Starting phenix.real_space_refine on Sun Aug 24 17:26:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ae1_15378/08_2025/8ae1_15378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ae1_15378/08_2025/8ae1_15378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ae1_15378/08_2025/8ae1_15378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ae1_15378/08_2025/8ae1_15378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ae1_15378/08_2025/8ae1_15378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ae1_15378/08_2025/8ae1_15378.map" } resolution = 3.25 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= 0.003 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: 5 Type Number sf(0) Gaussians Ca 18 9.91 5 S 18 5.16 5 C 13332 2.51 5 N 3819 2.21 5 O 4317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21504 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7162 Classifications: {'peptide': 953} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 922} Chain: "B" Number of atoms: 7162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7162 Classifications: {'peptide': 953} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 922} Chain: "C" Number of atoms: 7162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7162 Classifications: {'peptide': 953} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 922} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 4.10, per 1000 atoms: 0.19 Number of scatterers: 21504 At special positions: 0 Unit cell: (168.168, 157.248, 136.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 18 19.99 S 18 16.00 O 4317 8.00 N 3819 7.00 C 13332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 896 " - pdb=" SG CYS A 929 " distance=2.03 Simple disulfide: pdb=" SG CYS B 896 " - pdb=" SG CYS B 929 " distance=2.03 Simple disulfide: pdb=" SG CYS C 896 " - pdb=" SG CYS C 929 " 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: 1.13 Conformation dependent library (CDL) restraints added in 760.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 34 sheets defined 8.9% alpha, 52.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 217 through 252 removed outlier: 3.650A pdb=" N ARG A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 4.231A pdb=" N PHE A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.589A pdb=" N LEU A 325 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.907A pdb=" N TYR A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.577A pdb=" N THR A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 456' Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 784 through 788 removed outlier: 3.847A pdb=" N ASN A 787 " --> pdb=" O ASP A 784 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 788 " --> pdb=" O ASN A 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 784 through 788' Processing helix chain 'A' and resid 870 through 875 removed outlier: 3.922A pdb=" N GLY A 875 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 924 removed outlier: 3.501A pdb=" N GLN A 923 " --> pdb=" O ASN A 920 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 924 " --> pdb=" O LEU A 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 920 through 924' Processing helix chain 'B' and resid 217 through 252 removed outlier: 3.693A pdb=" N ARG B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 4.199A pdb=" N PHE B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.627A pdb=" N LEU B 325 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.778A pdb=" N TYR B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.557A pdb=" N THR B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 456' Processing helix chain 'B' and resid 591 through 596 removed outlier: 3.501A pdb=" N GLN B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.908A pdb=" N ASN B 787 " --> pdb=" O ASP B 784 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 788 " --> pdb=" O ASN B 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 784 through 788' Processing helix chain 'B' and resid 870 through 875 removed outlier: 3.887A pdb=" N GLY B 875 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 924 removed outlier: 3.608A pdb=" N SER B 924 " --> pdb=" O LEU B 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 252 removed outlier: 3.601A pdb=" N ARG C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 removed outlier: 4.219A pdb=" N PHE C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.648A pdb=" N LEU C 325 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.738A pdb=" N TYR C 354 " --> pdb=" O PRO C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.586A pdb=" N THR C 455 " --> pdb=" O THR C 451 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 456 " --> pdb=" O GLY C 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 456' Processing helix chain 'C' and resid 591 through 596 Processing helix chain 'C' and resid 688 through 693 Processing helix chain 'C' and resid 784 through 788 removed outlier: 3.870A pdb=" N ASN C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 788 " --> pdb=" O ASN C 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 784 through 788' Processing helix chain 'C' and resid 870 through 875 removed outlier: 3.994A pdb=" N GLY C 875 " --> pdb=" O LEU C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 924 removed outlier: 3.618A pdb=" N SER C 924 " --> pdb=" O LEU C 921 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 254 through 256 Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 384 removed outlier: 4.176A pdb=" N GLY A 382 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER A 265 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR A 384 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY A 263 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 262 " --> pdb=" O TYR A1163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A1163 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A1060 " --> pdb=" O GLY A1082 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A1035 