Starting phenix.real_space_refine on Sat Jul 4 06:23:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lvt_23542/07_2026/7lvt_23542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lvt_23542/07_2026/7lvt_23542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lvt_23542/07_2026/7lvt_23542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lvt_23542/07_2026/7lvt_23542.map" model { file = "/net/cci-nas-00/data/ceres_data/7lvt_23542/07_2026/7lvt_23542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lvt_23542/07_2026/7lvt_23542.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 11816 2.51 5 N 3448 2.21 5 O 3612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18944 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 690} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLU:plan': 18, 'TYR:plan': 16, 'ARG:plan': 14, 'ASP:plan': 17, 'ASN:plan1': 10, 'PHE:plan': 16, 'GLN:plan1': 9, 'TRP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 540 Chain: "B" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 691} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLU:plan': 18, 'TYR:plan': 16, 'ARG:plan': 14, 'ASP:plan': 17, 'ASN:plan1': 10, 'PHE:plan': 16, 'GLN:plan1': 9, 'TRP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 540 Chain: "C" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 689} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLU:plan': 18, 'TYR:plan': 16, 'ARG:plan': 14, 'ASP:plan': 17, 'ASN:plan1': 10, 'PHE:plan': 16, 'GLN:plan1': 9, 'TRP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 540 Chain: "D" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 4736 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 691} Chain breaks: 5 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLU:plan': 18, 'TYR:plan': 16, 'ARG:plan': 14, 'ASP:plan': 17, 'ASN:plan1': 10, 'PHE:plan': 16, 'GLN:plan1': 9, 'TRP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 540 Time building chain proxies: 3.99, per 1000 atoms: 0.21 Number of scatterers: 18944 At special positions: 0 Unit cell: (124.944, 162.208, 187.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 3612 8.00 N 3448 7.00 C 11816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 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: 1.31 Conformation dependent library (CDL) restraints added in 931.6 milliseconds 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5416 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 37 sheets defined 50.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.946A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.544A pdb=" N LEU A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 195 Proline residue: A 192 - end of helix Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.319A pdb=" N GLU A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 317 through 337 Processing helix chain 'A' and resid 355 through 365 removed outlier: 4.145A pdb=" N ASN A 361 " --> pdb=" O PRO A 357 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 457 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.593A pdb=" N LYS A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 556 removed outlier: 3.638A pdb=" N ASN A 556 " --> pdb=" O PHE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 575 removed outlier: 3.649A pdb=" N LEU A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 581 removed outlier: 3.625A pdb=" N VAL A 579 " --> pdb=" O CYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 661 removed outlier: 3.995A pdb=" N VAL A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 675 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'A' and resid 719 through 730 Processing helix chain 'A' and resid 738 through 746 Processing helix chain 'A' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS A 776 " --> pdb=" O PRO A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 removed outlier: 3.858A pdb=" N PHE A 823 " --> pdb=" O ILE A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 833 removed outlier: 3.804A pdb=" N LEU A 830 " --> pdb=" O LEU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.547A pdb=" N ALA A 837 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 838 " --> pdb=" O PHE A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 838' Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.515A pdb=" N TYR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 303 removed outlier: 4.336A pdb=" N ALA B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 337 Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 454 through 457 Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 498 through 506 Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.593A pdb=" N LYS B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 554 Processing helix chain 'B' and resid 559 through 581 removed outlier: 4.128A pdb=" N LEU B 567 " --> pdb=" O TRP B 563 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 568 " --> pdb=" O MET B 564 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 574 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 579 " --> pdb=" O CYS B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 664 removed outlier: 3.966A pdb=" N ILE B 638 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE B 642 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU B 664 " --> pdb=" O VAL B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 698 through 711 Processing helix chain 'B' and resid 711 through 716 Processing helix chain 'B' and resid 719 through 730 Processing helix chain 'B' and resid 738 through 746 Processing helix chain 'B' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS B 776 " --> pdb=" O PRO B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET B 792 " --> pdb=" O