Starting phenix.real_space_refine on Fri Mar 15 19:50:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io8_35611/03_2024/8io8_35611_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io8_35611/03_2024/8io8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io8_35611/03_2024/8io8_35611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io8_35611/03_2024/8io8_35611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io8_35611/03_2024/8io8_35611_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io8_35611/03_2024/8io8_35611_updated.pdb" } 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 Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 710": "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: 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: 6.93, per 1000 atoms: 0.55 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 - 3.50 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: 4.22 Conformation dependent library (CDL) restraints added in 2.2 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... running ksdssp... Secondary structure from input PDB file: 74 helices and 8 sheets defined 44.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 15 through 37 removed outlier: 3.560A pdb=" N ALA A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) 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: 3.521A 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 92 through 105 Proline residue: A 96 - end of helix removed outlier: 3.625A pdb=" N LEU A 99 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 101 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 184 through 194 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) removed outlier: 5.017A pdb=" N HIS A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASN A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.627A 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: 4.017A 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 355 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 368 through 375 removed outlier: 6.177A pdb=" N GLY A 373 " --> pdb=" O THR A 370 " (cutoff:3.500A) 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 403 through 415 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 450 through 455 removed outlier: 3.630A pdb=" N ASP A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY A 455 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 494 through 515 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) removed outlier: 4.791A pdb=" N SER A 501 " --> pdb=" O VAL A 498 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 503 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 512 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 514 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 555 Processing helix chain 'A' and resid 569 through 579 Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 681 through 687 Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.664A pdb=" N HIS A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 717 No H-bonds generated for 'chain 'A' and resid 715 through 717' Processing helix chain 'A' and resid 732 through 738 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 removed outlier: 3.597A pdb=" N ALA B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) 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: 3.517A 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 92 through 105 Proline residue: B 96 - end of helix removed outlier: 3.617A pdb=" N LEU B 99 " --> pdb=" O PRO B 96 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 101 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 184 through 194 removed outlier: 3.628A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N HIS B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LYS B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 223 No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing helix chain 'B' and resid 226 through 235 Processing helix chain 'B' and resid 248 through 274 removed outlier: 4.597A 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: 4.047A 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: 3.971A 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 368 through 375 removed outlier: 6.214A pdb=" N GLY B 373 " --> pdb=" O THR B 370 " (cutoff:3.500A) 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 403 through 415 Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.616A pdb=" N ASP B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY B 455 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'B' and resid 494 through 515 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) removed outlier: 4.805A pdb=" N SER B 501 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 503 " --> pdb=" O ASP B 500 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 512 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 514 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 569 