Starting phenix.real_space_refine on Sun Nov 17 03:31:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/11_2024/8ioa_35613.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/11_2024/8ioa_35613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/11_2024/8ioa_35613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/11_2024/8ioa_35613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/11_2024/8ioa_35613.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/11_2024/8ioa_35613.cif" } resolution = 2.63 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= 0.004 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 7972 2.51 5 N 2252 2.21 5 O 2308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12570 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "B" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.03, per 1000 atoms: 1.12 Number of scatterers: 12570 At special positions: 0 Unit cell: (98.4, 107.42, 99.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 4 15.00 Mg 2 11.99 O 2308 8.00 N 2252 7.00 C 7972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 3.4 seconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2932 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 10 sheets defined 51.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 63 through 82 removed outlier: 3.566A pdb=" N HIS A 73 " --> pdb=" O PHE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 106 removed outlier: 3.589A pdb=" N LEU A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 118 through 129 removed outlier: 4.018A pdb=" N PHE A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.599A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 247 through 275 removed outlier: 4.230A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 337 through 342 removed outlier: 5.990A pdb=" N GLU A 340 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.939A pdb=" N ILE A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.741A pdb=" N ARG A 363 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N SER A 365 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 367 " --> pdb=" O MET A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 401 through 416 removed outlier: 4.236A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 449 through 455 removed outlier: 4.007A pdb=" N GLU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.614A pdb=" N LEU A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 499 through 516 Processing helix chain 'A' and resid 547 through 556 removed outlier: 3.957A pdb=" N ASP A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 636 through 653 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 680 through 688 Processing helix chain 'A' and resid 702 through 709 removed outlier: 4.083A pdb=" N HIS A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 716 removed outlier: 3.545A pdb=" N HIS A 715 " --> pdb=" O ARG A 712 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 716 " --> pdb=" O HIS A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 712 through 716' Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 755 through 758 removed outlier: 3.739A pdb=" N ARG A 758 " --> pdb=" O PRO A 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 758' Processing helix chain 'A' and resid 761 through 783 Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'B' and resid 14 through 38 Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.509A pdb=" N ILE B 53 " --> pdb=" O PRO B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 82 removed outlier: 3.600A pdb=" N HIS B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 106 removed outlier: 3.561A pdb=" N LEU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 118 through 129 removed outlier: 4.006A pdb=" N PHE B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.633A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 removed outlier: 3.570A pdb=" N LEU B 196 " --> pdb=" O ASN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 247 through 275 removed outlier: 4.231A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 337 through 342 removed outlier: 5.988A pdb=" N GLU B 340 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.721A pdb=" N ARG B 363 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 401 through 416 removed outlier: 4.297A pdb=" N LEU B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.528A pdb=" N VAL B 439 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 3.978A pdb=" N GLU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 454 " --> pdb=" O PRO