Starting phenix.real_space_refine on Fri Jul 19 11:35:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4g_41030/07_2024/8t4g_41030.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4g_41030/07_2024/8t4g_41030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4g_41030/07_2024/8t4g_41030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4g_41030/07_2024/8t4g_41030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4g_41030/07_2024/8t4g_41030.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4g_41030/07_2024/8t4g_41030.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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 31 5.16 5 C 4890 2.51 5 N 1355 2.21 5 O 1445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 222": "OD1" <-> "OD2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 497": "OE1" <-> "OE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 591": "OE1" <-> "OE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "B ASP 631": "OD1" <-> "OD2" Residue "C ASP 3": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7721 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3417 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 18, 'TRANS': 510} Chain breaks: 2 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 545 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 400 Chain: "B" Number of atoms: 4225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4225 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 530} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG A 529 " occ=0.51 ... (3 atoms not shown) pdb=" CB ARG A 529 " occ=0.51 Time building chain proxies: 5.43, per 1000 atoms: 0.70 Number of scatterers: 7721 At special positions: 0 Unit cell: (69.637, 110.748, 132.562, 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 31 16.00 O 1445 8.00 N 1355 7.00 C 4890 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 73.6% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.871A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 218 removed outlier: 3.993A pdb=" N PHE A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 270 removed outlier: 3.740A pdb=" N PHE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 324 Processing helix chain 'A' and resid 324 through 340 Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 340 through 373 removed outlier: 4.541A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 437 removed outlier: 3.634A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 476 removed outlier: 3.714A pdb=" N MET A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 546 through 552 removed outlier: 3.842A pdb=" N LEU A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.994A pdb=" N TYR A 572 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.844A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 644 through 660 Processing helix chain 'A' and resid 674 through 688 Processing helix chain 'A' and resid 689 through 694 removed outlier: 3.676A pdb=" N ARG A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 709 removed outlier: 3.784A pdb=" N GLU A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'B' and resid 133 through 145 removed outlier: 3.557A pdb=" N LEU B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 181 removed outlier: 3.680A pdb=" N LEU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 188 through 234 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.592A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 266 through 289 Processing helix chain 'B' and resid 289 through 338 removed outlier: 4.046A pdb=" N LEU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.586A pdb=" N GLY B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 402 removed outlier: 3.604A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 449 removed outlier: 3.749A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 517 removed outlier: 4.013A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.663A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 590 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'B' and resid 633 through 636 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 648 through 653 removed outlier: 4.765A pdb=" N ASP B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 668 removed outlier: 3.820A pdb=" N THR B 665 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 524 removed outlier: 5.880A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 533 through 535 removed outlier: 6.741A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 712 through 716 removed outlier: 6.686A pdb=" N ILE A 712 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY A 723 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.895A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 546 through 548 removed outlier: 6.478A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1701 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: 2.33 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2615 1.34 - 1.46: 879 1.46 - 1.57: 4299 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 7846 Sorted by residual: bond pdb=" C VAL B 547 " pdb=" O VAL B 547 " ideal model delta sigma weight residual 1.236 1.222 0.014 1.02e-02 9.61e+03 1.83e+00 bond pdb=" CA