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A1016 " --> pdb=" O SER A 998 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 996 " --> pdb=" O GLY A1018 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 980 " --> pdb=" O PHE A 999 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 953 " --> pdb=" O HIS A 939 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 850 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ALA A 832 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG A 816 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL A 834 " --> pdb=" O SER A 814 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER A 814 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ARG A 836 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LEU A 812 " --> pdb=" O ARG A 836 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ALA A 838 " --> pdb=" O ASN A 810 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASN A 810 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLN A 840 " --> pdb=" O THR A 808 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N THR A 808 " --> pdb=" O GLN A 840 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ASP A 842 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ARG A 806 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 809 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 792 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR A 790 " --> pdb=" O ASP A 813 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 793 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 774 " --> pdb=" O GLY A 793 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 795 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY A 772 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN A 755 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 682 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY A 757 " --> pdb=" O TYR A 680 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR A 680 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 759 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 678 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS A 761 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 603 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL A 562 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 522 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 500 " --> pdb=" O GLY A 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 389 removed outlier: 4.268A pdb=" N ILE A 262 " --> pdb=" O TYR A1163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A1163 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A1060 " --> pdb=" O GLY A1082 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A1035 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A1016 " --> pdb=" O SER A 998 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 996 " --> pdb=" O GLY A1018 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 980 " --> pdb=" O PHE A 999 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 953 " --> pdb=" O HIS A 939 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 850 " --> pdb=" O GLY A 938 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 346 removed outlier: 3.950A pdb=" N SER A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA6, first strand: chain 'A' and resid 426 through 428 Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 438 Processing sheet with id=AA8, first strand: chain 'A' and resid 465 through 467 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 476 Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 506 Processing sheet with id=AB2, first strand: chain 'A' and resid 725 through 729 Processing sheet with id=AB3, first strand: chain 'A' and resid 879 through 880 removed outlier: 3.535A pdb=" N ARG A 891 " --> pdb=" O SER A 880 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.541A pdb=" N ASP A 972 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1088 through 1091 Processing sheet with id=AB6, first strand: chain 'A' and resid 1165 through 1166 Processing sheet with id=AB7, first strand: chain 'B' and resid 378 through 384 removed outlier: 4.102A pdb=" N GLY B 382 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER B 265 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR B 384 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY B 263 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 262 " --> pdb=" O TYR B1163 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B1163 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B1060 " --> pdb=" O GLY B1082 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B1053 " --> pdb=" O ASN B1046 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE B1035 " --> pdb=" O THR B1023 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B1016 " --> pdb=" O SER B 998 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 996 " --> pdb=" O GLY B1018 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 980 " --> pdb=" O PHE B 999 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 953 " --> pdb=" O HIS B 939 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 932 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 850 " --> pdb=" O GLY B 938 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ALA B 832 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG B 816 " --> pdb=" O ALA B 832 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL B 834 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER B 814 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ARG B 836 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU B 812 " --> pdb=" O ARG B 836 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ALA B 838 " --> pdb=" O ASN B 810 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ASN B 810 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N GLN B 840 " --> pdb=" O THR B 808 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR B 808 " --> pdb=" O GLN B 840 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASP B 842 