GLY B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 Processing helix chain 'B' and resid 822 through 835 removed outlier: 3.682A pdb=" N LEU B 830 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 831 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 834 " --> pdb=" O LEU B 830 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 835 " --> pdb=" O VAL B 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.702A pdb=" N LEU C 55 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.752A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 178 through 191 removed outlier: 5.471A pdb=" N GLU C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.718A pdb=" N ALA C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.021A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 317 through 337 removed outlier: 3.568A pdb=" N VAL C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 519 through 524 removed outlier: 3.593A pdb=" N LYS C 524 " --> pdb=" O TYR C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 556 removed outlier: 3.638A pdb=" N ASN C 556 " --> pdb=" O PHE C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 575 removed outlier: 3.648A pdb=" N LEU C 567 " --> pdb=" O TRP C 563 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 582 removed outlier: 3.590A pdb=" N VAL C 579 " --> pdb=" O CYS C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 661 removed outlier: 3.944A pdb=" N VAL C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 698 through 711 Processing helix chain 'C' and resid 711 through 716 Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 738 through 746 Processing helix chain 'C' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS C 776 " --> pdb=" O PRO C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET C 792 " --> pdb=" O GLY C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 826 removed outlier: 3.859A pdb=" N PHE C 823 " --> pdb=" O ILE C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 833 removed outlier: 3.805A pdb=" N LEU C 830 " --> pdb=" O LEU C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 838 removed outlier: 3.504A pdb=" N ALA C 837 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE C 838 " --> pdb=" O PHE C 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 834 through 838' Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 152 through 168 Processing helix chain 'D' and resid 178 through 185 Processing helix chain 'D' and resid 185 through 191 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 246 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 266 through 271 Processing helix chain 'D' and resid 286 through 303 removed outlier: 3.877A pdb=" N ALA D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 337 Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 498 through 506 Processing helix chain 'D' and resid 519 through 524 removed outlier: 3.594A pdb=" N LYS D 524 " --> pdb=" O TYR D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 554 Processing helix chain 'D' and resid 559 through 581 removed outlier: 4.128A pdb=" N LEU D 567 " --> pdb=" O TRP D 563 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 568 " --> pdb=" O MET D 564 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 574 " --> pdb=" O CYS D 570 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 579 " --> pdb=" O CYS D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 664 removed outlier: 4.079A pdb=" N ILE D 638 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE D 642 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU D 664 " --> pdb=" O VAL D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 698 through 711 Processing helix chain 'D' and resid 711 through 716 Processing helix chain 'D' and resid 719 through 730 Processing helix chain 'D' and resid 738 through 746 Processing helix chain 'D' and resid 772 through 787 removed outlier: 4.155A pdb=" N LYS D 776 " --> pdb=" O PRO D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 799 removed outlier: 3.508A pdb=" N MET D 792 " --> pdb=" O GLY D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 821 Processing helix chain 'D' and resid 822 through 835 removed outlier: 3.674A pdb=" N LEU D 830 " --> pdb=" O LEU D 826 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL D 831 " --> pdb=" O ALA D 827 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 834 " --> pdb=" O LEU D 830 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 835 " --> pdb=" O VAL D 831 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 80 removed outlier: 3.562A pdb=" N ILE A 38 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N ALA A 105 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ARG A 37 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE A 107 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY A 39 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS A 129 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 149 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN A 131 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A 384 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR A 150 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 201 removed outlier: 4.350A pdb=" N TYR A 225 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA4, first strand: chain 'A' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU A 433 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 435 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 528 Processing sheet with id=AA7, first strand: chain 'A' and resid 533 through 535 removed outlier: 3.928A pdb=" N MET A 533 " --> pdb=" O TYR A 763 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 682 removed outlier: 6.572A pdb=" N GLU