Starting phenix.real_space_refine on Thu May 15 06:42:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io8_35611/05_2025/8io8_35611.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io8_35611/05_2025/8io8_35611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8io8_35611/05_2025/8io8_35611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io8_35611/05_2025/8io8_35611.map" model { file = "/net/cci-nas-00/data/ceres_data/8io8_35611/05_2025/8io8_35611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io8_35611/05_2025/8io8_35611.cif" } resolution = 2.17 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= 0.005 sd= 0.047 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 10 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 7962 2.51 5 N 2258 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12596 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Chain: "B" Number of atoms: 6240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.75, per 1000 atoms: 0.62 Number of scatterers: 12596 At special positions: 0 Unit cell: (100.86, 109.06, 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 10 15.00 Mg 2 11.99 O 2332 8.00 N 2258 7.00 C 7962 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: 3.32 Conformation dependent library (CDL) restraints added in 1.7 seconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 52.2% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.560A pdb=" N ALA A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 63 through 82 removed outlier: 3.521A pdb=" N HIS A 73 " --> pdb=" O PHE A 69 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.709A 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: 4.119A pdb=" N PHE A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.520A pdb=" N THR A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.635A 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 219 through 224 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 247 through 275 removed outlier: 4.627A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.539A pdb=" N SER A 312 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 337 through 342 removed outlier: 5.976A pdb=" N GLU A 340 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 4.003A pdb=" N ILE A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.673A pdb=" N ARG A 363 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 removed outlier: 6.177A pdb=" N GLY A 373 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 402 through 416 Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.630A pdb=" N ASP A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 494 through 498 removed outlier: 4.340A pdb=" N HIS A 497 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 498 " --> pdb=" O PHE A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 498' Processing helix chain 'A' and resid 499 through 516 Processing helix chain 'A' and resid 547 through 554 removed outlier: 4.021A pdb=" N ASP A 551 " --> pdb=" O PRO A 547 " (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 635 through 653 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 680 through 688 Processing helix chain 'A' and resid 701 through 709 removed outlier: 4.339A pdb=" N ILE A 705 " --> pdb=" O TYR A 701 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 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: 3.634A 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 removed outlier: 3.597A pdb=" N ALA B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 63 through 82 removed outlier: 3.517A pdb=" N HIS B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 105 removed outlier: 3.703A 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: 4.098A pdb=" N PHE B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.628A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 247 through 275 removed outlier: 4.597A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.560A pdb=" N SER B 312 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 337 through 342 removed outlier: 5.956A pdb=" N GLU B 340 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.971A pdb=" N ILE B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.739A pdb=" N ARG B 363 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 376 removed outlier: 6.214A pdb=" N GLY B 373 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 402 through 416 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.616A pdb=" N ASP B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 494 through 498 removed outlier: 4.382A pdb=" N HIS B 497 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 498 " --> pdb=" O PHE B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 494 through 498' Processing helix chain 'B' and resid 499 through 