B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 499 through 516 Processing helix chain 'B' and resid 547 through 556 removed outlier: 3.973A pdb=" N ASP B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 636 through 653 Processing helix chain 'B' and resid 665 through 669 Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 702 through 709 removed outlier: 4.069A pdb=" N HIS B 706 " --> pdb=" O PRO B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 removed outlier: 3.542A pdb=" N HIS B 715 " --> pdb=" O ARG B 712 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN B 716 " --> pdb=" O HIS B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 712 through 716' Processing helix chain 'B' and resid 731 through 739 Processing helix chain 'B' and resid 742 through 754 Processing helix chain 'B' and resid 755 through 758 removed outlier: 3.509A pdb=" N ARG B 758 " --> pdb=" O PRO B 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 758' Processing helix chain 'B' and resid 761 through 783 Processing helix chain 'B' and resid 786 through 791 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 177 removed outlier: 6.492A pdb=" N VAL A 172 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 207 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N CYS A 174 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N HIS A 209 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 176 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 465 removed outlier: 8.381A pdb=" N MET A 465 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 422 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY A 487 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LEU A 529 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 489 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER A 531 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 491 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 443 removed outlier: 5.472A pdb=" N LYS A 442 " --> pdb=" O SER A 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.514A pdb=" N VAL A 630 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN A 697 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A 632 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 171 through 177 removed outlier: 6.498A pdb=" N VAL B 172 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE B 207 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N CYS B 174 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS B 209 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE B 176 " --> pdb=" O HIS B 209 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 397 through 400 removed outlier: 4.708A pdb=" N SER B 397 " --> pdb=" O GLN B 598 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 464 through 465 removed outlier: 8.414A pdb=" N MET B 465 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 422 " --> pdb=" O MET B 465 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY B 487 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LEU B 529 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE B 489 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER B 531 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B 491 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443 removed outlier: 5.545A pdb=" N LYS B 442 " --> pdb=" O SER B 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 613 through 615 removed outlier: 6.551A pdb=" N VAL B 629 " --> pdb=" O ARG B 659 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL B 661 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 631 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL B 663 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER B 633 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 630 " --> pdb=" O ILE B 695 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASN B 697 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 632 " --> pdb=" O ASN B 697 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1516 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: 4.83 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2091 1.30 - 1.43: 3541 1.43 - 1.55: 7246 1.55 - 1.68: 8 1.68 - 1.81: 46 Bond restraints: 12932 Sorted by residual: bond pdb=" C ASN A 697 " pdb=" O ASN A 697 " ideal model delta sigma weight residual 1.235 1.172 0.064 1.22e-02 6.72e+03 2.72e+01 bond pdb=" O1A TPP A 802 " pdb=" PA TPP A 802 " ideal model delta sigma weight residual 1.479 1.524 -0.045 1.00e-02 1.00e+04 2.01e+01 bond pdb=" O1A TPP B 801 " pdb=" PA TPP B 801 " ideal model