through 579 Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 636 through 652 Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 702 through 708 removed outlier: 3.650A pdb=" N HIS B 706 " --> pdb=" O PRO B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'B' and resid 732 through 738 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 84 through 89 removed outlier: 6.695A pdb=" N ALA A 203 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N CYS A 174 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 205 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE A 176 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 207 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LEU A 208 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 287 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 398 through 400 Processing sheet with id= C, 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: 6.867A pdb=" N HIS A 486 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N PHE A 423 " --> pdb=" O HIS A 486 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE A 488 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN A 527 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing sheet with id= D, 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: 7.545A pdb=" N ALA A 632 " --> pdb=" O PRO A 693 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 695 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N CYS A 634 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN A 697 " --> pdb=" O CYS A 634 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.695A pdb=" N ALA B 203 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N CYS B 174 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 205 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE B 176 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 207 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N LEU B 208 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 287 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id= F, 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= G, 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: 6.898A pdb=" N HIS B 486 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE B 423 " --> pdb=" O HIS B 486 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE B 488 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN B 527 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing sheet with id= H, 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: 7.571A pdb=" N ALA B 632 " --> pdb=" O PRO B 693 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE B 695 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N CYS B 634 " --> pdb=" O ILE B 695 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN B 697 " --> pdb=" O CYS B 634 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1152 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: 4.26 Time building geometry restraints manager: 4.70 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: 91.25 - 100.96: 12 100.96 - 110.67: 4477 110.67 - 120.37: 7907 120.37 - 130.08: 5131 130.08 - 139.79: 161 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: 7175 17.64 - 35.28: 364 35.28 - 52.91: 72 52.91 - 70.55: 13 70.55 - 88.19: 6 Dihedral angle restraints: 7630 sinusoidal: 3088 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 7627 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: 121 2.59 - 3.16: 10722 3.16 - 3.74: 20728 3.74 - 4.32: 31634 4.32 - 4.90: 49946 Nonbonded interactions: 113151 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 113146 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' 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: 3.100 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: 12.090 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.330 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.090 ------------------------------------------------------------------------------- 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= 0.410 Angle : 0.672 15.878 17688 Z= 0.341 Chirality : 0.049 0.270 1892 Planarity : 0.004 0.054 2318 Dihedral : 11.362 88.191 4706 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.359 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: 1.5440 time to fit residues: 211.0897 Evaluate side-chains 94 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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: 0.3980 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 730 ASN B 781 GLN B 791 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12952 Z= 0.253 Angle : 0.517 8.404 17688 Z= 0.258 Chirality : 0.044 0.188 1892 Planarity : 0.004 0.047 2318 Dihedral : 7.674 110.762 1800 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.06 % Allowed : 6.64 % Favored : 92.31 % 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: 0.59 (0.21), residues: 1572 helix: 1.06 (0.19), residues: 704 sheet: 0.97 (0.39), residues: 180 loop : -0.40 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 61 HIS 0.007 0.001 HIS B 719 PHE 0.008 0.001 PHE B 129 TYR 0.010 0.001 TYR B 87 ARG 0.004 0.000 ARG B 682 *********************** 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 104 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.528 Fit side-chains REVERT: A 217 ASN cc_start: 0.8674 (m-40) cc_final: 0.8334 (m110) REVERT: A 721 ARG cc_start: 0.7841 (mmt-90) cc_final: 0.7450 (mmt-90) REVERT: A 729 ILE cc_start: 0.8766 (mm) cc_final: 0.8285 (tp) REVERT: A 758 ARG cc_start: 0.7729 (mtt90) cc_final: 0.7428 (mmt90) REVERT: B 82 ASP cc_start: 0.8381 (t0) cc_final: 0.8169 (t70) REVERT: B 217 ASN cc_start: 0.8659 (m-40) cc_final: 0.8367 (m110) REVERT: B 325 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: B 514 LYS cc_start: 0.8781 (tttt) cc_final: 0.8566 (ttmt) outliers start: 14 outliers final: 9 residues processed: 97 average time/residue: 1.5651 time to fit residues: 164.2714 Evaluate side-chains 91 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 551 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain B residue 325 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 78 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 126 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1277 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= 0.175 Angle : 0.468 7.902 17688 Z= 0.231 Chirality : 0.042 0.170 1892 Planarity : 0.004 0.044 2318 Dihedral : 7.144 96.882 1800 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.28 % Allowed : 7.16 % Favored : 91.55 % 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: 0.77 (0.21), residues: 1572 helix: 1.34 (0.20), residues: 706 sheet: 0.72 (0.39), residues: 192 loop : -0.38 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 61 HIS 0.005 0.001 HIS B 719 PHE 0.007 0.001 PHE B 489 TYR 0.008 0.001 TYR A 480 ARG 0.004 0.000 ARG B 711 *********************** 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 106 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.435 Fit side-chains REVERT: A 217 ASN cc_start: 0.8589 (m-40) cc_final: 0.8262 (m-40) REVERT: A 721 ARG cc_start: 0.7801 (mmt-90) cc_final: 0.7445 (mmt-90) REVERT: A 729 ILE cc_start: 0.8792 (mm) cc_final: 0.8318 (tp) REVERT: B 82 ASP cc_start: 0.8359 (t0) cc_final: 0.8143 (t70) REVERT: B 217 ASN cc_start: 0.8630 (m-40) cc_final: 0.8328 (m-40) REVERT: B 514 LYS cc_start: 0.8785 (tttt) cc_final: 0.8564 (ttmt) REVERT: B 516 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7970 (mp0) outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 1.4804 time to fit residues: 153.9326 Evaluate side-chains 91 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 551 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 740 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12952 Z= 0.248 Angle : 0.494 8.211 17688 Z= 0.244 Chirality : 0.043 0.173 1892 Planarity : 0.004 0.042 2318 Dihedral : 6.863 87.209 1798 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.43 % Allowed : 7.47 % Favored : 91.10 % 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: 0.75 (0.21), residues: 1572 helix: 1.38 (0.20), residues: 706 sheet: 0.59 (0.39), residues: 192 loop : -0.42 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 24 HIS 0.005 0.001 HIS B 719 PHE 0.011 0.001 PHE A 233 TYR 0.010 0.001 TYR B 87 ARG 0.002 0.000 ARG B 682 *********************** 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 102 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 1.324 Fit side-chains REVERT: A 217 ASN cc_start: 0.8636 (m-40) cc_final: 0.8255 (m110) REVERT: A 721 ARG cc_start: 0.7832 (mmt-90) cc_final: 0.7455 (mmt-90) REVERT: A 729 ILE cc_start: 0.8826 (mm) cc_final: 0.8288 (tp) REVERT: B 82 ASP cc_start: 0.8344 (t0) cc_final: 0.8129 (t70) REVERT: B 217 ASN cc_start: 0.8620 (m-40) cc_final: 0.8273 (m110) REVERT: B 514 LYS cc_start: 0.8776 (tttt) cc_final: 0.8556 (ttmt) REVERT: B 516 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7959 (mp0) outliers start: 19 outliers final: 12 residues processed: 94 average time/residue: 1.6091 time to fit residues: 164.2407 Evaluate side-chains 96 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 434 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 38 optimal weight: 0.0570 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1439 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= 0.161 Angle : 0.453 7.729 17688 Z= 0.223 Chirality : 0.041 0.143 1892 Planarity : 0.004 0.041 2318 Dihedral : 6.619 85.498 1798 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.28 % Allowed : 7.84 % Favored : 90.87 % 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: 0.89 (0.21), residues: 1572 helix: 1.50 (0.20), residues: 706 sheet: 0.67 (0.39), residues: 192 loop : -0.35 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 61 HIS 0.004 0.001 HIS B 719 PHE 0.006 0.001 PHE A 233 TYR 0.007 0.001 TYR A 480 ARG 0.004 