A 680 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU A 735 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 682 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLU A 737 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 539 " --> pdb=" O ILE A 754 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 75 through 83 removed outlier: 6.036A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLN B 81 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 131 removed outlier: 8.056A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ASN B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.277A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 225 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.277A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 225 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 368 through 370 Processing sheet with id=AB5, first strand: chain 'B' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU B 433 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS B 481 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 435 " --> pdb=" O LYS B 481 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB7, first strand: chain 'B' and resid 526 through 528 Processing sheet with id=AB8, first strand: chain 'B' and resid 533 through 535 removed outlier: 3.927A pdb=" N MET B 533 " --> pdb=" O TYR B 763 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 680 through 682 removed outlier: 6.572A pdb=" N GLU B 680 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU B 735 " --> pdb=" O GLU B 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY B 682 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLU B 737 " --> pdb=" O GLY B 682 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 539 " --> pdb=" O ILE B 754 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 76 through 83 removed outlier: 6.235A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN C 81 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 201 through 203 removed outlier: 7.821A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 256 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 279 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 389 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 404 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AC5, first strand: chain 'C' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU C 433 " --> pdb=" O ASP C 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL C 435 " --> pdb=" O LYS C 481 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC7, first strand: chain 'C' and resid 526 through 528 Processing sheet with id=AC8, first strand: chain 'C' and resid 533 through 535 removed outlier: 3.927A pdb=" N MET C 533 " --> pdb=" O TYR C 763 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 680 through 682 removed outlier: 6.573A pdb=" N GLU C 680 " --> pdb=" O ALA C 733 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU C 735 " --> pdb=" O GLU C 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY C 682 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU C 737 " --> pdb=" O GLY C 682 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 539 " --> pdb=" O ILE C 754 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 75 through 83 Processing sheet with id=AD2, first strand: chain 'D' and resid 129 through 131 removed outlier: 7.992A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ASN D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 198 through 203 removed outlier: 6.436A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR D 225 " --> pdb=" O THR D 171 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=AD5, first strand: chain 'D' and resid 388 through 395 removed outlier: 3.690A pdb=" N GLY D 403 " --> pdb=" O ILE D 391 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER D 393 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS D 401 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS D 395 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 404 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 478 through 482 removed outlier: 6.824A pdb=" N LEU D 433 " --> pdb=" O ASP D 479 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS D 481 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL D 435 " --> pdb=" O LYS D 481 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 528 Processing sheet with id=AD9, first strand: chain 'D' and resid 533 through 535 removed outlier: 3.927A pdb=" N MET D 533 " --> pdb=" O TYR D 763 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 680 through 682 removed outlier: 6.574A pdb=" N GLU D 680 " --> pdb=" O ALA D 733 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 735 " --> pdb=" O GLU D 680 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY D 682 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU D 737 " --> pdb=" O GLY D 682 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 539 " --> pdb=" O ILE D 754 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3141 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: 3.80 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3343 1.31 - 1.44: 4746 1.44 - 1.56: 10956 1.56 - 1.68: 39 1.68 - 1.81: 120 Bond restraints: 19204 Sorted by residual: bond pdb=" C TRP C 296 " pdb=" O TRP C 296 " ideal model delta sigma weight residual 1.237 1.318 -0.081 1.17e-02 7.31e+03 4.84e+01 bond pdb=" C PRO B 304 " pdb=" O PRO B 304 " ideal model delta sigma weight residual 1.240 1.187 0.053 1.12e-02 7.97e+03 2.26e+01 bond pdb=" N ARG C 300 " pdb=" CA ARG C 300 " ideal model delta sigma weight residual 1.457 1.514 -0.056 1.29e-02 6.01e+03 1.91e+01 bond pdb=" C GLU D 267 " pdb=" O GLU D 267 " ideal model delta sigma weight residual 