516 Processing helix chain 'B' and resid 547 through 554 removed outlier: 4.020A pdb=" N ASP B 551 " --> pdb=" O PRO B 547 " (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 635 through 653 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 701 through 709 removed outlier: 4.295A pdb=" N ILE B 705 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS B 706 " --> pdb=" O PRO B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 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: 3.578A 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 84 through 89 removed outlier: 6.237A pdb=" N ASN A 84 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA A 173 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 86 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL A 175 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 88 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLY A 177 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 170 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU A 205 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 172 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A 207 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N CYS A 174 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS A 209 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 176 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU A 239 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL A 288 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 241 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ARG A 290 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 243 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 464 through 466 removed outlier: 8.316A pdb=" N MET A 465 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 422 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLY A 487 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N LEU A 529 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 489 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 531 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR A 491 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 442 through 443 removed outlier: 5.347A pdb=" N LYS A 442 " --> pdb=" O SER A 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.649A pdb=" N VAL A 629 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL A 661 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 631 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 663 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER A 633 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 630 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASN A 697 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA A 632 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.279A pdb=" N ASN B 84 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA B 173 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 86 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL B 175 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 88 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLY B 177 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU B 239 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 288 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE B 241 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ARG B 290 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 243 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 300 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 397 through 400 removed outlier: 4.670A pdb=" N SER B 397 " --> pdb=" O GLN B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 466 removed outlier: 8.273A pdb=" N MET B 465 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 422 " --> pdb=" O MET B 465 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY B 487 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU B 529 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE B 489 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER B 531 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR B 491 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 442 through 443 removed outlier: 5.337A pdb=" N LYS B 442 " --> pdb=" O SER B 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 613 through 615 removed outlier: 6.670A pdb=" N VAL B 629 " --> pdb=" O ARG B 659 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL B 661 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE B 631 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL B 663 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER B 633 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 630 " --> pdb=" O ILE B 695 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN B 697 