Starting phenix.real_space_refine on Thu Aug 6 02:55:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10er_75116/08_2026/10er_75116.cif Found real_map, /net/cci-nas-00/data/ceres_data/10er_75116/08_2026/10er_75116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10er_75116/08_2026/10er_75116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10er_75116/08_2026/10er_75116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10er_75116/08_2026/10er_75116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10er_75116/08_2026/10er_75116.map" } resolution = 3.2 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= 0.000 sd= 0.013 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 42 5.16 5 C 8012 2.51 5 N 2156 2.21 5 O 2386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12596 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 6298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6298 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 57, 'TRANS': 739} Chain breaks: 1 Restraints were copied for chains: A Time building chain proxies: 5.95, per 1000 atoms: 0.47 Number of scatterers: 12596 At special positions: 0 Unit cell: (100.01, 165.77, 98.64, 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 42 16.00 O 2386 8.00 N 2156 7.00 C 8012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 598.0 milliseconds 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 26 sheets defined 16.6% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.521A pdb=" N ASP B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 3.661A pdb=" N ALA B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 154' Processing helix chain 'B' and resid 315 through 327 Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.634A pdb=" N PHE B 378 " --> pdb=" O CYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.830A pdb=" N TRP B 722 " --> pdb=" O ALA B 719 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA B 724 " --> pdb=" O LEU B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 748 removed outlier: 3.509A pdb=" N ASP B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 748 " --> pdb=" O ALA B 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 744 through 748' Processing helix chain 'B' and resid 749 through 768 removed outlier: 3.805A pdb=" N VAL B 754 " --> pdb=" O VAL B 750 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 794 removed outlier: 3.561A pdb=" N MET B 786 " --> pdb=" O TYR B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 813 removed outlier: 3.835A pdb=" N LEU B 812 " --> pdb=" O ASN B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 835 removed outlier: 3.682A pdb=" N TYR B 831 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 834 " --> pdb=" O VAL B 830 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 835 " --> pdb=" O TYR B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 840 Processing helix chain 'B' and resid 862 through 875 removed outlier: 3.824A pdb=" N ASP B 866 " --> pdb=" O THR B 862 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 912 removed outlier: 3.602A pdb=" N ILE B 897 " --> pdb=" O ALA B 893 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR B 911 " --> pdb=" O TRP B 907 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 912 " --> pdb=" O LEU B 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.520A pdb=" N ASP A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.660A pdb=" N ALA A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 154' Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.634A pdb=" N PHE A 378 " --> pdb=" O CYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.829A pdb=" N TRP A 722 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 724 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 748 removed outlier: 3.509A pdb=" N ASP A 747 " --> pdb=" O GLU A 744 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 748 " --> pdb=" O ALA A 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 744 through 748' Processing helix chain 'A' and resid 749 through 768 removed outlier: 3.805A pdb=" N VAL A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 removed outlier: 3.561A pdb=" N MET A 786 " --> pdb=" O TYR A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.836A pdb=" N LEU A 812 " --> pdb=" O ASN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.682A pdb=" N TYR A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 835 " --> pdb=" O TYR A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 862 through 875 removed outlier: 3.824A pdb=" N ASP A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 912 removed outlier: 3.602A pdb=" N ILE A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 911 " --> pdb=" O TRP A 907 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.109A pdb=" N GLY B 179 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 182 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.792A