1.237 1.288 -0.052 1.19e-02 7.06e+03 1.89e+01 bond pdb=" C LEU B 301 " pdb=" O LEU B 301 " ideal model delta sigma weight residual 1.233 1.287 -0.054 1.46e-02 4.69e+03 1.37e+01 ... (remaining 19199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 23327 2.10 - 4.19: 2465 4.19 - 6.29: 364 6.29 - 8.39: 63 8.39 - 10.48: 17 Bond angle restraints: 26236 Sorted by residual: angle pdb=" N PRO B 304 " pdb=" CA PRO B 304 " pdb=" C PRO B 304 " ideal model delta sigma weight residual 110.70 100.22 10.48 1.22e+00 6.72e-01 7.38e+01 angle pdb=" N SER D 738 " pdb=" CA SER D 738 " pdb=" C SER D 738 " ideal model delta sigma weight residual 111.75 121.99 -10.24 1.28e+00 6.10e-01 6.40e+01 angle pdb=" N SER C 738 " pdb=" CA SER C 738 " pdb=" C SER C 738 " ideal model delta sigma weight residual 111.75 121.98 -10.23 1.28e+00 6.10e-01 6.39e+01 angle pdb=" N SER B 738 " pdb=" CA SER B 738 " pdb=" C SER B 738 " ideal model delta sigma weight residual 111.75 121.98 -10.23 1.28e+00 6.10e-01 6.38e+01 angle pdb=" N SER A 738 " pdb=" CA SER A 738 " pdb=" C SER A 738 " ideal model delta sigma weight residual 111.75 121.93 -10.18 1.28e+00 6.10e-01 6.32e+01 ... (remaining 26231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 10453 16.98 - 33.95: 783 33.95 - 50.93: 155 50.93 - 67.91: 23 67.91 - 84.88: 6 Dihedral angle restraints: 11420 sinusoidal: 3088 harmonic: 8332 Sorted by residual: dihedral pdb=" CA GLU C 48 " pdb=" C GLU C 48 " pdb=" N PRO C 49 " pdb=" CA PRO C 49 " ideal model delta harmonic sigma weight residual 180.00 150.41 29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" C GLU D 48 " pdb=" N GLU D 48 " pdb=" CA GLU D 48 " pdb=" CB GLU D 48 " ideal model delta harmonic sigma weight residual -122.60 -136.79 14.19 0 2.50e+00 1.60e-01 3.22e+01 dihedral pdb=" CA ILE D 638 " pdb=" C ILE D 638 " pdb=" N TRP D 639 " pdb=" CA TRP D 639 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 11417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2363 0.092 - 0.185: 590 0.185 - 0.277: 174 0.277 - 0.369: 34 0.369 - 0.461: 3 Chirality restraints: 3164 Sorted by residual: chirality pdb=" CA PHE C 583 " pdb=" N PHE C 583 " pdb=" C PHE C 583 " pdb=" CB PHE C 583 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CA GLU D 48 " pdb=" N GLU D 48 " pdb=" C GLU D 48 " pdb=" CB GLU D 48 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 3161 not shown) Planarity restraints: 3496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 178 " 0.027 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C ASP A 178 " -0.098 2.00e-02 2.50e+03 pdb=" O ASP A 178 " 0.037 2.00e-02 2.50e+03 pdb=" N SER A 179 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 297 " -0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C SER B 297 " 0.088 2.00e-02 2.50e+03 pdb=" O SER B 297 " -0.033 2.00e-02 2.50e+03 pdb=" N MET B 298 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 298 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" C MET B 298 " -0.067 2.00e-02 2.50e+03 pdb=" O MET B 298 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU B 299 " 0.023 2.00e-02 2.50e+03 ... (remaining 3493 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 236 2.63 - 3.19: 16783 3.19 - 3.76: 29198 3.76 - 4.33: 36625 4.33 - 4.90: 60629 Nonbonded interactions: 143471 Sorted by model distance: nonbonded pdb=" CB ALA B 706 " pdb=" O LYS C 697 " model vdw 2.057 3.460 nonbonded pdb=" O MET A 247 " pdb=" OH TYR A 254 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP B 260 " pdb=" OG1 THR B 318 " model vdw 2.306 3.040 nonbonded pdb=" O LYS A 385 " pdb=" OG SER A 407 " model vdw 2.309 3.040 nonbonded pdb=" O ALA D 100 " pdb=" OG SER D 344 " model vdw 2.319 3.040 ... (remaining 143466 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.520 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 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 : 0.008 0.081 19208 Z= 0.520 Angle : 1.359 10.481 26244 Z= 0.950 Chirality : 0.092 0.461 3164 Planarity : 0.007 0.074 3496 Dihedral : 13.036 84.885 5992 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.40 % Favored : 93.32 % Rotamer: Outliers : 0.96 % Allowed : 9.25 % Favored : 89.79 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.14), residues: 2828 helix: -1.41 (0.12), residues: 1321 sheet: -2.48 (0.21), residues: 468 loop : -2.19 (0.17), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 306 TYR 0.037 0.002 TYR A 328 PHE 0.035 0.002 PHE B 59 TRP 0.014 0.002 TRP D 368 HIS 0.016 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00777 / 0.52 (19204) covalent geometry : angle 1.35906 / 0.95 (26236) SS BOND : bond 0.00262 / 0.13 ( 4) SS BOND : angle 0.83552 / 0.70 ( 8) hydrogen bonds : bond 0.15644 / 10.09 ( 1081) hydrogen bonds : angle 7.11802 / 4.91 ( 3141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9472 (mt) cc_final: 0.9170 (mp) REVERT: A 132 THR cc_start: 0.8792 (p) cc_final: 0.8323 (t) REVERT: A 166 TYR cc_start: 0.9110 (t80) cc_final: 0.8627 (t80) REVERT: A 196 ASN cc_start: 0.8372 (p0) cc_final: 0.8003 (p0) REVERT: A 250 GLU cc_start: 0.6514 (mt-10) cc_final: 0.6108 (pt0) REVERT: A 282 LEU cc_start: 0.9689 (mm) cc_final: 0.9484 (mm) outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 0.0688 time to fit residues: 8.3633 Evaluate side-chains 59 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.054234 restraints weight = 22770.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.055954 restraints weight = 12470.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057149 restraints weight = 8054.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.057887 restraints weight = 5816.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058478 restraints weight = 4644.081| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4444 moved from start: 7.