Starting phenix.real_space_refine on Fri Mar 15 19:27:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/03_2024/8ioa_35613_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/03_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_35613/03_2024/8ioa_35613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/03_2024/8ioa_35613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/03_2024/8ioa_35613_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioa_35613/03_2024/8ioa_35613_updated.pdb" } 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 Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.02, per 1000 atoms: 1.04 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 - 3.50 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: 4.99 Conformation dependent library (CDL) restraints added in 4.7 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... running ksdssp... Secondary structure from input PDB file: 75 helices and 7 sheets defined 43.3% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 15 through 37 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.566A pdb=" N HIS A 73 " --> pdb=" O PHE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.561A pdb=" N GLU A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 182' Processing helix chain 'A' and resid 184 through 194 removed outlier: 3.599A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N HIS A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYS A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.230A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 324 through 337 removed outlier: 4.115A pdb=" N TYR A 337 " --> pdb=" O TRP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 351 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 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 401 through 415 removed outlier: 4.236A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.795A pdb=" N ASP A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 454' Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 500 through 515 Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.571A pdb=" N VAL A 553 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 579 Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 637 through 652 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 681 through 687 Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.551A pdb=" N ILE A 705 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 removed outlier: 4.518A pdb=" N ASN A 716 " --> pdb=" O HIS A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 743 through 753 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 762 through 782 Processing helix chain 'A' and resid 787 through 790 No H-bonds generated for 'chain 'A' and resid 787 through 790' Processing helix chain 'B' and resid 15 through 37 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.600A pdb=" N HIS B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.633A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N HIS B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LYS B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE B 195 " --> pdb=" O HIS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 235 Processing helix chain 'B' and resid 248 through 274 removed outlier: 4.231A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 324 through 337 removed outlier: 4.151A pdb=" N TYR B 337 " --> pdb=" O TRP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.969A pdb=" N ILE B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 401 through 415 removed outlier: 4.297A pdb=" N LEU B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.867A pdb=" N ASP B 454 " --> pdb=" O PRO B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'B' and resid 493 through 495 No H-bonds generated for 'chain 'B' and resid 493 through 495' Processing helix chain 'B' and resid 500 through 515 Processing helix chain 'B' and resid 547 through 555 removed outlier: 3.556A pdb=" N VAL B 553 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 555 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 579 Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 637 through 652 Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 702 through 708 removed outlier: 3.577A pdb=" N ILE B 705 " --> pdb=" O PRO B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 4.442A pdb=" N ASN B 716 " --> pdb=" O HIS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 743 through 753 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 762 through 782 Processing helix chain 'B' and resid 787 through 790 No H-bonds generated for 'chain 'B' and resid 787 through 790' Processing sheet with id= A, first strand: chain 'A' and resid 171 through 177 removed outlier: 6.691A pdb=" N ALA A 203 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N CYS A 174 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 205 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE A 176 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 207 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N LEU A 208 