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA B 632 " --> pdb=" O ASN B 697 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1488 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: 4.21 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2097 1.31 - 1.43: 3632 1.43 - 1.56: 7158 1.56 - 1.68: 16 1.68 - 1.81: 49 Bond restraints: 12952 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.695 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.609 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C LEU B 640 " pdb=" O LEU B 640 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.17e-02 7.31e+03 2.02e+01 bond pdb=" C LEU A 640 " pdb=" O LEU A 640 " ideal model delta sigma weight residual 1.237 1.184 0.052 1.17e-02 7.31e+03 2.01e+01 ... (remaining 12947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 17545 3.18 - 6.35: 120 6.35 - 9.53: 20 9.53 - 12.70: 2 12.70 - 15.88: 1 Bond angle restraints: 17688 Sorted by residual: angle pdb=" N LYS A 556 " pdb=" CA LYS A 556 " pdb=" C LYS A 556 " ideal model delta sigma weight residual 110.28 100.00 10.28 1.48e+00 4.57e-01 4.82e+01 angle pdb=" N ARG B 753 " pdb=" CA ARG B 753 " pdb=" C ARG B 753 " ideal model delta sigma weight residual 111.36 117.57 -6.21 1.09e+00 8.42e-01 3.25e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 111.07 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O3A TPP A 802 " pdb=" PB TPP A 802 " pdb=" O3B TPP A 802 " ideal model delta sigma weight residual 104.26 111.17 -6.91 1.33e+00 5.64e-01 2.69e+01 angle pdb=" N ALA B 558 " pdb=" CA ALA B 558 " pdb=" C ALA B 558 " ideal model delta sigma weight residual 113.01 107.02 5.99 1.20e+00 6.94e-01 2.49e+01 ... (remaining 17683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 7176 17.64 - 35.28: 368 35.28 - 52.91: 74 52.91 - 70.55: 13 70.55 - 88.19: 7 Dihedral angle restraints: 7638 sinusoidal: 3096 harmonic: 4542 Sorted by residual: dihedral pdb=" CA GLY A 294 " pdb=" C GLY A 294 " pdb=" N TRP A 295 " pdb=" CA TRP A 295 " ideal model delta harmonic sigma weight residual 180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLY B 294 " pdb=" C GLY B 294 " pdb=" N TRP B 295 " pdb=" CA TRP B 295 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU A 85 " pdb=" C LEU A 85 " pdb=" N ILE A 86 " pdb=" CA ILE A 86 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 7635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1499 0.054 - 0.108: 321 0.108 - 0.162: 58 0.162 - 0.216: 10 0.216 - 0.270: 4 Chirality restraints: 1892 Sorted by residual: chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA THR A 554 " pdb=" N THR A 554 " pdb=" C THR A 554 " pdb=" CB THR A 554 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA THR B 554 " pdb=" N THR B 554 " pdb=" C THR B 554 " pdb=" CB THR B 554 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1889 not shown) Planarity restraints: 2318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 786 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO B 787 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 787 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 787 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 536 " -0.009 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C ARG A 536 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG A 536 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN A 537 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 276 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C GLY A 276 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY A 276 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 277 " 0.010 2.00e-02 2.50e+03 ... (remaining 2315 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 122 2.59 - 3.16: 10610 3.16 - 3.74: 20674 3.74 - 4.32: 31356 4.32 - 4.90: 49929 Nonbonded interactions: 112691 Sorted by model distance: nonbonded pdb=" OD1 ASP B 178 " pdb="MG MG B 803 " model vdw 2.008 2.170 nonbonded pdb=" O TYR B 213 " pdb="MG MG B 803 " model vdw 2.017 2.170 nonbonded pdb=" O3B TPP B 802 " pdb="MG MG B 803 " model vdw 2.028 2.170 nonbonded pdb=" OD1 ASP A 178 " pdb="MG MG A 803 " model vdw 2.056 2.170 nonbonded pdb=" O1A TPP A 802 " pdb="MG MG A 803 " model vdw 2.072 2.170 ... (remaining 112686 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.350 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.620 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 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 : 0.006 0.146 12952 Z= 0.302 Angle : 0.672 15.878 17688 Z= 0.341 Chirality : 0.049 0.270 1892 Planarity : 0.004 0.054 2318 Dihedral : 11.485 88.191 4714 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.08 % Allowed : 2.56 % Favored : 97.36 % 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: 0.23 (0.21), residues: 