pdb=" N THR B 170 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 206 through 211 removed outlier: 4.704A pdb=" N VAL B 209 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ALA B 219 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TRP B 211 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS B 217 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 264 through 267 removed outlier: 3.989A pdb=" N VAL B 264 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 272 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE B 266 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 294 through 297 removed outlier: 3.508A pdb=" N LYS B 294 " --> pdb=" O VAL A 883 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 880 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 348 through 353 removed outlier: 6.789A pdb=" N TYR B 348 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 365 " --> pdb=" O TYR B 348 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 350 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 363 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 384 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN B 394 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR B 386 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL B 392 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 415 through 419 removed outlier: 7.805A pdb=" N MET B 415 " --> pdb=" O THR B 433 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR B 433 " --> pdb=" O MET B 415 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER B 417 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 431 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN B 419 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 429 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 449 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU B 465 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET B 451 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU B 463 " --> pdb=" O MET B 451 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 476 through 477 removed outlier: 3.641A pdb=" N LEU B 484 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP B 498 " --> pdb=" O VAL B 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 527 removed outlier: 3.538A pdb=" N SER B 526 " --> pdb=" O ASN B 555 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 555 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 570 " --> pdb=" O ARG B 580 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ARG B 580 " --> pdb=" O LEU B 570 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 529 through 531 Processing sheet with id=AB2, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AB3, first strand: chain 'B' and resid 592 through 596 removed outlier: 6.059A pdb=" N VAL B 593 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER B 615 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 652 through 659 removed outlier: 3.560A pdb=" N THR B 669 " --> pdb=" O SER B 731 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 729 " --> pdb=" O TYR B 671 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU B 687 " --> pdb=" O LEU B 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 801 through 804 removed outlier: 3.509A pdb=" N ARG B 880 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 294 " --> pdb=" O VAL B 883 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.108A pdb=" N GLY A 179 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 182 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.792A pdb=" N THR A 170 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 206 through 211 removed outlier: 4.703A pdb=" N VAL A 209 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ALA A 219 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TRP A 211 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS A 217 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 264 through 267 removed outlier: 3.989A pdb=" N VAL A 264 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 272 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 266 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 348 through 353 removed outlier: 6.789A pdb=" N TYR A 348 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 365 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER A 350 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 363 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 384 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN A 394 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N THR A 386 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL A 392 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 415 through 419 removed outlier: 7.806A pdb=" N MET A 415 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR A 433 " --> pdb=" O MET A 415 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER A 417 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 431 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 419 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 429 " --> pdb=" O ASN A 419 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 449 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 465 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET A 451 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A 463 " --> pdb=" O MET A 451 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 476 through 477 removed outlier: 3.641A pdb=" N LEU A 484 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP A 498 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.539A pdb=" N SER A 526 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 555 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 570 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ARG A 580 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 529 through 531 Processing sheet with id=AC6, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AC7, first strand: chain 'A' and resid 592 through 596 removed outlier: 6.059A pdb=" N VAL A 593 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 615 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 652 through 659 removed outlier: 3.560A pdb=" N THR A 669 " --> pdb=" O SER A 731 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 729 " --> pdb=" O TYR A 671 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 687 " --> pdb=" O LEU A 730 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 900 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: 2.04 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4136 1.34 - 1.46: 2893 1.46 - 1.58: 5823 1.58 - 1.70: 0 1.70 - 1.81: 68 Bond restraints: 12920 Sorted by residual: bond pdb=" C ARG B 367 " pdb=" N PRO B 368 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.12e-02 7.97e+03 6.97e+00 bond pdb=" C ARG A 367 " pdb=" N PRO A 368 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.12e-02 7.97e+03 6.48e+00 bond pdb=" N THR B 717 " pdb=" CA THR B 717 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.51e+00 bond pdb=" N THR A 717 " pdb=" CA THR A 717 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.40e+00 bond pdb=" C GLU B 455 " pdb=" N PRO B 456 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 1.01e+00 ... (remaining 12915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 16786 0.90 - 1.81: 561 1.81 - 2.71: 157 2.71 - 3.61: 59 3.61 - 4.52: 11 Bond angle restraints: 17574 Sorted by residual: angle pdb=" N TRP A 630 " pdb=" CA TRP A 630 " pdb=" C TRP A 630 " ideal model delta sigma weight residual 109.81 114.08 -4.27 2.21e+00 2.05e-01 3.74e+00 angle pdb=" N GLY A 801 " pdb=" CA GLY A 801 " pdb=" C GLY A 801 " ideal model delta sigma weight residual 110.90 113.83 -2.93 1.53e+00 4.27e-01 3.67e+00 angle pdb=" N GLY B 801 " pdb=" CA GLY B 801 " pdb=" C GLY B 801 " ideal model delta sigma weight residual 110.90 113.83 -2.93 1.53e+00 4.27e-01 3.66e+00 angle pdb=" CA LYS B 285 " pdb=" C LYS B 285 " pdb=" N LYS B 286 " ideal model delta sigma weight residual 114.90 117.52 -2.62 1.37e+00 5.33e-01 3.65e+00 angle pdb=" N TRP B 630 " pdb=" CA TRP B 630 " pdb=" C TRP B 630 " ideal model delta sigma weight residual 109.81 114.02 -4.21 2.21e+00 2.05e-01 3.63e+00 ... (remaining 17569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7006 17.99 - 35.97: 608 35.97 - 53.96: 132 53.96 - 71.94: 16 71.94 - 89.93: 16 Dihedral angle restraints: 7778 sinusoidal: 3160 harmonic: 4618 Sorted by residual: dihedral pdb=" CB GLU B 261 " pdb=" CG GLU B 261 " pdb=" CD GLU B 261 " pdb=" OE1 GLU B 261 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 261 " pdb=" CG GLU A 261 " pdb=" CD GLU A 261 " pdb=" OE1 GLU A 261 " ideal model delta sinusoidal sigma weight residual 0.00 89.63 -89.63 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 853 " pdb=" CG GLU A 853 " pdb=" CD GLU A 853 " pdb=" OE1 GLU A 853 " ideal model delta sinusoidal sigma weight residual 0.00 -89.34 89.34 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1245 0.028 - 0.056: 413 0.056 - 0.084: 107 0.084 - 0.112: 116 0.112 - 0.140: 35 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CA ILE A 404 " pdb=" N ILE A 404 " pdb=" C ILE A 404 " pdb=" CB ILE A 404 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE B 404 " pdb=" N ILE B 404 " pdb=" C ILE B 404 " pdb=" CB ILE B 404 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 276 " pdb=" N ILE B 276 " pdb=" C ILE B 276 " pdb=" CB ILE B 276 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1913 not shown) Planarity restraints: 2290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 630 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO A 631 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 631 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 631 