delta sigma weight residual 1.479 1.523 -0.044 1.00e-02 1.00e+04 1.90e+01 bond pdb=" CA ASN A 697 " pdb=" CB ASN A 697 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.43e-02 4.89e+03 7.76e+00 bond pdb=" CG ASN A 697 " pdb=" OD1 ASN A 697 " ideal model delta sigma weight residual 1.231 1.181 0.050 1.90e-02 2.77e+03 6.93e+00 ... (remaining 12927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 17291 1.42 - 2.85: 250 2.85 - 4.27: 89 4.27 - 5.70: 18 5.70 - 7.12: 8 Bond angle restraints: 17656 Sorted by residual: angle pdb=" N ASN B 621 " pdb=" CA ASN B 621 " pdb=" C ASN B 621 " ideal model delta sigma weight residual 111.14 116.88 -5.74 1.08e+00 8.57e-01 2.83e+01 angle pdb=" O3A TPP A 802 " pdb=" PB TPP A 802 " pdb=" O3B TPP A 802 " ideal model delta sigma weight residual 104.26 111.21 -6.95 1.33e+00 5.64e-01 2.72e+01 angle pdb=" O2B TPP B 801 " pdb=" PB TPP B 801 " pdb=" O3A TPP B 801 " ideal model delta sigma weight residual 104.26 111.04 -6.78 1.33e+00 5.64e-01 2.59e+01 angle pdb=" N LEU B 666 " pdb=" CA LEU B 666 " pdb=" C LEU B 666 " ideal model delta sigma weight residual 111.28 116.13 -4.85 1.09e+00 8.42e-01 1.98e+01 angle pdb=" N ARG B 39 " pdb=" CA ARG B 39 " pdb=" C ARG B 39 " ideal model delta sigma weight residual 114.56 108.93 5.63 1.27e+00 6.20e-01 1.96e+01 ... (remaining 17651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7167 17.89 - 35.79: 365 35.79 - 53.68: 55 53.68 - 71.58: 10 71.58 - 89.47: 1 Dihedral angle restraints: 7598 sinusoidal: 3040 harmonic: 4558 Sorted by residual: dihedral pdb=" CA TRP B 295 " pdb=" C TRP B 295 " pdb=" N THR B 296 " pdb=" CA THR B 296 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.52e+00 dihedral pdb=" CA GLU B 466 " pdb=" CB GLU B 466 " pdb=" CG GLU B 466 " pdb=" CD GLU B 466 " ideal model delta sinusoidal sigma weight residual -180.00 -120.11 -59.89 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU B 733 " pdb=" CB LEU B 733 " pdb=" CG LEU B 733 " pdb=" CD1 LEU B 733 " ideal model delta sinusoidal sigma weight residual 180.00 121.03 58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 7595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1356 0.041 - 0.082: 367 0.082 - 0.123: 154 0.123 - 0.164: 9 0.164 - 0.204: 2 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA LYS A 214 " pdb=" N LYS A 214 " pdb=" C LYS A 214 " pdb=" CB LYS A 214 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASN B 621 " pdb=" N ASN B 621 " pdb=" C ASN B 621 " pdb=" CB ASN B 621 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA LEU B 666 " pdb=" N LEU B 666 " pdb=" C LEU B 666 " pdb=" CB LEU B 666 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1885 not shown) Planarity restraints: 2324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 453 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C GLU A 453 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU A 453 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 454 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 696 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C PHE A 696 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE A 696 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 697 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 213 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C TYR A 213 " -0.037 2.00e-02 2.50e+03 pdb=" O TYR A 213 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 214 " 0.012 2.00e-02 2.50e+03 ... (remaining 2321 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 63 2.47 - 3.08: 9046 3.08 - 3.69: 19389 3.69 - 4.29: 30610 4.29 - 4.90: 51276 Nonbonded interactions: 110384 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O3B TPP A 802 " model vdw 1.866 2.170 nonbonded pdb=" O1A TPP B 801 " pdb="MG MG B 802 " model vdw 2.068 2.170 nonbonded pdb=" O1B TPP B 801 " pdb="MG MG B 802 " model vdw 2.097 2.170 nonbonded pdb=" OD1 ASN A 211 " pdb="MG MG A 801 " model vdw 2.102 2.170 nonbonded pdb=" OD1 ASP A 178 " pdb="MG MG A 801 " model vdw 2.123 2.170 ... (remaining 110379 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 702 or resid 704 through 718 or resid 720 throug \ h 796)) selection = (chain 'B' and (resid 9 through 702 or resid 704 through 718 or resid 720 throug \ h 796)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.670 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: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 39.700 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 : 0.005 0.064 12932 Z= 0.330 Angle : 0.517 7.119 17656 Z= 0.278 Chirality : 