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 19208 Z= 0.397 Angle : 1.094 16.213 26244 Z= 0.705 Chirality : 0.058 0.586 3164 Planarity : 0.007 0.087 3496 Dihedral : 8.419 154.667 3008 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 2.12 % Allowed : 5.66 % Favored : 92.22 % Rotamer: Outliers : 0.89 % Allowed : 7.10 % Favored : 92.01 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.73 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.15), residues: 2828 helix: 0.01 (0.14), residues: 1288 sheet: -2.38 (0.20), residues: 492 loop : -2.27 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 133 TYR 0.015 0.002 TYR B 166 PHE 0.013 0.001 PHE B 262 TRP 0.015 0.002 TRP D 405 HIS 0.011 0.002 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.40 (19204) covalent geometry : angle 1.09207 / 0.70 (26236) SS BOND : bond 0.02882 / 1.44 ( 4) SS BOND : angle 4.26033 / 3.38 ( 8) hydrogen bonds : bond 0.21794 / 15.82 ( 1081) hydrogen bonds : angle 7.22820 / 4.93 ( 3141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8944 (p) cc_final: 0.8249 (p) REVERT: A 143 ASP cc_start: 0.7987 (m-30) cc_final: 0.7179 (m-30) REVERT: A 166 TYR cc_start: 0.9038 (t80) cc_final: 0.8807 (t80) REVERT: A 196 ASN cc_start: 0.8495 (p0) cc_final: 0.8232 (p0) REVERT: A 221 SER cc_start: 0.8901 (t) cc_final: 0.8641 (p) REVERT: A 250 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6840 (pt0) REVERT: A 323 MET cc_start: 0.9619 (tpp) cc_final: 0.9263 (mmm) REVERT: A 325 ASP cc_start: 0.9182 (m-30) cc_final: 0.8920 (m-30) REVERT: A 385 LYS cc_start: 0.8445 (mmtm) cc_final: 0.7780 (tttt) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.0575 time to fit residues: 5.5434 Evaluate side-chains 47 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 280 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 233 optimal weight: 0.2980 chunk 271 optimal weight: 30.0000 chunk 270 optimal weight: 30.0000 chunk 279 optimal weight: 0.0970 chunk 192 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN A 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.074928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.057106 restraints weight = 22587.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058844 restraints weight = 12971.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.060092 restraints weight = 8588.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060928 restraints weight = 6270.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.061369 restraints weight = 4973.655| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4420 moved from start: 7.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 19208 Z= 0.253 Angle : 0.810 12.201 26244 Z= 0.497 Chirality : 0.044 0.248 3164 Planarity : 0.006 0.056 3496 Dihedral : 7.209 136.487 3008 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.53 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.16), residues: 2828 helix: 0.61 (0.14), residues: 1340 sheet: -1.86 (0.24), residues: 396 loop : -1.71 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 374 TYR 0.028 0.002 TYR D 324 PHE 0.013 0.001 PHE D 262 TRP 0.009 0.001 TRP D 368 HIS 0.008 0.001 HIS C 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.25 (19204) covalent geometry : angle 0.80924 / 0.50 (26236) SS BOND : bond 0.00725 / 0.36 ( 4) SS BOND : angle 1.50215 / 1.20 ( 8) hydrogen bonds : bond 0.11184 / 7.29 ( 1081) hydrogen bonds : angle 6.02557 / 4.09 ( 3141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: C 53 GLU cc_start: 0.8920 (pt0) cc_final: 0.8667 (mt-10) REVERT: C 143 ASP cc_start: 0.7265 (m-30) cc_final: 0.6563 (m-30) REVERT: C 182 LEU cc_start: 0.9167 (tp) cc_final: 0.8821 (tp) REVERT: C 221 SER cc_start: 0.8727 (t) cc_final: 0.8415 (p) REVERT: C 325 ASP cc_start: 0.9095 (m-30) cc_final: 0.8836 (m-30) REVERT: C 385 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7423 (tttt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0515 time to fit residues: 4.4981 Evaluate side-chains 45 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 278 optimal weight: 6.9990 chunk 167 optimal weight: 0.0050 chunk 50 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 40.0000 chunk 10 optimal weight: 0.1980 chunk 138 optimal weight: 40.0000 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 0.0970 chunk 206 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.075066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.056964 restraints weight = 22712.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.058768 restraints weight = 12771.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.060036 restraints weight = 8413.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.060956 restraints weight = 6150.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061309 restraints weight = 4822.980| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4452 moved from start: 7.