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 287 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 420 through 424 removed outlier: 6.892A pdb=" N HIS A 486 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N PHE A 423 " --> pdb=" O HIS A 486 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 488 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN A 527 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.554A pdb=" N VAL A 629 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL A 661 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 631 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL A 663 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 633 " --> pdb=" O VAL A 663 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 171 through 177 removed outlier: 6.724A pdb=" N ALA B 203 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS B 174 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 205 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE B 176 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 207 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N LEU B 208 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 287 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id= E, 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= F, first strand: chain 'B' and resid 464 through 466 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: 6.896A pdb=" N HIS B 486 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE B 423 " --> pdb=" O HIS B 486 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE B 488 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN B 527 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing sheet with id= G, 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) 434 hydrogen bonds defined for protein. 1231 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: 4.12 Time building geometry restraints manager: 5.36 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: 91.21 - 100.93: 14 100.93 - 110.66: 4551 110.66 - 120.38: 7902 120.38 - 130.10: 5028 130.10 - 139.82: 161 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 - 13.77: 6935 13.77 - 27.53: 499 27.53 - 41.30: 122 41.30 - 55.06: 25 55.06 - 68.83: 9 Dihedral angle restraints: 7590 sinusoidal: 3032 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 7587 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: 9094 3.08 - 3.69: 19471 3.69 - 4.29: 30871 4.29 - 4.90: 51337 Nonbonded interactions: 110836 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 110831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '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: 4.110 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: 12.300 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 47.680 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 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:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.030 ------------------------------------------------------------------------------- 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= 0.336 Angle : 0.517 7.119 17656 Z= 0.278 Chirality : 0.044 0.204 1888 Planarity : 0.004 0.038 2324 Dihedral : 10.643 68.825 4658 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 fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.487 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: 1.4637 time to fit residues: 164.9458 Evaluate side-chains 62 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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: 6.9990 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 677 HIS A 719 HIS B B 313 HIS B 537 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12932 Z= 0.178 Angle : 0.500 7.417 17656 Z= 0.252 Chirality : 0.042 0.135 1888 Planarity : 0.004 0.041 2324 Dihedral : 4.626 45.059 1742 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.20 % Allowed : 7.14 % 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: 1.71 (0.20), residues: 690 sheet: 0.25 (0.41), residues: 184 loop : -0.33 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 295 HIS 0.003 0.001 HIS B 326 PHE 0.011 0.001 PHE B 495 TYR 0.009 0.001 TYR B 480 ARG 0.008 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 89 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 1.483 Fit side-chains REVERT: A 681 ASP cc_start: 0.7940 (m-30) cc_final: 0.7733 (m-30) REVERT: B 681 ASP cc_start: 0.7923 (m-30) cc_final: 0.7659 (m-30) REVERT: B 721 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7962 (mmp-170) REVERT: B 734 GLU cc_start: 0.7987 (tt0) cc_final: 0.7704 (tt0) REVERT: B 749 ASP cc_start: 0.7733 (m-30) cc_final: 0.7450 (m-30) outliers start: 16 outliers final: 3 residues processed: 85 average time/residue: 1.1722 time to fit residues: 110.9247 Evaluate side-chains 64 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 500 ASP 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: 10.0000 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 0.0370 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12932 Z= 0.259 Angle : 0.493 6.195 17656 Z= 0.246 Chirality : 0.043 0.137 1888 Planarity : 0.004 0.042 2324 Dihedral : 4.500 41.128 1738 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.88 % Allowed : 6.99 % Favored : 91.13 % 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: 1.00 (0.22), residues: 1576 helix: 1.79 (0.20), residues: 692 sheet: 0.20 (0.41), residues: 184 loop : -0.31 (0.24), residues: 700 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 0.013 0.001 PHE B 495 TYR 0.008 0.001 TYR B 480 ARG 0.012 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 91 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 1.450 Fit side-chains REVERT: A 474 GLU cc_start: 0.8669 (tp30) cc_final: 0.8235 (tp30) REVERT: A 536 ARG cc_start: 0.8912 (tpp-160) cc_final: 0.8674 (mmt180) REVERT: A 681 ASP cc_start: 0.7983 (m-30) cc_final: 0.7769 (m-30) REVERT: B 474 GLU cc_start: 0.8665 (tp30) cc_final: 0.8425 (tp30) REVERT: B 681 ASP cc_start: 0.7943 (m-30) cc_final: 0.7722 (m-30) REVERT: B 721 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7992 (mmp-170) REVERT: B 734 GLU cc_start: 0.8047 (tt0) cc_final: 0.7738 (tt0) REVERT: B 738 ARG cc_start: 0.8292 (mmp80) cc_final: 0.8010 (ttm-80) outliers start: 25 outliers final: 8 residues processed: 88 average time/residue: 1.0921 time to fit residues: 107.1129 Evaluate side-chains 66 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 691 ASP 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: 0.9980 chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 95 optimal weight: 0.0980 chunk 142 optimal weight: 0.3980 chunk 150 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 B 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1421 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= 0.137 Angle : 0.462 6.576 17656 Z= 0.230 Chirality : 0.041 0.143 1888 Planarity : 0.004 0.043 2324 Dihedral : 4.316 43.075 1738 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.35 % Allowed : 7.82 % Favored : 90.83 % 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: 1.96 (0.21), residues: 670 sheet: 0.25 (0.40), residues: 186 loop : -0.18 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 295 HIS 0.010 0.001 HIS B 313 PHE 0.009 0.001 PHE A 125 TYR 0.011 0.001 TYR A 71 ARG 0.013 0.000 ARG A 758 *********************** 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 95 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 1.707 Fit side-chains REVERT: A 474 GLU cc_start: 0.8630 (tp30) cc_final: 0.8141 (tp30) REVERT: A 585 TYR cc_start: 0.8371 (m-80) cc_final: 0.8071 (m-80) REVERT: A 681 ASP cc_start: 0.7936 (m-30) cc_final: 0.7723 (m-30) REVERT: A 721 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7344 (mmp-170) REVERT: B 474 GLU cc_start: 0.8613 (tp30) cc_final: 0.8267 (tp30) REVERT: B 552 LEU cc_start: 0.8377 (tt) cc_final: 0.8112 (tp) REVERT: B 711 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8101 (mmp80) REVERT: B 734 GLU cc_start: 0.8042 (tt0) cc_final: 0.7758 (tt0) REVERT: B 738 ARG cc_start: 0.8321 (mmp80) cc_final: 0.8077 (ttm-80) outliers start: 18 outliers final: 5 residues processed: 91 average time/residue: 1.2479 time to fit residues: 125.1574 Evaluate side-chains 71 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 468 LEU Chi-restraints excluded: chain B residue 711 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12932 Z= 0.216 Angle : 0.480 5.972 17656 Z= 0.238 Chirality : 0.042 0.260 1888 Planarity : 0.004 0.049 2324 Dihedral : 4.350 46.070 1738 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.43 % Allowed : 8.57 % Favored : 90.00 % 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: 1.21 (0.22), residues: 1576 helix: 2.03 (0.21), residues: 668 sheet: 0.35 (0.41), residues: 186 loop : -0.20 (0.23), residues: 722 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 0.018 0.001 PHE A 495 TYR 0.009 0.001 TYR A 492 ARG 0.013 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 84 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 1.439 Fit side-chains REVERT: A 474 GLU cc_start: 0.8681 (tp30) cc_final: 0.8162 (tp30) REVERT: A 516 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7971 (mp0) REVERT: A 585 TYR cc_start: 0.8413 (m-80) cc_final: 0.8120 (m-80) REVERT: A 681 ASP cc_start: 0.7959 (m-30) cc_final: 0.7748 (m-30) REVERT: A 721 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7324 (mmp-170) REVERT: B 474 GLU cc_start: 0.8644 (tp30) cc_final: 0.8367 (tp30) REVERT: B 711 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8108 (mmp80) REVERT: B 721 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7982 (mmp-170) REVERT: B 734 GLU cc_start: 0.8036 (tt0) cc_final: 0.7765 (tt0) REVERT: B 738 ARG cc_start: 0.8364 (mmp80) cc_final: 0.8118 (ttm-80) outliers start: 19 outliers final: 9 residues processed: 82 average time/residue: 1.1885 time to fit residues: 108.0605 Evaluate side-chains 71 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 571 CYS 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 571 CYS 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: 4.