0.044 0.204 1888 Planarity : 0.004 0.038 2324 Dihedral : 10.790 89.473 4666 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.53 % Allowed : 4.06 % Favored : 95.41 % 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: 0.69 (0.22), residues: 1576 helix: 1.53 (0.20), residues: 674 sheet: 0.31 (0.41), residues: 188 loop : -0.51 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 295 HIS 0.003 0.001 HIS A 756 PHE 0.010 0.001 PHE B 233 TYR 0.008 0.001 TYR B 480 ARG 0.002 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.442 Fit side-chains REVERT: A 474 GLU cc_start: 0.8793 (tp30) cc_final: 0.8538 (tp30) REVERT: A 681 ASP cc_start: 0.8040 (m-30) cc_final: 0.7823 (m-30) REVERT: A 734 GLU cc_start: 0.7949 (tt0) cc_final: 0.7593 (tt0) REVERT: B 474 GLU cc_start: 0.8763 (tp30) cc_final: 0.8321 (tp30) REVERT: B 478 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 500 ASP cc_start: 0.8420 (t0) cc_final: 0.8191 (t0) REVERT: B 681 ASP cc_start: 0.7970 (m-30) cc_final: 0.7739 (m-30) outliers start: 7 outliers final: 2 residues processed: 104 average time/residue: 1.5508 time to fit residues: 174.7358 Evaluate side-chains 62 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 613 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 217 ASN A 544 HIS A 677 HIS A 719 HIS B B 128 GLN B 313 HIS B 537 GLN B 544 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 0.034 12932 Z= 0.192 Angle : 0.545 6.811 17656 Z= 0.280 Chirality : 0.044 0.137 1888 Planarity : 0.005 0.044 2324 Dihedral : 5.592 82.567 1750 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.20 % Allowed : 6.69 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.22), residues: 1576 helix: 1.67 (0.20), residues: 700 sheet: 0.18 (0.41), residues: 172 loop : -0.30 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 295 HIS 0.003 0.001 HIS B 326 PHE 0.011 0.001 PHE B 495 TYR 0.013 0.001 TYR A 108 ARG 0.007 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.444 Fit side-chains REVERT: A 674 GLU cc_start: 0.8113 (mp0) cc_final: 0.7901 (mp0) REVERT: A 681 ASP cc_start: 0.7942 (m-30) cc_final: 0.7737 (m-30) REVERT: A 721 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7588 (mmp-170) REVERT: A 749 ASP cc_start: 0.7662 (m-30) cc_final: 0.7453 (m-30) REVERT: B 474 GLU cc_start: 0.8541 (tp30) cc_final: 0.7969 (tp30) REVERT: B 681 ASP cc_start: 0.7935 (m-30) cc_final: 0.7727 (m-30) REVERT: B 721 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7992 (mmp-170) REVERT: B 734 GLU cc_start: 0.7953 (tt0) cc_final: 0.7666 (tt0) REVERT: B 749 ASP cc_start: 0.7760 (m-30) cc_final: 0.7508 (m-30) outliers start: 16 outliers final: 3 residues processed: 89 average time/residue: 1.3491 time to fit residues: 132.1623 Evaluate side-chains 68 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 721 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 HIS B 677 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12932 Z= 0.380 Angle : 0.567 6.612 17656 Z= 0.289 Chirality : 0.046 0.140 1888 Planarity : 0.005 0.039 2324 Dihedral : 5.605 86.647 1746 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.28 % Allowed : 7.07 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.22), residues: 1576 helix: 1.75 (0.20), residues: 688 sheet: 0.01 (0.40), residues: 174 loop : -0.30 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 295 HIS 0.010 0.001 HIS B 313 PHE 0.018 0.002 PHE A 495 TYR 0.011 0.001 TYR B 492 ARG 0.011 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 1.473 Fit side-chains REVERT: A 474 GLU cc_start: 0.8683 (tp30) cc_final: 0.8285 (tp30) REVERT: A 536 ARG cc_start: 0.8950 (tpp-160) cc_final: 0.8694 (mmt180) REVERT: A 681 ASP cc_start: 0.7982 (m-30) cc_final: 0.7776 (m-30) REVERT: A 721 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7541 (mmp-170) REVERT: A 734 GLU cc_start: 0.8108 (tt0) cc_final: 0.7809 (tt0) REVERT: A 749 ASP cc_start: 0.7683 (m-30) cc_final: 0.7328 (m-30) REVERT: B 674 GLU cc_start: 0.8061 (mp0) cc_final: 0.7827 (mp0) REVERT: B 681 ASP cc_start: 0.7958 (m-30) cc_final: 0.7743 (m-30) REVERT: B 721 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8025 (mmp-170) REVERT: B 734 GLU cc_start: 0.8052 (tt0) cc_final: 0.7744 (tt0) REVERT: B 738 ARG cc_start: 0.8341 (mmp80) cc_final: 0.8060 (ttm-80) REVERT: B 749 ASP cc_start: 0.7754 (m-30) cc_final: 0.7484 (m-30) outliers start: 17 outliers final: 6 residues processed: 85 average time/residue: 1.1817 time to fit residues: 111.8505 Evaluate side-chains 69 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 677 HIS B 