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19208 Z= 0.180 Angle : 0.690 8.750 26244 Z= 0.414 Chirality : 0.042 0.163 3164 Planarity : 0.004 0.033 3496 Dihedral : 6.790 137.386 3008 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2828 helix: 1.04 (0.14), residues: 1384 sheet: -1.47 (0.24), residues: 460 loop : -1.47 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 184 TYR 0.026 0.001 TYR A 324 PHE 0.009 0.001 PHE B 42 TRP 0.007 0.001 TRP D 405 HIS 0.004 0.001 HIS C 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.18 (19204) covalent geometry : angle 0.68944 / 0.41 (26236) SS BOND : bond 0.00506 / 0.25 ( 4) SS BOND : angle 1.05853 / 0.86 ( 8) hydrogen bonds : bond 0.07920 / 4.90 ( 1081) hydrogen bonds : angle 5.78282 / 3.89 ( 3141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.178 Fit side-chains REVERT: C 53 GLU cc_start: 0.8833 (pt0) cc_final: 0.8557 (pm20) REVERT: C 135 LYS cc_start: 0.9310 (pttm) cc_final: 0.9095 (ptpt) REVERT: C 176 TYR cc_start: 0.8131 (p90) cc_final: 0.7756 (p90) REVERT: C 182 LEU cc_start: 0.9185 (tp) cc_final: 0.8893 (tp) REVERT: C 200 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7521 (tptt) REVERT: C 221 SER cc_start: 0.8738 (t) cc_final: 0.8438 (p) REVERT: C 323 MET cc_start: 0.9596 (tpp) cc_final: 0.9304 (tpp) REVERT: C 325 ASP cc_start: 0.9097 (m-30) cc_final: 0.8795 (m-30) REVERT: C 385 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7346 (tttt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0574 time to fit residues: 4.6069 Evaluate side-chains 43 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 281 optimal weight: 30.0000 chunk 118 optimal weight: 40.0000 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 195 optimal weight: 30.0000 chunk 92 optimal weight: 0.4980 chunk 242 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 199 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.075530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.057732 restraints weight = 22922.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.059561 restraints weight = 12934.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.060784 restraints weight = 8423.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.061631 restraints weight = 6176.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.062267 restraints weight = 4934.764| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4442 moved from start: 7.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19208 Z= 0.164 Angle : 0.657 8.031 26244 Z= 0.395 Chirality : 0.041 0.160 3164 Planarity : 0.004 0.029 3496 Dihedral : 6.785 136.506 3008 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.95 % Favored : 94.77 % Rotamer: Outliers : 0.30 % Allowed : 2.96 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2828 helix: 1.43 (0.15), residues: 1364 sheet: -1.38 (0.24), residues: 456 loop : -1.36 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 184 TYR 0.019 0.001 TYR D 324 PHE 0.008 0.001 PHE B 42 TRP 0.006 0.001 TRP D 405 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 (19204) covalent geometry : angle 0.65672 / 0.40 (26236) SS BOND : bond 0.00395 / 0.20 ( 4) SS BOND : angle 1.12448 / 0.91 ( 8) hydrogen bonds : bond 0.07595 / 4.75 ( 1081) hydrogen bonds : angle 5.55225 / 3.74 ( 3141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.125 Fit side-chains REVERT: C 53 GLU cc_start: 0.8831 (pt0) cc_final: 0.8588 (pm20) REVERT: C 132 THR cc_start: 0.8707 (p) cc_final: 0.8057 (p) REVERT: C 176 TYR cc_start: 0.8352 (p90) cc_final: 0.8092 (p90) REVERT: C 200 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7418 (tptt) REVERT: C 221 SER cc_start: 0.8721 (t) cc_final: 0.8412 (p) REVERT: C 323 MET cc_start: 0.9579 (tpp) cc_final: 0.9227 (mmm) REVERT: C 325 ASP cc_start: 0.9075 (m-30) cc_final: 0.8846 (m-30) REVERT: C 385 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7268 (tttt) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.0513 time to fit residues: 4.2281 Evaluate side-chains 43 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 127 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 118 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 19 optimal weight: 0.4980 chunk 157 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 98 GLN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.075577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057571 restraints weight = 23072.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.059356 restraints weight = 13028.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.060651 restraints weight = 8622.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.061562 restraints weight = 6295.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.062051 restraints weight = 4958.633| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4451 moved from start: 7.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19208 Z= 0.164 Angle : 0.651 8.222 26244 Z= 0.392 Chirality : 0.040 0.150 3164 Planarity : 0.004 0.032 3496 Dihedral : 6.712 138.041 3008 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.38 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2828 helix: 1.54 (0.15), residues: 1380 sheet: -1.23 (0.25), residues: 436 loop : -1.11 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 142 TYR 0.025 0.001 TYR D 324 PHE 0.013 0.001 PHE C 42 TRP 0.006 0.001 TRP D 405 HIS 0.002 0.000 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (19204) covalent geometry : angle 0.65089 / 0.39 (26236) SS BOND : bond 0.00932 / 0.47 ( 4) SS BOND : angle 1.24424 / 1.00 ( 8) hydrogen bonds : bond 0.07353 / 4.54 ( 1081) hydrogen bonds : angle 5.44900 / 3.67 ( 3141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.182 Fit side-chains REVERT: C 132 THR cc_start: 0.8671 (p) cc_final: 0.8362 (p) REVERT: C 176 TYR cc_start: 0.8477 (p90) cc_final: 0.8137 (p90) REVERT: C 200 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7444 (tptt) REVERT: C 221 SER cc_start: 0.8771 (t) cc_final: 0.8484 (p) REVERT: C 237 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8399 (tm-30) REVERT: C 323 MET cc_start: 0.9538 (tpp) cc_final: 0.9187 (tpp) REVERT: C 324 TYR cc_start: 0.8874 (t80) cc_final: 0.8222 (t80) REVERT: C 325 ASP cc_start: 0.9077 (m-30) cc_final: 0.8866 (m-30) REVERT: C 385 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7108 (tttt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0486 time to fit residues: 3.9752 Evaluate side-chains 45 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 87 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 119 optimal weight: 0.4980 chunk 49 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 241 optimal weight: 0.7980 chunk 266 optimal weight: 0.2980 chunk 51 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.076097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.057988 restraints weight = 22984.