1572 helix: 0.53 (0.19), residues: 700 sheet: 0.96 (0.38), residues: 184 loop : -0.36 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.005 0.001 HIS A 699 PHE 0.009 0.002 PHE B 129 TYR 0.012 0.001 TYR B 87 ARG 0.003 0.000 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.20134 ( 551) hydrogen bonds : angle 6.00980 ( 1488) covalent geometry : bond 0.00613 (12952) covalent geometry : angle 0.67234 (17688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.404 Fit side-chains REVERT: A 217 ASN cc_start: 0.8706 (m-40) cc_final: 0.8396 (m110) REVERT: A 729 ILE cc_start: 0.8814 (mm) cc_final: 0.8269 (tp) REVERT: B 217 ASN cc_start: 0.8649 (m-40) cc_final: 0.8369 (m110) REVERT: B 514 LYS cc_start: 0.8853 (tttt) cc_final: 0.8578 (ttmt) outliers start: 1 outliers final: 2 residues processed: 127 average time/residue: 1.6227 time to fit residues: 221.3569 Evaluate side-chains 94 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.2980 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 128 GLN B 730 ASN B 781 GLN B 791 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.086667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.067774 restraints weight = 19552.778| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.16 r_work: 0.2732 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12952 Z= 0.126 Angle : 0.521 10.768 17688 Z= 0.261 Chirality : 0.044 0.178 1892 Planarity : 0.004 0.049 2318 Dihedral : 7.726 87.416 1808 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.75 % Allowed : 6.56 % Favored : 92.68 % 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: 0.85 (0.21), residues: 1572 helix: 1.25 (0.19), residues: 714 sheet: 1.12 (0.39), residues: 176 loop : -0.25 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 61 HIS 0.006 0.001 HIS B 544 PHE 0.007 0.001 PHE B 125 TYR 0.011 0.001 TYR B 108 ARG 0.004 0.000 ARG B 682 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 551) hydrogen bonds : angle 4.03234 ( 1488) covalent geometry : bond 0.00284 (12952) covalent geometry : angle 0.52088 (17688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.296 Fit side-chains REVERT: A 217 ASN cc_start: 0.8781 (m-40) cc_final: 0.8574 (m-40) REVERT: A 556 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7856 (mmtm) REVERT: A 721 ARG cc_start: 0.8285 (mmt-90) cc_final: 0.7920 (mmt-90) REVERT: A 729 ILE cc_start: 0.8752 (mm) cc_final: 0.8140 (tp) REVERT: B 82 ASP cc_start: 0.8958 (t0) cc_final: 0.8657 (t70) REVERT: B 149 GLU cc_start: 0.7942 (pt0) cc_final: 0.7455 (pm20) REVERT: B 217 ASN cc_start: 0.8746 (m-40) cc_final: 0.8424 (m-40) REVERT: B 514 LYS cc_start: 0.9131 (tttt) cc_final: 0.8753 (ttmt) REVERT: B 516 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8539 (mp0) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 1.5973 time to fit residues: 175.6289 Evaluate side-chains 93 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 9 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 97 optimal weight: 7.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 ASN B 740 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.086373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.067329 restraints weight = 19634.534| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.21 r_work: 0.2715 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12952 Z= 0.127 Angle : 0.501 11.466 17688 Z= 0.248 Chirality : 0.043 0.179 1892 Planarity : 0.004 0.044 2318 Dihedral : 7.442 84.327 1808 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.83 % Allowed : 7.16 % Favored : 92.01 % 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: 1572 helix: 1.61 (0.19), residues: 712 sheet: 1.02 (0.39), residues: 176 loop : -0.26 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 24 HIS 0.008 0.001 HIS B 544 PHE 0.007 0.001 PHE A 233 TYR 0.009 0.001 TYR B 108 ARG 0.003 0.000 ARG B 682 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 551) hydrogen bonds : angle 3.80641 ( 1488) covalent geometry : bond 0.00292 (12952) covalent geometry : angle 0.50149 (17688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.315 Fit side-chains REVERT: A 217 ASN cc_start: 0.8764 (m-40) cc_final: 0.8408 (m-40) REVERT: A 681 ASP cc_start: 0.8327 (m-30) cc_final: 0.8037 (m-30) REVERT: A 721 ARG cc_start: 0.8288 (mmt-90) cc_final: 0.7920 (mmt-90) REVERT: A 729 ILE cc_start: 0.8737 (mm) cc_final: 0.8164 (tp) REVERT: B 82 ASP cc_start: 0.8959 (t0) cc_final: 0.8658 (t70) REVERT: B 149 GLU cc_start: 0.7976 (pt0) cc_final: 0.7453 (pm20) REVERT: B 217 ASN cc_start: 0.8701 (m-40) cc_final: 0.8342 (m-40) REVERT: B 508 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8789 (ttpp) REVERT: B 514 LYS cc_start: 0.9143 (tttt) cc_final: 0.8771 (ttmt) REVERT: B 516 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8626 (mp0) outliers start: 11 outliers final: 4 residues processed: 99 average time/residue: 1.5749 time to fit residues: 167.8462 Evaluate side-chains 91 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.067515 restraints weight = 19401.042| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.18 r_work: 0.2720 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12952 Z= 0.127 Angle : 0.498 11.966 17688 Z= 0.246 Chirality : 0.043 0.186 1892 Planarity : 0.004 0.042 2318 Dihedral : 7.116 81.296 1802 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.68 % Allowed : 7.69 % Favored : 91.63 % 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: 1.20 (0.22), residues: 1572 helix: 1.69 (0.19), residues: 724 sheet: 0.98 (0.40), residues: 176 loop : -0.19 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 444 HIS 0.005 0.001 HIS B 544 PHE 0.008 0.001 PHE A 233 TYR 0.009 0.001 TYR B 108 ARG 0.003 0.000 ARG B 711 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 551) hydrogen bonds : angle 3.70722 ( 1488) covalent geometry : bond 0.00295 (12952) covalent geometry : angle 0.49812 (17688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 1.334 Fit side-chains REVERT: A 217 ASN cc_start: 0.8781 (m-40) cc_final: 0.8396 (m-40) REVERT: A 681 ASP cc_start: 0.8305 (m-30) cc_final: 0.8009 (m-30) REVERT: A 721 ARG cc_start: 0.8302 (mmt-90) cc_final: 0.7921 (mmt-90) REVERT: A 729 ILE cc_start: 0.8774 (mm) cc_final: 0.8201 (tp) REVERT: B 82 ASP cc_start: 0.8950 (t0) cc_final: 0.8613 (t70) REVERT: B 149 GLU cc_start: 0.7966 (pt0) cc_final: 0.7414 (pm20) REVERT: B 217 ASN cc_start: 0.8717 (m-40) cc_final: 0.8347 (m-40) REVERT: B 514 LYS cc_start: 0.9103 (tttt) cc_final: 0.8737 (ttmt) REVERT: B 516 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8608 (mp0) outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 1.5791 time to fit residues: 163.4419 Evaluate side-chains 92 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 152 optimal weight: 0.1980 chunk 38 optimal weight: 0.0970 chunk 128 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 146 optimal weight: 0.7980 chunk 109 optimal weight: 0.0030 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.090161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.071297 restraints weight = 19575.435| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.20 r_work: 0.2799 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12952 Z= 0.081 Angle : 0.454 11.114 17688 Z= 0.223 Chirality : 0.041 0.168 1892 Planarity : 0.004 0.041 2318 Dihedral : 6.842 80.450 1802 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.90 % Allowed : 7.69 % Favored : 91.40 % 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: 1.33 (0.22), residues: 1572 helix: 1.85 (0.19), residues: 724 sheet: 0.95 (0.40), residues: 180 loop : -0.16 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 703 HIS 0.005 0.001 HIS B 544 PHE 0.008 0.001 PHE A 125 TYR 0.010 0.001 TYR B 480 ARG 0.006 0.000 ARG B 758 Details of bonding type rmsd hydrogen bonds : bond 0.02545 ( 551) hydrogen bonds : angle 3.49494 ( 1488) covalent geometry : bond 0.00173 (12952) covalent geometry : angle 0.45415 (17688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.355 Fit side-chains REVERT: A 82 ASP cc_start: 0.8960 (t0) cc_final: 0.8669 (t70) REVERT: A 681 ASP cc_start: 0.8212 (m-30) cc_final: 0.8006 (m-30) REVERT: A 721 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.7968 (mmt-90) REVERT: A 729 ILE cc_start: 0.8778 (mm) cc_final: 0.8257 (tp) REVERT: A 758 ARG cc_start: 0.7801 (mmt90) cc_final: 0.7591 (mmt90) REVERT: B 82 ASP cc_start: 0.8963 (t0) cc_final: 0.8630 (t70) REVERT: B 149 GLU cc_start: 0.7821 (pt0) cc_final: 0.7276 (pm20) REVERT: B 217 ASN cc_start: 0.8585 (m-40) cc_final: 0.8208 (m-40) REVERT: B 514 LYS cc_start: 0.9122 (tttt) cc_final: 0.8765 (ttmt) REVERT: B 516 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8557 (mp0) outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 1.5090 time to fit residues: 161.5715 Evaluate side-chains 88 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.086207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.067210 restraints weight = 19717.073| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.20 r_work: 0.2716 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12952 Z= 0.141 Angle : 0.504 12.798 17688 Z= 0.247 Chirality : 0.043 0.176 1892 Planarity : 0.004 0.040 2318 Dihedral : 7.163 85.529 1802 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.68 % Allowed : 8.37 % Favored : 90.95 % 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: 1572 helix: 1.82 (0.19), residues: 724 sheet: 1.03 (0.40), residues: 176 loop : -0.16 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 794 