VAL B 547 " pdb=" CB VAL B 547 " ideal model delta sigma weight residual 1.544 1.526 0.017 1.32e-02 5.74e+03 1.66e+00 bond pdb=" C PHE B 195 " pdb=" O PHE B 195 " ideal model delta sigma weight residual 1.236 1.222 0.015 1.15e-02 7.56e+03 1.63e+00 bond pdb=" CA VAL B 467 " pdb=" CB VAL B 467 " ideal model delta sigma weight residual 1.533 1.547 -0.015 1.14e-02 7.69e+03 1.63e+00 bond pdb=" C LEU A 241 " pdb=" N GLU A 242 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.27e-02 6.20e+03 1.62e+00 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.78: 160 105.78 - 112.84: 4294 112.84 - 119.89: 2529 119.89 - 126.95: 3637 126.95 - 134.01: 69 Bond angle restraints: 10689 Sorted by residual: angle pdb=" N VAL B 485 " pdb=" CA VAL B 485 " pdb=" C VAL B 485 " ideal model delta sigma weight residual 113.47 109.64 3.83 1.01e+00 9.80e-01 1.44e+01 angle pdb=" C PHE B 194 " pdb=" N PHE B 195 " pdb=" CA PHE B 195 " ideal model delta sigma weight residual 120.65 116.07 4.58 1.32e+00 5.74e-01 1.21e+01 angle pdb=" CA GLN A 451 " pdb=" CB GLN A 451 " pdb=" CG GLN A 451 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.34e+00 angle pdb=" N VAL B 419 " pdb=" CA VAL B 419 " pdb=" C VAL B 419 " ideal model delta sigma weight residual 110.62 113.22 -2.60 1.02e+00 9.61e-01 6.52e+00 angle pdb=" N GLU A 242 " pdb=" CA GLU A 242 " pdb=" C GLU A 242 " ideal model delta sigma weight residual 111.07 108.48 2.59 1.07e+00 8.73e-01 5.84e+00 ... (remaining 10684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4153 17.89 - 35.77: 410 35.77 - 53.66: 99 53.66 - 71.54: 12 71.54 - 89.43: 9 Dihedral angle restraints: 4683 sinusoidal: 1562 harmonic: 3121 Sorted by residual: dihedral pdb=" CA PHE A 339 " pdb=" C PHE A 339 " pdb=" N LEU A 340 " pdb=" CA LEU A 340 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP B 237 " pdb=" CB ASP B 237 " pdb=" CG ASP B 237 " pdb=" OD1 ASP B 237 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU B 351 " pdb=" CG GLU B 351 " pdb=" CD GLU B 351 " pdb=" OE1 GLU B 351 " ideal model delta sinusoidal sigma weight residual 0.00 -87.56 87.56 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 4680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 755 0.027 - 0.054: 346 0.054 - 0.080: 108 0.080 - 0.107: 54 0.107 - 0.134: 15 Chirality restraints: 1278 Sorted by residual: chirality pdb=" CB THR A 294 " pdb=" CA THR A 294 " pdb=" OG1 THR A 294 " pdb=" CG2 THR A 294 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA MET A 374 " pdb=" N MET A 374 " pdb=" C MET A 374 " pdb=" CB MET A 374 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE A 699 " pdb=" N ILE A 699 " pdb=" C ILE A 699 " pdb=" CB ILE A 699 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 1275 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 567 " 0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 568 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 467 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C VAL B 467 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL B 467 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 468 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 672 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C ILE B 672 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE B 672 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU B 673 " -0.007 2.00e-02 2.50e+03 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1739 2.78 - 3.31: 7829 3.31 - 3.84: 12702 3.84 - 4.37: 12818 4.37 - 4.90: 23874 Nonbonded interactions: 58962 Sorted by model distance: nonbonded pdb=" O LEU A 338 " pdb=" OG SER A 418 " model vdw 2.254 2.440 nonbonded pdb=" OE1 GLU B 307 " pdb=" OH TYR B 376 " model vdw 2.259 2.440 nonbonded pdb=" O GLU B 593 " pdb=" OG1 THR B 598 " model vdw 2.288 2.440 nonbonded pdb=" OD1 ASN B 250 " pdb=" OG SER B 254 " model vdw 2.318 2.440 nonbonded pdb=" NH1 ARG B 327 " pdb=" OE1 GLN B 361 " model vdw 2.363 2.520 ... (remaining 58957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.51 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: 3.430 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.260 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 0.026 7846 Z= 0.222 Angle : 0.534 7.314 10689 Z= 0.294 Chirality : 0.038 0.134 1278 Planarity : 0.003 0.063 1397 Dihedral : 15.823 89.430 2673 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.14 % Allowed : 19.35 % Favored : 80.51 % 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: 2.80 (0.26), residues: 1079 helix: 2.78 (0.19), residues: 708 sheet: -0.55 (0.73), residues: 59 loop : 0.18 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.012 0.001 HIS B 670 PHE 0.009 0.001 PHE B 201 TYR 0.010 0.001 TYR B 422 ARG 0.002 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.808 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2131 time to fit residues: 28.1202 Evaluate side-chains 97 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7846 Z= 0.187 Angle : 0.467 5.980 10689 Z= 0.242 Chirality : 0.037 0.124 1278 Planarity : 0.003 0.055 1397 Dihedral : 3.864 51.350 1157 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.54 % Allowed : 18.64 % Favored : 78.81 % 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: 2.90 (0.27), residues: 1079 helix: 2.79 (0.19), residues: 726 sheet: -0.46 (0.73), residues: 58 loop : 0.20 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.010 0.001 HIS B 670 PHE 0.017 0.001 PHE B 588 TYR 0.009 0.001 TYR B 422 ARG 0.002 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.946 Fit side-chains REVERT: A 404 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8037 (tp30) outliers start: 18 outliers final: 13 residues processed: 116 average time/residue: 0.2173 time to fit residues: 34.3228 Evaluate side-chains 108 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.0170 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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: 0.7874 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7846 Z= 0.177 Angle : 0.452 5.975 10689 Z= 0.232 Chirality : 0.036 0.125 1278 Planarity : 0.003 0.050 1397 Dihedral : 3.702 50.919 1157 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.82 % Allowed : 20.76 % Favored : 76.41 % 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: 2.96 (0.27), residues: 1079 helix: 2.89 (0.19), residues: 725 sheet: -0.46 (0.73), residues: 58 loop : 0.09 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.009 0.001 HIS B 670 PHE 0.009 0.001 PHE B 201 TYR 0.008 0.001 TYR B 422 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.884 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 116 average time/residue: 0.2084 time to fit residues: 32.9093 Evaluate side-chains 110 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7895 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7846 Z= 0.207 Angle : 0.480 8.975 10689 Z= 0.242 Chirality : 0.037 0.128 1278 Planarity : 0.003 0.046 1397 Dihedral : 3.624 51.093 1157 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.81 % Allowed : 20.76 % Favored : 75.42 % 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: 2.93 (0.27), residues: 1079 helix: 2.87 (0.19), residues: 725 sheet: -0.50 (0.73), residues: 58 loop : 0.06 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.010 0.001 HIS B 670 PHE 0.009 0.001 PHE B 201 TYR 0.010 0.001 TYR B 172 ARG 0.002 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.893 Fit side-chains REVERT: A 404 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8026 (tp30) REVERT: B 168 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8336 (mp) outliers start: 27 outliers final: 20 residues processed: 117 average time/residue: 0.2128 time to fit residues: 33.8673 Evaluate side-chains 115 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 88 optimal weight: 0.0370 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.0060 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7846 Z= 0.182 Angle : 0.464 7.584 10689 Z= 0.234 Chirality : 0.036 0.124 1278 Planarity : 0.003 0.044 1397 Dihedral : 3.529 51.425 1157 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.39 % Allowed : 21.89 % Favored : 74.72 % 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: 3.02 (0.27), residues: 1079 helix: 2.96 (0.19), residues: 725 sheet: -0.56 (0.73), residues: 58 loop : 0.06 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.009 0.001 HIS B 670 PHE 0.009 0.001 PHE B 201 TYR 0.009 0.001 TYR B 172 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.792 Fit side-chains REVERT: A 404 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8008 (tp30) REVERT: B 269 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8636 (t0) REVERT: B 404 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8138 (mp) outliers start: 24 outliers final: 18 residues processed: 118 average time/residue: 0.2062 time to fit residues: 32.8915 Evaluate side-chains 111 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7890 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7846 Z= 0.196 Angle : 0.475 7.158 10689 Z= 0.239 Chirality : 0.037 0.179 1278 Planarity : 0.003 0.043 1397 Dihedral : 3.512 51.588 1157 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.81 % Allowed : 22.74 % Favored : 73.45 % 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: 2.99 (0.27), residues: 1079 helix: 2.94 (0.19), residues: 725 sheet: -0.59 (0.73), residues: 58 loop : 0.04 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.008 0.001 HIS B 670 PHE 0.009 0.001 PHE B 201 TYR 0.021 0.001 TYR B 541 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.913 Fit side-chains REVERT: B 168 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8361 (mp) REVERT: B 269 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8647 (t0) REVERT: B 404 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8148 (mp) outliers start: 27 outliers final: 22 residues processed: 117 average time/residue: 0.1997 time to fit residues: 31.7757 Evaluate side-chains 116 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7846 Z= 0.170 Angle : 0.464 6.951 10689 Z= 0.234 Chirality : 0.036 0.131 1278 Planarity : 0.003 0.042 1397 Dihedral : 3.442 51.638 1157 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.53 % Allowed : 23.59 % Favored : 72.88 % 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: 3.07 (0.27), residues: 1079 helix: 3.00 (0.19), residues: 726 sheet: -0.58 (0.73), residues: 58 loop : 0.08 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.008 