0.000 ARG B 711 *********************** 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 104 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.313 Fit side-chains REVERT: A 217 ASN cc_start: 0.8552 (m-40) cc_final: 0.8191 (m-40) REVERT: A 721 ARG cc_start: 0.7828 (mmt-90) cc_final: 0.7460 (mmt-90) REVERT: A 729 ILE cc_start: 0.8865 (mm) cc_final: 0.8339 (tp) REVERT: A 758 ARG cc_start: 0.7658 (mmt90) cc_final: 0.7447 (mmt90) REVERT: B 82 ASP cc_start: 0.8311 (t0) cc_final: 0.8097 (t70) REVERT: B 217 ASN cc_start: 0.8605 (m-40) cc_final: 0.8283 (m-40) REVERT: B 514 LYS cc_start: 0.8784 (tttt) cc_final: 0.8583 (ttmt) REVERT: B 516 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: B 593 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8835 (pmtt) outliers start: 17 outliers final: 8 residues processed: 98 average time/residue: 1.5169 time to fit residues: 160.8149 Evaluate side-chains 95 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 551 ASP Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 636 ASP 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 50 optimal weight: 0.0170 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.9578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1481 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= 0.158 Angle : 0.452 7.834 17688 Z= 0.222 Chirality : 0.041 0.137 1892 Planarity : 0.004 0.040 2318 Dihedral : 6.561 84.457 1798 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.13 % Allowed : 8.30 % 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: 0.93 (0.21), residues: 1572 helix: 1.56 (0.20), residues: 706 sheet: 0.63 (0.39), residues: 192 loop : -0.34 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 509 HIS 0.006 0.001 HIS B 544 PHE 0.007 0.001 PHE A 233 TYR 0.008 0.001 TYR B 87 ARG 0.003 0.000 ARG B 711 *********************** 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 99 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.510 Fit side-chains REVERT: A 217 ASN cc_start: 0.8512 (m-40) cc_final: 0.8145 (m-40) REVERT: A 721 ARG cc_start: 0.7825 (mmt-90) cc_final: 0.7448 (mmt-90) REVERT: A 729 ILE cc_start: 0.8896 (mm) cc_final: 0.8380 (tp) REVERT: B 82 ASP cc_start: 0.8312 (t0) cc_final: 0.8091 (t70) REVERT: B 217 ASN cc_start: 0.8594 (m-40) cc_final: 0.8280 (m-40) REVERT: B 516 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: B 593 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8832 (pmtt) outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 1.5324 time to fit residues: 152.6136 Evaluate side-chains 93 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 551 ASP Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 759 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1525 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= 0.165 Angle : 0.452 7.866 17688 Z= 0.222 Chirality : 0.042 0.137 1892 Planarity : 0.004 0.039 2318 Dihedral : 6.549 83.691 1798 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.21 % Allowed : 8.45 % Favored : 90.35 % 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: 0.96 (0.22), residues: 1572 helix: 1.59 (0.20), residues: 706 sheet: 0.61 (0.39), residues: 192 loop : -0.33 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 24 HIS 0.004 0.001 HIS B 544 PHE 0.007 0.001 PHE A 233 TYR 0.009 0.001 TYR B 87 ARG 0.004 0.000 ARG B 711 *********************** 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 100 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.387 Fit side-chains REVERT: A 217 ASN cc_start: 0.8542 (m-40) cc_final: 0.8195 (m-40) REVERT: A 721 ARG cc_start: 0.7775 (mmt-90) cc_final: 0.7568 (mmt-90) REVERT: B 82 ASP cc_start: 0.8334 (t0) cc_final: 0.8107 (t70) REVERT: B 217 ASN cc_start: 0.8582 (m-40) cc_final: 0.8245 (m-40) REVERT: B 516 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: B 593 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8792 (pmtt) outliers start: 16 outliers final: 12 residues processed: 94 average time/residue: 1.3886 time to fit residues: 141.9446 Evaluate side-chains 97 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 636 ASP 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 60 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.0030 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12952 Z= 0.243 Angle : 0.485 8.313 17688 Z= 0.240 Chirality : 0.043 0.149 1892 Planarity : 0.004 0.039 2318 Dihedral : 6.743 85.197 1798 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 1.36 % Allowed : 8.37 % Favored : 90.27 % 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: 0.89 (0.21), residues: 1572 helix: 1.52 (0.20), residues: 706 sheet: 0.53 (0.39), residues: 192 loop : -0.33 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 794 HIS 0.005 0.001 HIS B 544 PHE 0.012 0.001 PHE A 233 TYR 0.010 0.001 TYR B 87 ARG 0.003 0.000 ARG B 711 *********************** 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 100 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.371 