HIS 0.006 0.001 HIS A 544 PHE 0.010 0.001 PHE A 233 TYR 0.010 0.001 TYR B 108 ARG 0.005 0.000 ARG B 758 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 551) hydrogen bonds : angle 3.66437 ( 1488) covalent geometry : bond 0.00332 (12952) covalent geometry : angle 0.50398 (17688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.327 Fit side-chains REVERT: A 681 ASP cc_start: 0.8264 (m-30) cc_final: 0.8008 (m-30) REVERT: A 713 HIS cc_start: 0.8729 (m170) cc_final: 0.8500 (m-70) REVERT: A 721 ARG cc_start: 0.8317 (mmt-90) cc_final: 0.7928 (mmt-90) REVERT: A 729 ILE cc_start: 0.8795 (mm) cc_final: 0.8205 (tp) REVERT: A 758 ARG cc_start: 0.7866 (mmt90) cc_final: 0.7645 (mmt90) REVERT: B 82 ASP cc_start: 0.8987 (t0) cc_final: 0.8665 (t70) REVERT: B 217 ASN cc_start: 0.8739 (m-40) cc_final: 0.8330 (m-40) REVERT: B 514 LYS cc_start: 0.9112 (tttt) cc_final: 0.8759 (ttmt) outliers start: 9 outliers final: 4 residues processed: 88 average time/residue: 1.5561 time to fit residues: 148.2602 Evaluate side-chains 86 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 154 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 115 optimal weight: 0.1980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.087118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.068146 restraints weight = 19544.357| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.19 r_work: 0.2736 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12952 Z= 0.111 Angle : 0.485 13.097 17688 Z= 0.237 Chirality : 0.042 0.174 1892 Planarity : 0.004 0.041 2318 Dihedral : 7.101 86.410 1802 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.75 % Allowed : 8.52 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1572 helix: 1.91 (0.20), residues: 712 sheet: 1.01 (0.40), residues: 178 loop : -0.12 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 703 HIS 0.005 0.001 HIS B 544 PHE 0.007 0.001 PHE A 233 TYR 0.009 0.001 TYR B 108 ARG 0.004 0.000 ARG B 758 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 551) hydrogen bonds : angle 3.59527 ( 1488) covalent geometry : bond 0.00259 (12952) covalent geometry : angle 0.48537 (17688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.391 Fit side-chains REVERT: A 82 ASP cc_start: 0.8948 (t0) cc_final: 0.8659 (t70) REVERT: A 556 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8081 (mmtm) REVERT: A 681 ASP cc_start: 0.8264 (m-30) cc_final: 0.8014 (m-30) REVERT: A 713 HIS cc_start: 0.8732 (m170) cc_final: 0.8501 (m-70) REVERT: A 729 ILE cc_start: 0.8810 (mm) cc_final: 0.8182 (tp) REVERT: A 758 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7657 (mmt90) REVERT: B 82 ASP cc_start: 0.8963 (t0) cc_final: 0.8625 (t70) REVERT: B 217 ASN cc_start: 0.8679 (m-40) cc_final: 0.8272 (m-40) REVERT: B 514 LYS cc_start: 0.9107 (tttt) cc_final: 0.8749 (ttmt) REVERT: B 516 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: B 758 ARG cc_start: 0.7813 (mmt90) cc_final: 0.7590 (mpt-90) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 1.5038 time to fit residues: 148.3261 Evaluate side-chains 89 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 93 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.086238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.067260 restraints weight = 19671.468| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.19 r_work: 0.2717 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12952 Z= 0.136 Angle : 0.505 13.623 17688 Z= 0.246 Chirality : 0.043 0.172 1892 Planarity : 0.004 0.040 2318 Dihedral : 7.121 84.701 1802 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 0.45 % Allowed : 8.90 % Favored : 90.65 % 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: 1.29 (0.22), residues: 1572 helix: 1.80 (0.19), residues: 724 sheet: 0.99 (0.40), residues: 176 loop : -0.18 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 703 HIS 0.005 0.001 HIS B 544 PHE 0.010 0.001 PHE B 233 TYR 0.010 0.001 TYR B 108 ARG 0.004 0.000 ARG B 515 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 551) hydrogen bonds : angle 3.63223 ( 1488) covalent geometry : bond 0.00320 (12952) covalent geometry : angle 0.50506 (17688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.420 Fit side-chains REVERT: A 82 ASP cc_start: 0.8949 (t0) cc_final: 0.8658 (t70) REVERT: A 302 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8469 (mppt) REVERT: A 681 ASP cc_start: 0.8319 (m-30) cc_final: 0.8066 (m-30) REVERT: A 713 HIS cc_start: 0.8737 (m170) cc_final: 0.8501 (m-70) REVERT: A 729 ILE cc_start: 0.8828 (mm) cc_final: 0.8258 (tp) REVERT: A 758 ARG cc_start: 0.7863 (mmt90) cc_final: 0.7644 (mmt90) REVERT: B 82 ASP cc_start: 0.8987 (t0) cc_final: 0.8662 (t70) REVERT: B 217 ASN cc_start: 0.8726 (m-40) cc_final: 0.8306 (m-40) REVERT: B 514 LYS cc_start: 