PHE 0.024 0.001 PHE A 141 TYR 0.018 0.001 TYR A 399 ARG 0.005 0.000 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LEU cc_start: 0.9473 (pp) cc_final: 0.9185 (tt) REVERT: A 236 MET cc_start: 0.8676 (mmm) cc_final: 0.8348 (mmm) REVERT: A 256 SER cc_start: 0.9282 (t) cc_final: 0.8837 (p) REVERT: A 301 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: A 341 MET cc_start: 0.9209 (tpp) cc_final: 0.8585 (tpp) REVERT: A 384 SER cc_start: 0.9064 (m) cc_final: 0.8755 (p) REVERT: A 455 CYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9269 (p) REVERT: A 503 ILE cc_start: 0.9777 (mm) cc_final: 0.9517 (tt) REVERT: A 557 MET cc_start: 0.9677 (mmt) cc_final: 0.9245 (tpp) REVERT: A 573 MET cc_start: 0.9234 (mmm) cc_final: 0.8879 (mmm) REVERT: B 1 MET cc_start: 0.9190 (tpp) cc_final: 0.8701 (tpp) REVERT: B 11 LEU cc_start: 0.9590 (tp) cc_final: 0.9214 (tp) REVERT: B 73 MET cc_start: 0.9578 (tpp) cc_final: 0.9320 (tpp) REVERT: B 164 MET cc_start: 0.8704 (ttm) cc_final: 0.8457 (ttm) REVERT: B 373 THR cc_start: 0.9348 (m) cc_final: 0.9125 (p) REVERT: B 424 PHE cc_start: 0.9228 (m-80) cc_final: 0.8749 (m-10) REVERT: B 444 MET cc_start: 0.9291 (tmm) cc_final: 0.9047 (tpt) REVERT: B 478 LYS cc_start: 0.9369 (mttm) cc_final: 0.8751 (mmtm) REVERT: B 503 MET cc_start: 0.9394 (mtp) cc_final: 0.9192 (mtm) REVERT: B 541 CYS cc_start: 0.9194 (m) cc_final: 0.8762 (m) REVERT: B 573 MET cc_start: 0.9607 (mmp) cc_final: 0.9223 (mmp) REVERT: B 592 MET cc_start: 0.7737 (mmm) cc_final: 0.7291 (mmm) outliers start: 22 outliers final: 19 residues processed: 108 average time/residue: 0.1663 time to fit residues: 26.7948 Evaluate side-chains 109 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 393 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.0370 chunk 65 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 ASN B 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8784 Z= 0.167 Angle : 0.739 13.845 11935 Z= 0.330 Chirality : 0.042 0.177 1390 Planarity : 0.004 0.038 1515 Dihedral : 5.299 64.999 1219 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.42 % Allowed : 19.56 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.38 (0.26), residues: 1101 helix: 1.56 (0.23), residues: 519 sheet: -0.26 (0.36), residues: 206 loop : -1.27 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 22 HIS 0.003 0.001 HIS B 524 PHE 0.024 0.001 PHE A 141 TYR 0.020 0.001 TYR B 569 ARG 0.005 0.000 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8601 (mmm) cc_final: 0.8256 (mmm) REVERT: A 256 SER cc_start: 0.9312 (t) cc_final: 0.8827 (p) REVERT: A 384 SER cc_start: 0.9025 (m) cc_final: 0.8730 (p) REVERT: A 503 ILE cc_start: 0.9771 (mm) cc_final: 0.9480 (tt) REVERT: A 556 MET cc_start: 0.9727 (ttm) cc_final: 0.9448 (tpp) REVERT: A 557 MET cc_start: 0.9675 (mmt) cc_final: 0.9238 (tpp) REVERT: A 573 MET cc_start: 0.9220 (mmm) cc_final: 0.8861 (mmm) REVERT: B 1 MET cc_start: 0.9183 (tpp) cc_final: 0.8794 (tpp) REVERT: B 164 MET cc_start: 0.8685 (ttm) cc_final: 0.8457 (ttm) REVERT: B 373 THR cc_start: 0.9348 (m) cc_final: 0.9131 (p) REVERT: B 444 MET cc_start: 0.9274 (tmm) cc_final: 0.9043 (tpt) REVERT: B 503 MET cc_start: 0.9389 (mtp) cc_final: 0.9061 (mtt) REVERT: B 541 CYS cc_start: 0.9165 (m) cc_final: 0.8739 (m) REVERT: B 573 MET