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 630 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO B 631 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 631 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 631 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 404 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 405 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 405 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 405 " 0.024 5.00e-02 4.00e+02 ... (remaining 2287 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 7155 3.06 - 3.52: 11676 3.52 - 3.98: 17682 3.98 - 4.44: 19583 4.44 - 4.90: 34100 Nonbonded interactions: 90196 Sorted by model distance: nonbonded pdb=" N ILE B 406 " pdb=" N ALA B 407 " model vdw 2.595 2.560 nonbonded pdb=" N ILE A 406 " pdb=" N ALA A 407 " model vdw 2.596 2.560 nonbonded pdb=" N ILE B 372 " pdb=" N VAL B 373 " model vdw 2.620 2.560 nonbonded pdb=" N ILE A 372 " pdb=" N VAL A 373 " model vdw 2.620 2.560 nonbonded pdb=" N ALA B 346 " pdb=" O ALA B 346 " model vdw 2.632 2.496 ... (remaining 90191 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.002 0.035 12920 Z= 0.103 Angle : 0.460 4.518 17574 Z= 0.248 Chirality : 0.040 0.140 1916 Planarity : 0.004 0.044 2290 Dihedral : 14.297 89.930 4810 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.43 (0.21), residues: 1586 helix: 2.38 (0.40), residues: 180 sheet: 0.35 (0.27), residues: 402 loop : -1.12 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.007 0.001 TYR A 645 PHE 0.005 0.000 PHE A 785 TRP 0.010 0.000 TRP A 489 HIS 0.001 0.000 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (12920) covalent geometry : angle 0.45965 / 0.25 (17574) hydrogen bonds : bond 0.17019 / 12.36 ( 340) hydrogen bonds : angle 5.48991 / 3.57 ( 900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: B 441 MET cc_start: 0.9125 (tmm) cc_final: 0.8815 (tmm) REVERT: B 607 MET cc_start: 0.7691 (tpp) cc_final: 0.7452 (tpt) REVERT: A 441 MET cc_start: 0.9130 (tmm) cc_final: 0.8838 (tmm) REVERT: A 521 TYR cc_start: 0.7768 (p90) cc_final: 0.7534 (p90) REVERT: A 607 MET cc_start: 0.7646 (tpp) cc_final: 0.7398 (tpt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0701 time to fit residues: 6.5397 Evaluate side-chains 45 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.0070 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 466 HIS B 577 ASN B 780 HIS A 466 HIS A 577 ASN A 780 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080964 restraints weight = 25130.997| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 4.21 r_work: 0.3079 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12920 Z= 0.080 Angle : 0.442 6.036 17574 Z= 0.221 Chirality : 0.040 0.135 1916 Planarity : 0.004 0.043 2290 Dihedral : 2.875 12.582 1744 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.36 % Allowed : 6.80 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.37 (0.21), residues: 1586 helix: 2.36 (0.40), residues: 184 sheet: 0.33 (0.26), residues: 412 loop : -1.06 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 906 TYR 0.019 0.001 TYR A 676 PHE 0.007 0.001 PHE B 785 TRP 0.006 0.000 TRP B 489 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.08 (12920) covalent geometry : angle 0.44224 / 0.22 (17574) hydrogen bonds : bond 0.02870 / 1.96 ( 340) hydrogen bonds : angle 4.31062 / 2.88 ( 900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: B 441 MET cc_start: 0.9102 (tmm) cc_final: 0.8739 (tmm) REVERT: B 607 MET cc_start: 0.7477 (tpp) cc_final: 0.7268 (tpt) REVERT: A 441 MET cc_start: 0.9106 (tmm) cc_final: 0.8761 (tmm) REVERT: A 521 TYR cc_start: 0.8067 (p90) cc_final: 0.7738 (p90) REVERT: A 898 MET cc_start: 0.8356 (mmt) cc_final: 0.7934 (mmt) outliers start: 5 outliers final: 1 residues processed: 57 average time/residue: 0.0900 time to fit residues: 8.4603 Evaluate side-chains 48 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 684 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 49 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 HIS A 899 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.114256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.073582 restraints weight = 25288.423| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 4.22 r_work: 0.2941 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12920 Z= 0.146 Angle : 0.516 5.384 17574 Z= 0.266 Chirality : 0.042 0.146 1916 Planarity : 0.004 0.044 2290 Dihedral : 3.445 13.728 1744 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.94 % Allowed : 8.10 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.65 (0.21), residues: 1586 helix: 1.29 (0.39), residues: 204 sheet: 0.30 (0.26), residues: 428 loop : -1.21 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 804 TYR 0.016 0.001 TYR B 749 PHE 0.014 0.001 PHE B 785 TRP 0.008 0.001 TRP B 825 HIS 0.006 0.001 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (12920) covalent