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12932 Z= 0.320 Angle : 0.506 5.814 17656 Z= 0.252 Chirality : 0.044 0.222 1888 Planarity : 0.004 0.049 2324 Dihedral : 4.481 49.320 1738 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.58 % Allowed : 8.57 % Favored : 89.85 % 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: 1.97 (0.21), residues: 676 sheet: 0.30 (0.41), residues: 186 loop : -0.23 (0.23), 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 0.020 0.001 PHE A 495 TYR 0.008 0.001 TYR B 492 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 81 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 1.596 Fit side-chains REVERT: A 474 GLU cc_start: 0.8695 (tp30) cc_final: 0.8367 (tp30) REVERT: A 516 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7902 (mp0) REVERT: A 585 TYR cc_start: 0.8508 (m-80) cc_final: 0.8154 (m-80) REVERT: A 681 ASP cc_start: 0.7971 (m-30) cc_final: 0.7769 (m-30) REVERT: A 721 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7382 (mmp-170) REVERT: B 474 GLU cc_start: 0.8642 (tp30) cc_final: 0.8343 (tp30) REVERT: B 681 ASP cc_start: 0.8035 (m-30) cc_final: 0.7750 (m-30) REVERT: B 711 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7918 (mtp85) REVERT: B 721 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8014 (mmp-170) REVERT: B 734 GLU cc_start: 0.8016 (tt0) cc_final: 0.7715 (tt0) REVERT: B 738 ARG cc_start: 0.8395 (mmp80) cc_final: 0.8155 (ttm-80) outliers start: 21 outliers final: 13 residues processed: 78 average time/residue: 1.1131 time to fit residues: 97.0575 Evaluate side-chains 75 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 571 CYS Chi-restraints excluded: chain A residue 691 ASP 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 571 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.0570 chunk 69 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1491 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= 0.152 Angle : 0.466 7.518 17656 Z= 0.232 Chirality : 0.041 0.197 1888 Planarity : 0.004 0.055 2324 Dihedral : 4.392 52.818 1738 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.50 % Allowed : 8.65 % Favored : 89.85 % 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: 1.25 (0.22), residues: 1576 helix: 2.06 (0.21), residues: 674 sheet: 0.32 (0.41), residues: 186 loop : -0.17 (0.23), residues: 716 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 0.014 0.001 PHE A 495 TYR 0.008 0.001 TYR B 480 ARG 0.014 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 86 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 1.560 Fit side-chains REVERT: A 474 GLU cc_start: 0.8668 (tp30) cc_final: 0.8116 (tp30) REVERT: A 516 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7867 (mp0) REVERT: A 585 TYR cc_start: 0.8392 (m-80) cc_final: 0.8110 (m-80) REVERT: A 681 ASP cc_start: 0.7942 (m-30) cc_final: 0.7732 (m-30) REVERT: A 721 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7285 (mmp-170) REVERT: A 749 ASP cc_start: 0.7511 (m-30) cc_final: 0.7307 (m-30) REVERT: B 474 GLU cc_start: 0.8626 (tp30) cc_final: 0.8344 (tp30) REVERT: B 711 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7911 (mtp85) REVERT: B 734 GLU cc_start: 0.8008 (tt0) cc_final: 0.7719 (tt0) REVERT: B 738 ARG cc_start: 0.8377 (mmp80) cc_final: 0.8169 (ttm-80) outliers start: 20 outliers final: 14 residues processed: 83 average time/residue: 1.0747 time to fit residues: 99.9220 Evaluate side-chains 78 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 312 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 721 ARG 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 504 ASN Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 711 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1520 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= 0.180 Angle : 0.462 6.059 17656 Z= 0.229 Chirality : 0.042 0.197 1888 Planarity : 0.004 0.060 2324 Dihedral : 4.371 54.153 1738 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.65 % Allowed : 8.72 % 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: 1.25 (0.22), residues: 1576 helix: 2.06 (0.21), residues: 674 sheet: 0.36 (0.41), residues: 186 loop : -0.19 (0.23), residues: 716 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 0.013 0.001 PHE A 495 TYR 0.008 0.001 TYR B 723 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 86 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 1.575 Fit side-chains REVERT: A 474 GLU cc_start: 0.8675 (tp30) cc_final: 0.8134 (tp30) REVERT: A 516 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7852 (mp0) REVERT: A 585 TYR cc_start: 0.8372 (m-80) cc_final: 0.8086 (m-80) REVERT: A 681 ASP cc_start: 0.7949 (m-30) cc_final: 0.7740 (m-30) REVERT: A 721 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7266 (mmp-170) REVERT: A 734 GLU cc_start: 0.8098 (tt0) cc_final: 0.7874 (tt0) REVERT: B 474 GLU cc_start: 0.8621 (tp30) cc_final: 0.8329 (tp30) REVERT: B 711 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7915 (mtp85) REVERT: B 721 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7965 (mmp-170) REVERT: B 734 GLU cc_start: 0.8000 (tt0) cc_final: 0.7699 (tt0) REVERT: B 738 ARG cc_start: 0.8365 (mmp80) cc_final: 