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.059769 restraints weight = 13386.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.060973 restraints weight = 8933.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.061836 restraints weight = 6615.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.062348 restraints weight = 5307.512| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4465 moved from start: 7.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19208 Z= 0.158 Angle : 0.652 8.423 26244 Z= 0.388 Chirality : 0.040 0.152 3164 Planarity : 0.004 0.030 3496 Dihedral : 6.659 137.875 3008 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.38 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2828 helix: 1.68 (0.15), residues: 1380 sheet: -1.23 (0.27), residues: 400 loop : -0.95 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 93 TYR 0.024 0.001 TYR B 324 PHE 0.011 0.001 PHE D 42 TRP 0.005 0.001 TRP D 405 HIS 0.001 0.000 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.16 (19204) covalent geometry : angle 0.65155 / 0.39 (26236) SS BOND : bond 0.00426 / 0.21 ( 4) SS BOND : angle 1.44745 / 1.17 ( 8) hydrogen bonds : bond 0.07153 / 4.41 ( 1081) hydrogen bonds : angle 5.43157 / 3.66 ( 3141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.178 Fit side-chains REVERT: C 110 SER cc_start: 0.8966 (t) cc_final: 0.8587 (p) REVERT: C 132 THR cc_start: 0.8666 (p) cc_final: 0.8408 (p) REVERT: C 176 TYR cc_start: 0.8669 (p90) cc_final: 0.8267 (p90) REVERT: C 182 LEU cc_start: 0.9152 (tp) cc_final: 0.8907 (tp) REVERT: C 200 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7399 (tptt) REVERT: C 221 SER cc_start: 0.8757 (t) cc_final: 0.8485 (p) REVERT: C 237 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8436 (tm-30) REVERT: C 323 MET cc_start: 0.9551 (tpp) cc_final: 0.9192 (tpp) REVERT: C 324 TYR cc_start: 0.8866 (t80) cc_final: 0.8388 (t80) REVERT: C 325 ASP cc_start: 0.9075 (m-30) cc_final: 0.8868 (m-30) REVERT: C 385 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7091 (tttt) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0452 time to fit residues: 3.9340 Evaluate side-chains 43 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 84 optimal weight: 8.9990 chunk 82 optimal weight: 0.0170 chunk 217 optimal weight: 0.0870 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 265 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 229 optimal weight: 0.3980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.076688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.058342 restraints weight = 23061.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.060144 restraints weight = 13432.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.061344 restraints weight = 8977.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.062264 restraints weight = 6667.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.062912 restraints weight = 5279.876| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4464 moved from start: 7.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19208 Z= 0.154 Angle : 0.644 8.665 26244 Z= 0.384 Chirality : 0.040 0.156 3164 Planarity : 0.004 0.029 3496 Dihedral : 6.598 137.772 3008 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.96 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2828 helix: 1.77 (0.15), residues: 1384 sheet: -1.08 (0.26), residues: 432 loop : -0.93 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 142 TYR 0.022 0.001 TYR D 328 PHE 0.014 0.001 PHE A 255 TRP 0.022 0.001 TRP A 296 HIS 0.002 0.000 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (19204) covalent geometry : angle 0.64391 / 0.38 (26236) SS BOND : bond 0.00289 / 0.14 ( 4) SS BOND : angle 1.29028 / 1.04 ( 8) hydrogen bonds : bond 0.07053 / 4.34 ( 1081) hydrogen bonds : angle 5.34417 / 3.61 ( 3141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.197 Fit side-chains REVERT: C 110 SER cc_start: 0.9004 (t) cc_final: 0.8706 (p) REVERT: C 176 TYR cc_start: 0.8746 (p90) cc_final: 0.8423 (p90) REVERT: C 200 LYS cc_start: 0.7923 (mtpt) cc_final: 0.7477 (tptt) REVERT: C 221 SER cc_start: 0.8780 (t) cc_final: 0.8548 (p) REVERT: C 237 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8580 (tm-30) REVERT: C 324 TYR cc_start: 0.8807 (t80) cc_final: 0.8457 (t80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0461 time to fit residues: 4.0174 Evaluate side-chains 42 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 164 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 186 optimal weight: 0.0270 chunk 234 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 chunk 92 optimal weight: 0.0270 chunk 15 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 chunk 21 optimal weight: 0.0010 chunk 188 optimal weight: 0.0050 overall best weight: 0.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 119 GLN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.077651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.059483 restraints weight = 22546.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061257 restraints weight = 13333.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.062512 restraints weight = 8995.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.063399 restraints weight = 6654.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063949 restraints weight = 5306.026| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4424 moved from start: 7.