cc_start: 0.9585 (mmp) cc_final: 0.9295 (mmp) REVERT: B 592 MET cc_start: 0.7755 (mmm) cc_final: 0.7291 (mmm) outliers start: 22 outliers final: 18 residues processed: 110 average time/residue: 0.1782 time to fit residues: 28.9811 Evaluate side-chains 107 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.3980 chunk 73 optimal weight: 0.1980 chunk 110 optimal weight: 0.0970 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 8784 Z= 0.241 Angle : 1.024 59.199 11935 Z= 0.552 Chirality : 0.045 0.509 1390 Planarity : 0.004 0.045 1515 Dihedral : 5.326 64.985 1213 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.31 % Allowed : 20.22 % Favored : 77.47 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.35 (0.26), residues: 1101 helix: 1.56 (0.23), residues: 519 sheet: -0.36 (0.36), residues: 206 loop : -1.27 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 22 HIS 0.003 0.001 HIS B 524 PHE 0.036 0.002 PHE A 458 TYR 0.016 0.001 TYR A 399 ARG 0.011 0.000 ARG B 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8603 (mmm) cc_final: 0.8256 (mmm) REVERT: A 256 SER cc_start: 0.9312 (t) cc_final: 0.8826 (p) REVERT: A 384 SER cc_start: 0.9026 (m) cc_final: 0.8730 (p) REVERT: A 503 ILE cc_start: 0.9772 (mm) cc_final: 0.9479 (tt) REVERT: A 556 MET cc_start: 0.9727 (ttm) cc_final: 0.9445 (tpp) REVERT: A 557 MET cc_start: 0.9674 (mmt) cc_final: 0.9239 (tpp) REVERT: A 573 MET cc_start: 0.9219 (mmm) cc_final: 0.8864 (mmm) REVERT: B 1 MET cc_start: 0.9091 (tpp) cc_final: 0.8795 (tpp) REVERT: B 164 MET cc_start: 0.8687 (ttm) cc_final: 0.8456 (ttm) REVERT: B 373 THR cc_start: 0.9347 (m) cc_final: 0.9132 (p) REVERT: B 444 MET cc_start: 0.9272 (tmm) cc_final: 0.9043 (tpt) REVERT: B 503 MET cc_start: 0.9372 (mtp) cc_final: 0.9056 (mtt) REVERT: B 541 CYS cc_start: 0.9170 (m) cc_final: 0.8740 (m) REVERT: B 573 MET cc_start: 0.9607 (mmp) cc_final: 0.9299 (mmp) REVERT: B 592 MET cc_start: 0.7726 (mmm) cc_final: 0.7292 (mmm) outliers start: 21 outliers final: 17 residues processed: 104 average time/residue: 0.1646 time to fit residues: 25.9070 Evaluate side-chains 105 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 313 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 0.0370 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.0470 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.047936 restraints weight = 42458.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.049523 restraints weight = 24674.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.050630 restraints weight = 16654.647| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 8784 Z= 0.241 Angle : 1.024 59.199 11935 Z= 0.552 Chirality : 0.045 0.509 1390 Planarity : 0.004 0.045 1515 Dihedral : 5.326 64.985 1213 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.87 % Allowed : 20.44 % Favored : 77.69 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.35 (0.26), residues: 1101 helix: 1.56 (0.23), residues: 519 sheet: -0.36 (0.36), residues: 206 loop : -1.27 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 22 HIS 0.003 0.001 HIS B 524 PHE 0.036 0.002 PHE A 458 TYR 0.016 0.001 TYR A 399 ARG 0.011 0.000 ARG B 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.46 seconds wall clock time: 33 minutes 52.25 seconds (2032.25 seconds total)