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ARG B 806 " --> pdb=" O ASP B 842 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 809 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 792 " --> pdb=" O THR B 811 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR B 790 " --> pdb=" O ASP B 813 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 795 " --> pdb=" O GLY B 772 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 772 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B 769 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA B 763 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B 675 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN B 765 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL B 673 " --> pdb=" O ASN B 765 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 603 " --> pdb=" O ARG B 630 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL B 562 " --> pdb=" O ARG B 549 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 522 " --> pdb=" O GLY B 500 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 500 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 387 through 389 removed outlier: 4.223A pdb=" N ILE B 262 " --> pdb=" O TYR B1163 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B1163 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B1060 " --> pdb=" O GLY B1082 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B1053 " --> pdb=" O ASN B1046 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE B1035 " --> pdb=" O THR B1023 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B1016 " --> pdb=" O SER B 998 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 996 " --> pdb=" O GLY B1018 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 980 " --> pdb=" O PHE B 999 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 953 " --> pdb=" O HIS B 939 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 932 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B 850 " --> pdb=" O GLY B 938 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 342 through 346 removed outlier: 3.902A pdb=" N SER B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 465 through 467 Processing sheet with id=AC2, first strand: chain 'B' and resid 473 through 476 removed outlier: 7.416A pdb=" N PHE C 425 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR C 394 " --> pdb=" O PHE C 425 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 505 through 506 Processing sheet with id=AC4, first strand: chain 'B' and resid 725 through 729 Processing sheet with id=AC5, first strand: chain 'B' and resid 879 through 880 Processing sheet with id=AC6, first strand: chain 'B' and resid 962 through 963 removed outlier: 3.567A pdb=" N ASP B 972 " --> pdb=" O VAL B 962 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1088 through 1091 Processing sheet with id=AC8, first strand: chain 'B' and resid 1165 through 1166 Processing sheet with id=AC9, first strand: chain 'C' and resid 378 through 384 removed outlier: 4.220A pdb=" N GLY C 382 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER C 265 " --> pdb=" O GLY C 382 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR C 384 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY C 263 " --> pdb=" O THR C 384 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE C 262 " --> pdb=" O TYR C1163 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR C1163 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C1035 " --> pdb=" O THR C1023 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C1016 " --> pdb=" O SER C 998 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 996 " --> pdb=" O GLY C1018 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 980 " --> pdb=" O PHE C 999 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 953 " --> pdb=" O HIS C 939 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 932 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 850 " --> pdb=" O GLY C 938 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA C 832 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG C 816 " --> pdb=" O ALA C 832 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N VAL C 834 " --> pdb=" O SER C 814 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER C 814 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ARG C 836 " --> pdb=" O LEU C 812 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N LEU C 812 " --> pdb=" O ARG C 836 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALA C 838 " --> pdb=" O ASN C 810 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ASN C 810 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLN C 840 " --> pdb=" O THR C 808 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR C 808 " --> pdb=" O GLN C 840 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ASP C 842 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG C 806 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 809 " --> pdb=" O GLY C 794 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR C 790 " --> pdb=" O ASP C 813 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 795 " --> pdb=" O GLY C 772 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 772 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 769 " --> pdb=" O LEU C 766 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA C 763 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU C 675 " --> pdb=" O ALA C 763 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASN C 765 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 673 " --> pdb=" O ASN C 765 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 603 " --> pdb=" O ARG C 630 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL C 562 " --> pdb=" O ARG C 549 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C 522 " --> pdb=" O GLY C 500 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 500 " --> pdb=" O GLY C 522 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 387 through 389 removed outlier: 4.258A pdb=" N ILE C 262 " --> pdb=" O TYR