geometry : angle 0.51568 / 0.27 (17574) hydrogen bonds : bond 0.04754 / 3.19 ( 340) hydrogen bonds : angle 4.37712 / 2.96 ( 900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.453 Fit side-chains REVERT: B 144 ARG cc_start: 0.8046 (ttt180) cc_final: 0.7842 (ttp80) REVERT: B 441 MET cc_start: 0.9138 (tmm) cc_final: 0.8726 (tmm) REVERT: B 607 MET cc_start: 0.7582 (tpp) cc_final: 0.7337 (tpt) REVERT: A 441 MET cc_start: 0.9136 (tmm) cc_final: 0.8737 (tmm) REVERT: A 521 TYR cc_start: 0.8094 (p90) cc_final: 0.7739 (p90) REVERT: A 607 MET cc_start: 0.7607 (tpt) cc_final: 0.7361 (tpt) REVERT: A 898 MET cc_start: 0.8653 (mmt) cc_final: 0.8225 (mmt) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 0.0792 time to fit residues: 7.7915 Evaluate side-chains 51 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 521 TYR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 135 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 899 HIS A 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.115084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.074232 restraints weight = 25226.740| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.29 r_work: 0.2954 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12920 Z= 0.107 Angle : 0.476 9.270 17574 Z= 0.242 Chirality : 0.042 0.140 1916 Planarity : 0.004 0.041 2290 Dihedral : 3.312 13.422 1744 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.51 % Allowed : 9.41 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.66 (0.21), residues: 1586 helix: 1.45 (0.39), residues: 200 sheet: 0.34 (0.26), residues: 426 loop : -1.27 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.010 0.001 TYR A 676 PHE 0.010 0.001 PHE B 785 TRP 0.007 0.001 TRP B 825 HIS 0.005 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (12920) covalent geometry : angle 0.47645 / 0.24 (17574) hydrogen bonds : bond 0.03593 / 2.39 ( 340) hydrogen bonds : angle 4.14827 / 2.80 ( 900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.440 Fit side-chains REVERT: B 144 ARG cc_start: 0.8078 (ttt180) cc_final: 0.7859 (ttp80) REVERT: B 441 MET cc_start: 0.9142 (tmm) cc_final: 0.8708 (tmm) REVERT: B 607 MET cc_start: 0.7596 (tpp) cc_final: 0.7371 (tpt) REVERT: B 834 MET cc_start: 0.7358 (ptp) cc_final: 0.7101 (ptp) REVERT: A 441 MET cc_start: 0.9156 (tmm) cc_final: 0.8745 (tmm) REVERT: A 521 TYR cc_start: 0.8134 (p90) cc_final: 0.7764 (p90) REVERT: A 607 MET cc_start: 0.7523 (tpt) cc_final: 0.7278 (tpt) REVERT: A 898 MET cc_start: 0.8531 (mmt) cc_final: 0.8107 (mmt) outliers start: 7 outliers final: 7 residues processed: 52 average time/residue: 0.0883 time to fit residues: 7.5453 Evaluate side-chains 53 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 521 TYR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 74 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 83 optimal weight: 0.0050 chunk 47 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 564 ASN A 564 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.112051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.071335 restraints weight = 25532.796| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 4.28 r_work: 0.2889 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12920 Z= 0.197 Angle : 0.560 7.784 17574 Z= 0.291 Chirality : 0.043 0.143 1916 Planarity : 0.004 0.048 2290 Dihedral : 3.820 14.548 1744 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.80 % Allowed : 10.35 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.93 (0.21), residues: 1586 helix: 1.01 (0.38), residues: 200 sheet: 0.19 (0.25), residues: 442 loop : -1.44 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 421 TYR 0.015 0.001 TYR B 749 PHE 0.016 0.001 PHE A 868 TRP 0.009 0.001 TRP B 825 HIS 0.006 0.002 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (12920) covalent geometry : angle 0.56031 / 0.29 (17574) hydrogen bonds : bond 0.05171 / 3.44 ( 340) hydrogen bonds : angle 4.44909 / 3.02 ( 900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.593 Fit side-chains REVERT: B 144 ARG cc_start: 0.7985 (ttt180) cc_final: 0.7774 (ttp80) REVERT: B 441 MET cc_start: 0.9194 (tmm) cc_final: 0.8770 (tmm) REVERT: B 607 MET cc_start: 0.7792 (tpp) cc_final: 0.7536 (tpp) REVERT: A 441 MET cc_start: 0.9170 (tmm) cc_final: 0.8755 (tmm) REVERT: A 521 TYR cc_start: 0.8229 (p90) cc_final: 0.7973 (p90) outliers start: 11 outliers final: 8 residues processed: 56 average time/residue: 0.0780 time to fit residues: 7.4310 Evaluate side-chains 55 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 521 TYR Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 106 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 23 optimal weight: 0.0670 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.114501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.073870 restraints weight = 25026.555| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 