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19208 Z= 0.157 Angle : 0.670 8.661 26244 Z= 0.392 Chirality : 0.040 0.157 3164 Planarity : 0.004 0.030 3496 Dihedral : 6.596 137.399 3008 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.96 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2828 helix: 1.74 (0.15), residues: 1388 sheet: -0.98 (0.26), residues: 432 loop : -0.95 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 142 TYR 0.019 0.001 TYR D 324 PHE 0.011 0.001 PHE A 255 TRP 0.020 0.002 TRP A 296 HIS 0.001 0.000 HIS D 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.16 (19204) covalent geometry : angle 0.66979 / 0.39 (26236) SS BOND : bond 0.00222 / 0.11 ( 4) SS BOND : angle 1.37554 / 1.11 ( 8) hydrogen bonds : bond 0.06898 / 4.27 ( 1081) hydrogen bonds : angle 5.32894 / 3.60 ( 3141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.162 Fit side-chains REVERT: C 132 THR cc_start: 0.8688 (p) cc_final: 0.8081 (p) REVERT: C 176 TYR cc_start: 0.8682 (p90) cc_final: 0.8342 (p90) REVERT: C 200 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7579 (tptt) REVERT: C 221 SER cc_start: 0.8839 (t) cc_final: 0.8614 (p) REVERT: C 237 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8539 (tm-30) REVERT: C 248 MET cc_start: 0.9107 (tpp) cc_final: 0.8872 (tpp) REVERT: C 323 MET cc_start: 0.9460 (tpp) cc_final: 0.9215 (mmm) REVERT: C 324 TYR cc_start: 0.8798 (t80) cc_final: 0.8342 (t80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0441 time to fit residues: 3.8449 Evaluate side-chains 46 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 61 optimal weight: 30.0000 chunk 226 optimal weight: 0.0870 chunk 245 optimal weight: 0.0570 chunk 111 optimal weight: 0.0270 chunk 234 optimal weight: 0.0020 chunk 228 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 159 optimal weight: 0.0370 chunk 45 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 overall best weight: 0.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.078541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.061042 restraints weight = 22745.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.062663 restraints weight = 14016.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.063779 restraints weight = 9686.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064558 restraints weight = 7368.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065018 restraints weight = 6017.067| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4421 moved from start: 7.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19208 Z= 0.155 Angle : 0.656 8.526 26244 Z= 0.386 Chirality : 0.040 0.156 3164 Planarity : 0.004 0.028 3496 Dihedral : 6.569 136.866 3008 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.38 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2828 helix: 1.77 (0.15), residues: 1388 sheet: -0.89 (0.26), residues: 432 loop : -0.92 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 300 TYR 0.018 0.001 TYR B 324 PHE 0.009 0.001 PHE D 42 TRP 0.005 0.001 TRP A 296 HIS 0.001 0.000 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.16 (19204) covalent geometry : angle 0.65537 / 0.39 (26236) SS BOND : bond 0.00218 / 0.11 ( 4) SS BOND : angle 1.35159 / 1.09 ( 8) hydrogen bonds : bond 0.06836 / 4.24 ( 1081) hydrogen bonds : angle 5.26862 / 3.56 ( 3141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5656 Ramachandran restraints generated. 2828 Oldfield, 0 Emsley, 2828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.181 Fit side-chains REVERT: C 132 THR cc_start: 0.8624 (p) cc_final: 0.7904 (p) REVERT: C 200 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7466 (tptt) REVERT: C 217 GLU cc_start: 0.9291 (tp30) cc_final: 0.8831 (tp30) REVERT: C 221 SER cc_start: 0.8771 (t) cc_final: 0.8377 (p) REVERT: C 248 MET cc_start: 0.9197 (tpp) cc_final: 0.8871 (tpp) REVERT: C 323 MET cc_start: 0.9487 (tpp) cc_final: 0.9252 (mmm) REVERT: C 324 TYR cc_start: 0.8860 (t80) cc_final: 0.8417 (t80) REVERT: C 394 LEU cc_start: 0.9037 (tt) cc_final: 0.8828 (tt) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0435 time to fit residues: 3.7884 Evaluate side-chains 45 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 224 optimal weight: 0.2980 chunk 207 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 204 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.076597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.057921 restraints weight = 23273.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.059736 restraints weight = 13781.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.060950 restraints weight = 9303.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.061847 restraints weight = 6966.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062403 restraints weight = 5596.863| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4497 moved from start: 7.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19208 Z= 0.168 Angle : 0.671 8.456 26244 Z= 0.393 Chirality : 0.040 0.146 3164 Planarity : 0.004 0.029 3496 Dihedral : 6.616 136.414 3008 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2828 helix: 1.85 (0.15), residues: 1388 sheet: -0.92 (0.25), residues: 440 loop : -0.92 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.016 0.002 TYR B 324 PHE 0.016 0.001 PHE B 57 TRP 0.020 0.001 TRP C 296 HIS 0.002 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (19204) covalent geometry : angle 0.67078 / 0.39 (26236) SS BOND : bond 0.00190 / 0.10 ( 4) SS BOND : angle 1.18925 / 0.96 ( 8) hydrogen bonds : bond 0.06764 / 4.23 ( 1081) hydrogen bonds : angle 5.26783 / 3.55 ( 3141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1545.47 seconds wall clock time: 27 minutes 52.83 seconds (1672.83 seconds total)