0.8162 (ttm-80) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 1.1361 time to fit residues: 105.0454 Evaluate side-chains 81 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 312 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 721 ARG 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 504 ASN Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 721 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 544 HIS A 677 HIS B 537 GLN B 544 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12932 Z= 0.156 Angle : 0.455 6.802 17656 Z= 0.226 Chirality : 0.041 0.178 1888 Planarity : 0.004 0.062 2324 Dihedral : 4.333 55.754 1738 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.43 % Allowed : 9.02 % Favored : 89.55 % 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: 2.09 (0.21), residues: 674 sheet: 0.38 (0.41), residues: 186 loop : -0.18 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 295 HIS 0.004 0.001 HIS B 313 PHE 0.012 0.001 PHE A 495 TYR 0.008 0.001 TYR B 492 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 93 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 1.529 Fit side-chains REVERT: A 474 GLU cc_start: 0.8673 (tp30) cc_final: 0.8139 (tp30) REVERT: A 516 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7886 (mp0) REVERT: A 585 TYR cc_start: 0.8342 (m-80) cc_final: 0.8059 (m-80) REVERT: A 681 ASP cc_start: 0.7934 (m-30) cc_final: 0.7725 (m-30) REVERT: A 721 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7225 (mmp-170) REVERT: A 734 GLU cc_start: 0.8107 (tt0) cc_final: 0.7850 (tt0) REVERT: B 142 GLU cc_start: 0.8717 (mp0) cc_final: 0.7941 (mp0) REVERT: B 474 GLU cc_start: 0.8628 (tp30) cc_final: 0.8343 (tp30) REVERT: B 711 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7915 (mtp85) REVERT: B 721 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7920 (mmp-170) REVERT: B 734 GLU cc_start: 0.8020 (tt0) cc_final: 0.7730 (tt0) REVERT: B 738 ARG cc_start: 0.8377 (mmp80) cc_final: 0.8175 (ttm-80) outliers start: 19 outliers final: 11 residues processed: 90 average time/residue: 1.3028 time to fit residues: 129.7151 Evaluate side-chains 82 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 312 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 721 ARG 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 571 CYS 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: 5.9990 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 chunk 143 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12932 Z= 0.144 Angle : 0.462 6.248 17656 Z= 0.230 Chirality : 0.041 0.169 1888 Planarity : 0.004 0.064 2324 Dihedral : 4.337 59.567 1738 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.20 % Allowed : 9.77 % Favored : 89.02 % 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: 1.31 (0.22), residues: 1576 helix: 2.10 (0.21), residues: 674 sheet: 0.42 (0.41), residues: 186 loop : -0.16 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 295 HIS 0.005 0.001 HIS A 539 PHE 0.019 0.001 PHE B 495 TYR 0.008 0.001 TYR B 480 ARG 0.015 0.000 ARG A 758 ********************** 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 88 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.521 Fit side-chains REVERT: A 474 GLU cc_start: 0.8673 (tp30) cc_final: 0.8161 (tp30) REVERT: A 540 ASN cc_start: 0.7888 (m-40) cc_final: 0.6693 (t0) REVERT: A 681 ASP cc_start: 0.7931 (m-30) cc_final: 0.7722 (m-30) REVERT: A 721 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7884 (mtp180) REVERT: B 474 GLU cc_start: 0.8624 (tp30) cc_final: 0.8203 (tp30) REVERT: B 711 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8100 (mmp80) REVERT: B 734 GLU cc_start: 0.8038 (tt0) cc_final: 0.7752 (tt0) REVERT: B 738 ARG cc_start: 0.8380 (mmp80) cc_final: 0.8168 (ttm-80) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 1.1157 time to fit residues: 105.8023 Evaluate side-chains 78 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 312 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 571 CYS 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 571 CYS 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: 20.0000 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 0.0370 chunk 127 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.069964 restraints weight = 44386.354| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.96 r_work: 0.2748 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12932 Z= 0.152 Angle : 0.459 6.620 17656 Z= 0.228 Chirality : 0.041 0.159 1888 Planarity : 0.004 0.063 2324 Dihedral : 4.305 55.429 1738 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.13 % Allowed : 10.00 % Favored : 88.87 % 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: 1.32 (0.22), residues: 1576 helix: 2.09 (0.21), residues: 674 sheet: 0.42 (0.41), residues: 186 loop : -0.12 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 295 HIS 0.004 0.001 HIS B 313 PHE 0.011 0.001 PHE B 495 TYR 0.008 0.001 TYR B 480 ARG 0.015 0.000 ARG A 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.23 seconds wall clock time: 64 minutes 48.13 seconds (3888.13 seconds total)