0.001 HIS B 670 PHE 0.009 0.001 PHE B 201 TYR 0.010 0.001 TYR B 428 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.866 Fit side-chains REVERT: A 404 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8026 (tp30) REVERT: B 269 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8582 (t0) REVERT: B 623 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7617 (mtm-85) outliers start: 25 outliers final: 21 residues processed: 117 average time/residue: 0.2160 time to fit residues: 34.0639 Evaluate side-chains 116 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7901 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7846 Z= 0.213 Angle : 0.488 7.159 10689 Z= 0.246 Chirality : 0.037 0.130 1278 Planarity : 0.003 0.042 1397 Dihedral : 3.511 51.802 1157 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.67 % Allowed : 23.73 % Favored : 72.60 % 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: 2.98 (0.27), residues: 1079 helix: 2.92 (0.19), residues: 726 sheet: -0.61 (0.73), residues: 58 loop : 0.08 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.003 0.001 HIS B 171 PHE 0.009 0.001 PHE B 201 TYR 0.010 0.001 TYR B 172 ARG 0.002 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.964 Fit side-chains REVERT: A 404 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8030 (tp30) REVERT: B 168 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8367 (mp) REVERT: B 269 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8616 (t0) REVERT: B 404 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8157 (mp) outliers start: 26 outliers final: 21 residues processed: 115 average time/residue: 0.2111 time to fit residues: 33.2188 Evaluate side-chains 116 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 98 optimal weight: 0.0980 chunk 57 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 30.0000 chunk 86 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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: 0.7834 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7846 Z= 0.137 Angle : 0.455 7.635 10689 Z= 0.228 Chirality : 0.036 0.131 1278 Planarity : 0.003 0.042 1397 Dihedral : 3.376 51.712 1157 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.98 % Allowed : 25.28 % Favored : 72.74 % 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: 3.24 (0.27), residues: 1079 helix: 3.12 (0.19), residues: 725 sheet: -0.57 (0.72), residues: 58 loop : 0.20 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.000 HIS A 257 PHE 0.010 0.001 PHE B 201 TYR 0.025 0.001 TYR B 541 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.862 Fit side-chains REVERT: A 404 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8064 (tp30) REVERT: B 269 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8523 (t0) REVERT: B 623 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7613 (mtm-85) outliers start: 14 outliers final: 8 residues processed: 113 average time/residue: 0.2211 time to fit residues: 33.1998 Evaluate side-chains 109 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7846 Z= 0.242 Angle : 0.504 7.437 10689 Z= 0.253 Chirality : 0.037 0.133 1278 Planarity : 0.003 0.042 1397 Dihedral : 3.474 51.537 1157 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.84 % Allowed : 25.14 % Favored : 73.02 % 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: 3.03 (0.27), residues: 1079 helix: 2.95 (0.19), residues: 727 sheet: -0.63 (0.73), residues: 58 loop : 0.11 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 413 HIS 0.003 0.001 HIS B 171 PHE 0.009 0.001 PHE A 339 TYR 0.011 0.001 TYR B 172 ARG 0.002 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.885 Fit side-chains REVERT: A 404 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8062 (tp30) REVERT: B 168 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 269 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8617 (t0) REVERT: B 404 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8170 (mp) outliers start: 13 outliers final: 10 residues processed: 104 average time/residue: 0.2339 time to fit residues: 32.7751 Evaluate side-chains 106 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain C residue 1 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.165898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122348 restraints weight = 10458.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125590 restraints weight = 6164.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127706 restraints weight = 4494.705| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7846 Z= 0.212 Angle : 0.494 7.338 10689 Z= 0.249 Chirality : 0.037 0.135 1278 Planarity : 0.003 0.042 1397 Dihedral : 3.478 51.790 1157 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.12 % Allowed : 25.14 % Favored : 72.74 % 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: 3.01 (0.27), residues: 1079 helix: 2.94 (0.19), residues: 729 sheet: -0.67 (0.72), residues: 58 loop : 0.09 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.003 0.001 HIS B 171 PHE 0.009 0.001 PHE B 201 TYR 0.014 0.001 TYR B 428 ARG 0.001 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.08 seconds wall clock time: 33 minutes 34.92 seconds (2014.92 seconds total)