Fit side-chains REVERT: A 217 ASN cc_start: 0.8635 (m-40) cc_final: 0.8257 (m110) REVERT: A 460 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7671 (p0) REVERT: B 82 ASP cc_start: 0.8339 (t0) cc_final: 0.8116 (t70) REVERT: B 217 ASN cc_start: 0.8655 (m-40) cc_final: 0.8323 (m-40) REVERT: B 516 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: B 593 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8831 (pmtt) outliers start: 18 outliers final: 11 residues processed: 94 average time/residue: 1.4390 time to fit residues: 147.2791 Evaluate side-chains 96 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 636 ASP 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 131 optimal weight: 0.0470 chunk 140 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1582 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= 0.148 Angle : 0.446 7.685 17688 Z= 0.219 Chirality : 0.041 0.134 1892 Planarity : 0.004 0.039 2318 Dihedral : 6.507 83.587 1798 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.86 % Favored : 97.01 % Rotamer: Outliers : 1.21 % Allowed : 8.75 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1572 helix: 1.62 (0.20), residues: 706 sheet: 0.61 (0.40), residues: 192 loop : -0.26 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 61 HIS 0.004 0.001 HIS B 719 PHE 0.007 0.001 PHE A 233 TYR 0.007 0.001 TYR A 480 ARG 0.004 0.000 ARG B 711 *********************** 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 102 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 1.428 Fit side-chains REVERT: A 217 ASN cc_start: 0.8503 (m-40) cc_final: 0.8162 (m-40) REVERT: A 721 ARG cc_start: 0.7887 (mmt-90) cc_final: 0.7593 (mmt-90) REVERT: B 82 ASP cc_start: 0.8309 (t0) cc_final: 0.8089 (t70) REVERT: B 217 ASN cc_start: 0.8556 (m-40) cc_final: 0.8216 (m-40) REVERT: B 516 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 593 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8803 (pmtt) outliers start: 16 outliers final: 10 residues processed: 95 average time/residue: 1.4369 time to fit residues: 148.1979 Evaluate side-chains 95 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 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 551 ASP Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 636 ASP 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 148 optimal weight: 0.0670 chunk 90 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1729 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= 0.126 Angle : 0.435 7.445 17688 Z= 0.213 Chirality : 0.041 0.148 1892 Planarity : 0.004 0.039 2318 Dihedral : 6.374 81.068 1798 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.86 % Favored : 97.01 % Rotamer: Outliers : 0.90 % Allowed : 9.05 % Favored : 90.05 % 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: 1.69 (0.20), residues: 706 sheet: 0.63 (0.39), residues: 192 loop : -0.24 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 61 HIS 0.004 0.001 HIS B 719 PHE 0.006 0.001 PHE B 489 TYR 0.008 0.001 TYR A 480 ARG 0.004 0.000 ARG B 711 ********************** 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 100 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.190 Fit side-chains REVERT: A 217 ASN cc_start: 0.8484 (m-40) cc_final: 0.8191 (m-40) REVERT: A 681 ASP cc_start: 0.7874 (m-30) cc_final: 0.7669 (m-30) REVERT: A 721 ARG cc_start: 0.7884 (mmt-90) cc_final: 0.7593 (mmt-90) REVERT: B 82 ASP cc_start: 0.8335 (t0) cc_final: 0.8123 (t70) REVERT: B 217 ASN cc_start: 0.8456 (m-40) cc_final: 0.8153 (m-40) REVERT: B 593 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8756 (pmtt) outliers start: 12 outliers final: 9 residues processed: 94 average time/residue: 1.4344 time to fit residues: 146.5247 Evaluate side-chains 95 residues out of total 1326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 551 ASP Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 636 ASP 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 131 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.085829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.066993 restraints weight = 19470.022| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.17 r_work: 0.2709 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12952 Z= 0.225 Angle : 0.480 7.872 17688 Z= 0.237 Chirality : 0.043 0.164 1892 Planarity : 0.004 0.038 2318 Dihedral : 6.650 82.922 1798 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.88 % Rotamer: Outliers : 0.83 % Allowed : 9.20 % Favored : 89.97 % 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: 0.99 (0.22), residues: 1572 helix: 1.59 (0.20), residues: 706 sheet: 0.57 (0.39), residues: 192 loop : -0.26 (0.24), residues: 674 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 0.011 0.001 PHE A 233 TYR 0.010 0.001 TYR B 87 ARG 0.004 0.000 ARG B 711 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3917.16 seconds wall clock time: 70 minutes 24.88 seconds (4224.88 seconds total)