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12932 Z= 0.171 Angle : 0.499 5.327 17656 Z= 0.254 Chirality : 0.042 0.144 1888 Planarity : 0.004 0.044 2324 Dihedral : 5.451 89.261 1746 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.50 % Allowed : 7.07 % Favored : 91.43 % 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: 1.02 (0.22), residues: 1576 helix: 1.87 (0.20), residues: 688 sheet: -0.08 (0.40), residues: 174 loop : -0.26 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 295 HIS 0.008 0.001 HIS B 313 PHE 0.011 0.001 PHE B 495 TYR 0.010 0.001 TYR B 480 ARG 0.010 0.000 ARG A 738 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 1.611 Fit side-chains REVERT: A 537 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: A 585 TYR cc_start: 0.8885 (m-80) cc_final: 0.8680 (m-80) REVERT: A 674 GLU cc_start: 0.8080 (mp0) cc_final: 0.7825 (mp0) REVERT: A 721 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7456 (mmp-170) REVERT: A 734 GLU cc_start: 0.8038 (tt0) cc_final: 0.7770 (tt0) REVERT: A 749 ASP cc_start: 0.7620 (m-30) cc_final: 0.7282 (m-30) REVERT: B 277 GLU cc_start: 0.8014 (pp20) cc_final: 0.7799 (pp20) REVERT: B 721 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7999 (mmp-170) REVERT: B 734 GLU cc_start: 0.8073 (tt0) cc_final: 0.7816 (tt0) REVERT: B 738 ARG cc_start: 0.8328 (mmp80) cc_final: 0.8067 (ttm-80) REVERT: B 749 ASP cc_start: 0.7697 (m-30) cc_final: 0.7423 (m-30) outliers start: 20 outliers final: 6 residues processed: 95 average time/residue: 1.2763 time to fit residues: 134.1977 Evaluate side-chains 76 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 721 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 677 HIS B 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12932 Z= 0.247 Angle : 0.519 6.283 17656 Z= 0.264 Chirality : 0.044 0.256 1888 Planarity : 0.005 0.049 2324 Dihedral : 5.447 88.458 1746 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.65 % Allowed : 7.97 % Favored : 90.38 % 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: 1.08 (0.22), residues: 1576 helix: 1.93 (0.20), residues: 688 sheet: -0.03 (0.40), residues: 174 loop : -0.24 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 295 HIS 0.007 0.001 HIS B 313 PHE 0.012 0.001 PHE A 495 TYR 0.009 0.001 TYR B 492 ARG 0.011 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 1.496 Fit side-chains REVERT: A 516 GLU cc_start: 0.8035 (mp0) cc_final: 0.7816 (mp0) REVERT: A 537 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: A 721 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7442 (mmp-170) REVERT: A 734 GLU cc_start: 0.8029 (tt0) cc_final: 0.7744 (tt0) REVERT: A 749 ASP cc_start: 0.7652 (m-30) cc_final: 0.7320 (m-30) REVERT: B 474 GLU cc_start: 0.8637 (tp30) cc_final: 0.8342 (tp30) REVERT: B 674 GLU cc_start: 0.8146 (mp0) cc_final: 0.7878 (mp0) REVERT: B 711 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7934 (mtp85) REVERT: B 721 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8030 (mmp-170) REVERT: B 734 GLU cc_start: 0.8048 (tt0) cc_final: 0.7748 (tt0) REVERT: B 738 ARG cc_start: 0.8368 (mmp80) cc_final: 0.8116 (ttm-80) REVERT: B 749 ASP cc_start: 0.7716 (m-30) cc_final: 0.7461 (m-30) outliers start: 22 outliers final: 9 residues processed: 83 average time/residue: 1.2658 time to fit residues: 116.7414 Evaluate side-chains 78 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 677 HIS B 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12932 Z= 0.172 Angle : 0.500 6.099 17656 Z= 0.254 Chirality : 0.043 0.219 1888 Planarity : 0.004 0.053 2324 Dihedral : 5.360 86.799 1746 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.35 % Allowed : 8.27 % Favored : 90.38 % 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: 1.16 (0.22), residues: 1576 helix: 1.98 (0.20), residues: 688 sheet: 0.07 (0.40), residues: 170 loop : -0.20 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 295 HIS 0.007 0.001 HIS B 313 PHE 0.010 0.001 PHE B 495 TYR 0.009 0.001 TYR B 480 ARG 0.013 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.457 Fit side-chains REVERT: A 516 GLU cc_start: 0.8047 (mp0) cc_final: 0.7664 (mp0) REVERT: A 537 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7993 (pp30) REVERT: A 721 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7410 (mmp-170) REVERT: A 734 GLU cc_start: 0.8032 (tt0) cc_final: 0.7816 (tt0) REVERT: A 749 ASP cc_start: 0.7643 (m-30) cc_final: 0.7318 (m-30) REVERT: B 277 GLU cc_start: 0.7986 (pp20) cc_final: 0.7775 (pp20) REVERT: B 552 LEU cc_start: 0.8451 (tt) cc_final: 0.8165 (tp) REVERT: B 674 GLU cc_start: 0.8077 (mp0) cc_final: 0.7648 (mp0) REVERT: B 711 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7932 (mtp85) REVERT: B 721 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8009 (mmp-170) REVERT: B 734 GLU cc_start: 0.8020 (tt0) cc_final: 0.7755 (tt0) REVERT: B 738 ARG cc_start: 0.8356 (mmp80) cc_final: 0.8108 (ttm-80) REVERT: B 749 ASP cc_start: 0.7715 (m-30) cc_final: 0.7481 (m-30) outliers start: 18 outliers final: 8 residues processed: 89 average time/residue: 1.3653 time to fit residues: 133.3367 Evaluate side-chains 84 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 721 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 0.0670 chunk 94 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 677 HIS B 540 ASN B 677 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12932 Z= 0.149 Angle : 0.484 5.606 17656 Z= 0.245 Chirality : 0.042 0.198 1888 Planarity : 0.004 0.055 2324 Dihedral : 5.262 84.688 1746 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.50 % Allowed : 8.20 % Favored : 90.30 % 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: 1.22 (0.22), residues: 1576 helix: 2.01 (0.20), residues: 688 sheet: 0.16 (0.40), residues: 170 loop : -0.16 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 295 HIS 0.006 0.001 HIS B 313 PHE 0.009 0.001 PHE B 495 TYR 0.009 0.001 TYR B 480 ARG 0.013 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 1.271 Fit side-chains REVERT: A 516 GLU cc_start: 0.8015 (mp0) cc_final: 0.7795 (mp0) REVERT: A 537 GLN cc_start: 0.8432 (tt0) cc_final: 0.8006 (pp30) REVERT: A 721 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7373 (mmp-170) REVERT: A 749 ASP cc_start: 0.7641 (m-30) cc_final: 0.7324 (m-30) REVERT: B 552 LEU cc_start: 0.8425 (tt) cc_final: 0.8120 (tp) REVERT: B 674 GLU cc_start: 0.8053 (mp0) cc_final: 0.7627 (mp0) REVERT: B 711 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7909 (mtp85) REVERT: B 721 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7988 (mmp-170) REVERT: B 734 GLU cc_start: 0.8014 (tt0) cc_final: 0.7747 (tt0) REVERT: B 738 ARG cc_start: 0.8362 (mmp80) cc_final: 0.8129 (ttm-80) REVERT: B 749 ASP cc_start: 0.7705 (m-30) cc_final: 0.7481 (m-30) outliers start: 20 outliers final: 10 residues processed: 95 average time/residue: 1.2726 time to fit residues: 134.0014 Evaluate side-chains 81 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 0.0270 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 677 HIS B 677 HIS B 730 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12932 Z= 0.153 Angle : 0.496 5.615 17656 Z= 0.252 Chirality : 0.042 0.190 1888 Planarity : 0.004 0.059 2324 Dihedral : 5.192 82.269 1746 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.20 % Allowed : 8.57 % Favored : 90.23 % 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: 1.22 (0.22), residues: 1576 helix: 1.97 (0.20), residues: 690 sheet: 0.25 (0.40), residues: 170 loop : -0.14 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 295 HIS 0.005 0.001 HIS B 313 PHE 0.009 0.001 PHE B 495 TYR 0.009 0.001 TYR B 492 ARG 0.015 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 1.488 Fit side-chains REVERT: A 537 GLN cc_start: 0.8380 (tt0) cc_final: 0.8012 (pp30) REVERT: A 540 ASN cc_start: 0.7438 (m-40) cc_final: 0.6367 (t0) REVERT: A 721 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7308 (mmp-170) REVERT: A 749 ASP cc_start: 0.7645 (m-30) cc_final: 0.7333 (m-30) REVERT: B 516 GLU cc_start: 0.8071 (mp0) cc_final: 0.7572 (mp0) REVERT: B 552 LEU cc_start: 0.8395 (tt) cc_final: 0.8163 (tp) REVERT: B 674 GLU cc_start: 0.8062 (mp0) cc_final: 0.7620 (mp0) REVERT: B 711 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7917 (mtp85) REVERT: B 721 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8108 (mtp180) REVERT: B 734 GLU cc_start: 0.8038 (tt0) cc_final: 0.7768 (tt0) REVERT: B 738 ARG cc_start: 0.8394 (mmp80) cc_final: 0.8164 (ttm-80) outliers start: 16 outliers final: 10 residues processed: 93 average time/residue: 1.3022 time to fit residues: 133.5555 Evaluate side-chains 82 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 504 ASN Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 721 ARG Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0980 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.0070 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 139 optimal weight: 0.0170 chunk 92 optimal weight: 7.9990 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 HIS B 209 HIS B 540 ASN B 677 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12932 