0.9105 (tttt) cc_final: 0.8758 (ttmt) outliers start: 6 outliers final: 6 residues processed: 87 average time/residue: 1.6093 time to fit residues: 151.5793 Evaluate side-chains 88 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 65 optimal weight: 0.0010 chunk 132 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.7546 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.068895 restraints weight = 19529.837| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.20 r_work: 0.2751 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12952 Z= 0.097 Angle : 0.481 13.812 17688 Z= 0.233 Chirality : 0.042 0.158 1892 Planarity : 0.004 0.040 2318 Dihedral : 6.982 83.421 1802 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 0.53 % Allowed : 8.82 % Favored : 90.65 % 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: 1.38 (0.22), residues: 1572 helix: 1.93 (0.20), residues: 712 sheet: 0.86 (0.39), residues: 182 loop : -0.12 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 703 HIS 0.004 0.001 HIS B 544 PHE 0.007 0.001 PHE A 125 TYR 0.008 0.001 TYR B 108 ARG 0.005 0.000 ARG B 515 Details of bonding type rmsd hydrogen bonds : bond 0.02889 ( 551) hydrogen bonds : angle 3.54363 ( 1488) covalent geometry : bond 0.00221 (12952) covalent geometry : angle 0.48133 (17688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 1.472 Fit side-chains REVERT: A 82 ASP cc_start: 0.8952 (t0) cc_final: 0.8665 (t70) REVERT: B 82 ASP cc_start: 0.8970 (t0) cc_final: 0.8626 (t70) REVERT: B 217 ASN cc_start: 0.8646 (m-40) cc_final: 0.8235 (m-40) REVERT: B 444 TRP cc_start: 0.8902 (t-100) cc_final: 0.8692 (t-100) REVERT: B 514 LYS cc_start: 0.9097 (tttt) cc_final: 0.8744 (ttmt) outliers start: 7 outliers final: 6 residues processed: 88 average time/residue: 1.4457 time to fit residues: 138.3532 Evaluate side-chains 86 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.087736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.068704 restraints weight = 19585.726| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.20 r_work: 0.2746 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12952 Z= 0.104 Angle : 0.486 14.006 17688 Z= 0.235 Chirality : 0.042 0.158 1892 Planarity : 0.004 0.040 2318 Dihedral : 6.997 83.775 1802 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 0.38 % Allowed : 9.05 % Favored : 90.57 % 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: 1.41 (0.22), residues: 1572 helix: 1.93 (0.20), residues: 712 sheet: 1.02 (0.40), residues: 178 loop : -0.10 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 703 HIS 0.006 0.001 HIS B 544 PHE 0.007 0.001 PHE B 233 TYR 0.008 0.001 TYR B 108 ARG 0.004 0.000 ARG B 515 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 551) hydrogen bonds : angle 3.54648 ( 1488) covalent geometry : bond 0.00240 (12952) covalent geometry : angle 0.48558 (17688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 1.307 Fit side-chains REVERT: A 82 ASP cc_start: 0.8952 (t0) cc_final: 0.8667 (t70) REVERT: A 729 ILE cc_start: 0.8841 (mm) cc_final: 0.8207 (tp) REVERT: B 82 ASP cc_start: 0.8970 (t0) cc_final: 0.8649 (t70) REVERT: B 217 ASN cc_start: 0.8658 (m-40) cc_final: 0.8241 (m-40) REVERT: B 444 TRP cc_start: 0.8922 (t-100) cc_final: 0.8648 (t-100) REVERT: B 514 LYS cc_start: 0.9089 (tttt) cc_final: 0.8723 (ttmt) outliers start: 5 outliers final: 5 residues processed: 85 average time/residue: 1.5128 time to fit residues: 139.8052 Evaluate side-chains 85 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 1.9990 chunk 106 optimal weight: 0.0570 chunk 66 optimal weight: 7.9990 chunk 31 optimal weight: 0.0270 chunk 154 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.089120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.070089 restraints weight = 19398.377| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.20 r_work: 0.2776 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12952 Z= 0.087 Angle : 0.471 13.460 17688 Z= 0.227 Chirality : 0.041 0.152 1892 Planarity : 0.004 0.040 2318 Dihedral : 6.879 81.033 1802 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.69 % Rotamer: Outliers : 0.38 % Allowed : 9.20 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1572 helix: 1.99 (0.20), residues: 712 sheet: 0.92 (0.40), residues: 182 loop : -0.09 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 703 HIS 0.005 0.001 HIS B 544 PHE 0.007 0.001 PHE A 125 TYR 0.008 0.001 TYR B 480 ARG 0.005 0.000 ARG B 515 Details of bonding type rmsd hydrogen bonds : bond 0.02706 ( 551) hydrogen bonds : angle 3.48566 ( 1488) covalent geometry : bond 0.00197 (12952) covalent geometry : angle 0.47071 (17688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9262.14 seconds wall clock time: 160 minutes 14.15 seconds (9614.15 seconds total)