4.21 r_work: 0.2950 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12920 Z= 0.093 Angle : 0.472 6.907 17574 Z= 0.240 Chirality : 0.041 0.140 1916 Planarity : 0.004 0.042 2290 Dihedral : 3.419 14.750 1744 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.65 % Allowed : 10.71 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.79 (0.21), residues: 1586 helix: 1.40 (0.39), residues: 200 sheet: 0.11 (0.26), residues: 438 loop : -1.31 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.009 0.001 TYR B 749 PHE 0.010 0.001 PHE B 785 TRP 0.008 0.001 TRP B 722 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.09 (12920) covalent geometry : angle 0.47152 / 0.24 (17574) hydrogen bonds : bond 0.03263 / 2.15 ( 340) hydrogen bonds : angle 4.11830 / 2.78 ( 900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.396 Fit side-chains REVERT: B 144 ARG cc_start: 0.8095 (ttt180) cc_final: 0.7881 (ttp80) REVERT: B 441 MET cc_start: 0.9191 (tmm) cc_final: 0.8767 (tmm) REVERT: B 607 MET cc_start: 0.7798 (tpp) cc_final: 0.7580 (tpp) REVERT: A 441 MET cc_start: 0.9164 (tmm) cc_final: 0.8749 (tmm) REVERT: A 521 TYR cc_start: 0.8167 (p90) cc_final: 0.7917 (p90) REVERT: A 898 MET cc_start: 0.8516 (mmt) cc_final: 0.8066 (mmt) outliers start: 9 outliers final: 6 residues processed: 56 average time/residue: 0.0735 time to fit residues: 6.9992 Evaluate side-chains 52 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 121 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 24 optimal weight: 0.0040 chunk 118 optimal weight: 0.0000 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 466 HIS A 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.114601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.074088 restraints weight = 25167.062| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.21 r_work: 0.2951 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12920 Z= 0.099 Angle : 0.473 5.729 17574 Z= 0.241 Chirality : 0.041 0.139 1916 Planarity : 0.004 0.041 2290 Dihedral : 3.345 13.373 1744 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.58 % Allowed : 11.07 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.71 (0.21), residues: 1586 helix: 1.52 (0.39), residues: 200 sheet: 0.17 (0.26), residues: 438 loop : -1.28 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.009 0.001 TYR B 749 PHE 0.010 0.001 PHE B 785 TRP 0.007 0.001 TRP B 722 HIS 0.005 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (12920) covalent geometry : angle 0.47260 / 0.24 (17574) hydrogen bonds : bond 0.03386 / 2.23 ( 340) hydrogen bonds : angle 4.03551 / 2.73 ( 900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.477 Fit side-chains REVERT: B 144 ARG cc_start: 0.7942 (ttt180) cc_final: 0.7726 (ttp80) REVERT: B 441 MET cc_start: 0.9181 (tmm) cc_final: 0.8745 (tmm) REVERT: B 834 MET cc_start: 0.7496 (ptp) cc_final: 0.7281 (ptp) REVERT: A 415 MET cc_start: 0.6905 (mmm) cc_final: 0.6479 (mmp) REVERT: A 441 MET cc_start: 0.9168 (tmm) cc_final: 0.8751 (tmm) REVERT: A 521 TYR cc_start: 0.8237 (p90) cc_final: 0.7996 (p90) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.0835 time to fit residues: 7.3840 Evaluate side-chains 52 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 136 optimal weight: 0.0020 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 128 optimal weight: 0.0170 overall best weight: 0.7028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 466 HIS A 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.115184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.074588 restraints weight = 24974.269| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.21 r_work: 0.2964 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12920 Z= 0.090 Angle : 0.465 9.384 17574 Z= 0.235 Chirality : 0.041 0.138 1916 Planarity : 0.004 0.040 2290 Dihedral : 3.243 13.069 1744 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.65 % Allowed : 11.22 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.64 (0.21), residues: 1586 helix: 1.64 (0.39), residues: 200 sheet: 0.22 (0.26), residues: 438 loop : -1.25 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 421 TYR 0.007 0.001 TYR A 676 PHE 0.010 0.001 PHE B 785 TRP 0.008 0.001 TRP A 722 HIS 0.006 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.09 (12920) covalent geometry : angle 0.46503 / 0.23 (17574) hydrogen bonds : bond 0.03060 / 2.02 ( 340) hydrogen bonds : angle 3.94366 / 2.66 ( 900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.312 Fit side-chains REVERT: B 144 ARG cc_start: 0.8058 (ttt180) cc_final: 0.7845 (ttp80) REVERT: B 441 MET cc_start: 0.9187 (tmm) cc_final: 0.8755 (tmm) REVERT: B 834 MET cc_start: 0.7456 (ptp) cc_final: 0.7245 (ptp) REVERT: A 415 MET cc_start: 0.6836 (mmm) cc_final: 0.6432 (mmp) REVERT: A 441 MET cc_start: 0.9167 (tmm) cc_final: 0.8756 (tmm) REVERT: A 521 TYR cc_start: 0.8238 (p90) cc_final: 0.7996 (p90) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.0767 time to fit residues: 7.0023 Evaluate side-chains 53 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 92 optimal weight: 3.9990 chunk 114 optimal weight: 0.0870 chunk 125 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 466 HIS A 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.114899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074268 restraints weight = 25080.713| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.21 r_work: 0.2961 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12920 Z= 0.095 Angle : 0.468 8.458 17574 Z= 0.237 Chirality : 0.041 0.138 1916 Planarity : 0.004 0.040 2290 Dihedral : 3.247 12.956 1744 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.58 % Allowed : 11.65 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.62 (0.21), residues: 1586 helix: 1.67 (0.39), residues: 200 sheet: 0.23 (0.26), residues: 438 loop : -1.24 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 421 TYR 0.008 0.001 TYR B 749 PHE 0.010 0.001 PHE B 785 TRP 0.007 0.001 TRP B 722 HIS 0.006 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.09 (12920) covalent geometry : angle 0.46766 / 0.24 (17574) hydrogen bonds : bond 0.03241 / 2.13 ( 340) hydrogen bonds : angle 3.91847 / 2.65 ( 900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.370 Fit side-chains REVERT: B 144 ARG cc_start: 0.8052 (ttt180) cc_final: 0.7844 (ttp80) REVERT: B 441 MET cc_start: 0.9190 (tmm) cc_final: 0.8762 (tmm) REVERT: B 834 MET cc_start: 0.7491 (ptp) cc_final: 0.7285 (ptp) REVERT: A 415 MET cc_start: 0.6909 (mmm) cc_final: 0.6502 (mmp) REVERT: A 441 MET cc_start: 0.9191 (tmm) cc_final: 0.8795 (tmm) REVERT: A 521 TYR cc_start: 0.8276 (p90) cc_final: 0.7939 (p90) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.0796 time to fit residues: 7.5201 Evaluate side-chains 54 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 118 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 chunk 13 optimal weight: 0.0370 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 87 optimal weight: 0.0770 chunk 97 optimal weight: 0.0970 chunk 80 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.116457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.076108 restraints weight = 25091.966| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 4.21 r_work: 0.3001 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12920 Z= 0.079 Angle : 0.452 8.677 17574 Z= 0.226 Chirality : 0.041 0.135 1916 Planarity : 0.004 0.039 2290 Dihedral : 3.080 12.318 1744 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.43 % Allowed : 11.87 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.51 (0.21), residues: 1586 helix: 1.83 (0.39), residues: 200 sheet: 0.34 (0.27), residues: 420 loop : -1.18 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 494 TYR 0.007 0.001 TYR A 645 PHE 0.009 0.001 PHE B 785 TRP 0.008 0.001 TRP A 722 HIS 0.007 0.000 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.08 (12920) covalent geometry : angle 0.45158 / 0.23 (17574) hydrogen bonds : bond 0.02531 / 1.67 ( 340) hydrogen bonds : angle 3.79814 / 2.55 ( 900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: B 144 ARG cc_start: 0.8028 (ttt180) cc_final: 0.7822 (ttp80) REVERT: B 441 MET cc_start: 0.9189 (tmm) cc_final: 0.8746 (tmm) REVERT: B 834 MET cc_start: 0.7373 (ptp) cc_final: 0.7167 (ptp) REVERT: A 415 MET cc_start: 0.6692 (mmm) cc_final: 0.6297 (mmp) REVERT: A 441 MET cc_start: 0.9187 (tmm) cc_final: 0.8801 (tmm) REVERT: A 521 TYR cc_start: 0.8197 (p90) cc_final: 0.7868 (p90) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.0903 time to fit residues: 8.1851 Evaluate side-chains 55 residues out of total 1382 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 466 HIS A 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.113105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072440 restraints weight = 25309.067| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 4.21 r_work: 0.2920 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12920 Z= 0.147 Angle : 0.513 8.114 17574 Z= 0.263 Chirality : 0.042 0.141 1916 Planarity : 0.004 0.045 2290 Dihedral : 3.475 13.391 1744 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.43 % Allowed : 12.01 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.69 (0.21), residues: 1586 helix: 1.48 (0.38), residues: 200 sheet: 0.27 (0.26), residues: 448 loop : -1.32 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 421 TYR 0.014 0.001 TYR B 749 PHE 0.012 0.001 PHE B 785 TRP 0.008 0.001 TRP B 430 HIS 0.006 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (12920) covalent geometry : angle 0.51305 / 0.26 (17574) hydrogen bonds : bond 0.04353 / 2.88 ( 340) hydrogen bonds : angle 4.07783 / 2.75 ( 900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2533.47 seconds wall clock time: 43 minutes 56.31 seconds (2636.31 seconds total)