Z= 0.135 Angle : 0.487 6.760 17656 Z= 0.247 Chirality : 0.042 0.181 1888 Planarity : 0.004 0.061 2324 Dihedral : 5.081 79.505 1746 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.05 % Allowed : 9.32 % Favored : 89.62 % 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: 1.29 (0.22), residues: 1576 helix: 1.97 (0.20), residues: 692 sheet: 0.33 (0.40), residues: 170 loop : -0.07 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 295 HIS 0.005 0.001 HIS B 313 PHE 0.008 0.001 PHE A 125 TYR 0.009 0.001 TYR B 480 ARG 0.015 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 1.619 Fit side-chains REVERT: A 540 ASN cc_start: 0.7326 (m-40) cc_final: 0.6239 (t0) REVERT: A 721 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7283 (mmp-170) REVERT: A 749 ASP cc_start: 0.7627 (m-30) cc_final: 0.7313 (m-30) REVERT: B 516 GLU cc_start: 0.7975 (mp0) cc_final: 0.7766 (mp0) REVERT: B 540 ASN cc_start: 0.7599 (m-40) cc_final: 0.6664 (t0) REVERT: B 552 LEU cc_start: 0.8340 (tt) cc_final: 0.8119 (tp) REVERT: B 674 GLU cc_start: 0.8062 (mp0) cc_final: 0.7612 (mp0) REVERT: B 711 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7939 (mtp85) REVERT: B 721 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8117 (mtp180) REVERT: B 734 GLU cc_start: 0.8158 (tt0) cc_final: 0.7915 (tt0) REVERT: B 738 ARG cc_start: 0.8395 (mmp80) cc_final: 0.8173 (ttm-80) outliers start: 14 outliers final: 6 residues processed: 89 average time/residue: 1.1884 time to fit residues: 117.5347 Evaluate side-chains 78 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 721 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.0670 chunk 90 optimal weight: 0.0470 chunk 70 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 123 optimal weight: 0.3980 chunk 12 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 537 GLN A 677 HIS A 730 ASN B 537 GLN B 677 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12932 Z= 0.139 Angle : 0.498 7.249 17656 Z= 0.249 Chirality : 0.042 0.182 1888 Planarity : 0.005 0.064 2324 Dihedral : 5.043 76.869 1746 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.90 % Allowed : 9.40 % Favored : 89.70 % 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: 1.44 (0.22), residues: 1576 helix: 2.11 (0.20), residues: 680 sheet: 0.40 (0.41), residues: 170 loop : 0.05 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 295 HIS 0.005 0.001 HIS B 313 PHE 0.010 0.001 PHE B 688 TYR 0.010 0.001 TYR B 480 ARG 0.015 0.000 ARG A 515 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 2.133 Fit side-chains REVERT: A 540 ASN cc_start: 0.7104 (m-40) cc_final: 0.6036 (t0) REVERT: A 721 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7234 (mmp-170) REVERT: A 749 ASP cc_start: 0.7632 (m-30) cc_final: 0.7336 (m-30) REVERT: B 516 GLU cc_start: 0.7942 (mp0) cc_final: 0.7736 (mp0) REVERT: B 540 ASN cc_start: 0.7525 (m-40) cc_final: 0.6518 (t0) REVERT: B 674 GLU cc_start: 0.8052 (mp0) cc_final: 0.7556 (mp0) REVERT: B 711 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7936 (mtp85) REVERT: B 734 GLU cc_start: 0.8161 (tt0) cc_final: 0.7926 (tt0) REVERT: B 738 ARG cc_start: 0.8400 (mmp80) cc_final: 0.8173 (ttm-80) REVERT: B 791 GLN cc_start: 0.8802 (mt0) cc_final: 0.8557 (mt0) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 1.3043 time to fit residues: 123.4684 Evaluate side-chains 76 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 746 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 0.0070 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 0.0770 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN A 677 HIS B 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.071664 restraints weight = 45512.493| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.03 r_work: 0.2775 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.221 12932 Z= 0.250 Angle : 0.765 59.178 17656 Z= 0.441 Chirality : 0.057 1.653 1888 Planarity : 0.005 0.067 2324 Dihedral : 5.039 76.867 1746 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.90 % Allowed : 9.85 % Favored : 89.25 % Cbeta Deviations : 0.07 % 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: 1.44 (0.22), residues: 1576 helix: 2.10 (0.20), residues: 680 sheet: 0.40 (0.41), residues: 170 loop : 0.06 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 295 HIS 0.005 0.001 HIS B 313 PHE 0.009 0.001 PHE B 688 TYR 0.009 0.001 TYR B 480 ARG 0.014 0.000 ARG A 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3697.07 seconds wall clock time: 67 minutes 50.49 seconds (4070.49 seconds total)