C1163 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR C1163 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C1035 " --> pdb=" O THR C1023 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C1016 " --> pdb=" O SER C 998 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 996 " --> pdb=" O GLY C1018 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 980 " --> pdb=" O PHE C 999 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 953 " --> pdb=" O HIS C 939 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 932 " --> pdb=" O ARG C 856 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 850 " --> pdb=" O GLY C 938 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.948A pdb=" N SER C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AD4, first strand: chain 'C' and resid 725 through 729 Processing sheet with id=AD5, first strand: chain 'C' and resid 879 through 880 Processing sheet with id=AD6, first strand: chain 'C' and resid 962 through 963 removed outlier: 3.526A pdb=" N ASP C 972 " --> pdb=" O VAL C 962 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1088 through 1091 1312 hydrogen bonds defined for protein. 3597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7431 1.34 - 1.46: 4899 1.46 - 1.58: 9552 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 21912 Sorted by residual: bond pdb=" CG PRO B 494 " pdb=" CD PRO B 494 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.70e-02 1.37e+03 1.12e+00 bond pdb=" CG PRO A 494 " pdb=" CD PRO A 494 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.09e+00 bond pdb=" CA THR B1001 " pdb=" CB THR B1001 " ideal model delta sigma weight residual 1.525 1.543 -0.018 1.77e-02 3.19e+03 1.07e+00 bond pdb=" CG PRO C 494 " pdb=" CD PRO C 494 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.05e+00 bond pdb=" CA VAL A1029 " pdb=" CB VAL A1029 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 9.98e-01 ... (remaining 21907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 29203 1.37 - 2.73: 480 2.73 - 4.10: 85 4.10 - 5.47: 11 5.47 - 6.84: 2 Bond angle restraints: 29781 Sorted by residual: angle pdb=" C ALA C 634 " pdb=" N ASN C 635 " pdb=" CA ASN C 635 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.01e+00 angle pdb=" C LEU A1139 " pdb=" N ASN A1140 " pdb=" CA ASN A1140 " ideal model delta sigma weight residual 123.91 128.13 -4.22 1.66e+00 3.63e-01 6.47e+00 angle pdb=" N ASP B 513 " pdb=" CA ASP B 513 " pdb=" C ASP B 513 " ideal model delta sigma weight residual 109.71 106.22 3.49 1.41e+00 5.03e-01 6.12e+00 angle pdb=" C LEU B1139 " pdb=" N ASN B1140 " pdb=" CA ASN B1140 " ideal model delta sigma weight residual 123.91 127.93 -4.02 1.66e+00 3.63e-01 5.88e+00 angle pdb=" C ALA A 634 " pdb=" N ASN A 635 " pdb=" CA ASN A 635 " ideal model delta sigma weight residual 121.54 126.09 -4.55 1.91e+00 2.74e-01 5.67e+00 ... (remaining 29776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 11550 17.00 - 34.01: 869 34.01 - 51.01: 176 51.01 - 68.01: 25 68.01 - 85.01: 19 Dihedral angle restraints: 12639 sinusoidal: 4656 harmonic: 7983 Sorted by residual: dihedral pdb=" CA VAL C 511 " pdb=" C VAL C 511 " pdb=" N PHE C 512 " pdb=" CA PHE C 512 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA VAL A 511 " pdb=" C VAL A 511 " pdb=" N PHE A 512 " pdb=" CA PHE A 512 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA PRO A 469 " pdb=" C PRO A 469 " pdb=" N ALA A 470 " pdb=" CA ALA A 470 " ideal model delta harmonic sigma weight residual -180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 12636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2365 0.041 - 0.082: 558 0.082 - 0.123: 278 0.123 - 0.164: 17 0.164 - 0.205: 4 Chirality restraints: 3222 Sorted by residual: chirality pdb=" CB ILE B 693 " pdb=" CA ILE B 693 " pdb=" CG1 ILE B 693 " pdb=" CG2 ILE B 693 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASN C1140 " pdb=" N ASN C1140 " pdb=" C ASN C1140 " pdb=" CB ASN C1140 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ASN B1140 " pdb=" N ASN B1140 " pdb=" C ASN B1140 " pdb=" CB ASN B1140 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 3219 not shown) Planarity restraints: 4044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 512 " 0.013 2.00e-02 2.50e+03 1.06e-02 1.97e+00 pdb=" CG PHE A 512 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 512 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 512 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 512 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 512 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 512 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 512 " -0.012 2.00e-02 2.50e+03 9.90e-03 1.71e+00 pdb=" CG PHE C 512 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 512 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 512 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 512 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 512 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 512 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 468 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 469 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.017 5.00e-02 4.00e+02 ... (remaining 4041 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 823 2.71 - 3.26: 20197 3.26 - 3.81: 32447 3.81 - 4.35: 42220 4.35 - 4.90: 75873 Nonbonded interactions: 171560 Sorted by model distance: nonbonded pdb=" O CYS B 896 " pdb=" ND2 ASN B 900 " model vdw 2.165 3.120 nonbonded pdb=" O CYS C 896 " pdb=" ND2 ASN C 900 " model vdw 2.174 3.120 nonbonded pdb=" OG SER B 267 " pdb=" O PHE B 311 " model vdw 2.174 3.040 nonbonded pdb=" O CYS A 896 " pdb=" ND2 ASN A 900 " model vdw 2.174 3.120 nonbonded pdb=" OG SER C 267 " pdb=" O PHE C 311 " model vdw 2.174 3.040 ... (remaining 171555 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 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.810 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 0.029 21915 Z= 0.110 Angle : 0.469 6.836 29787 Z= 0.261 Chirality : 0.044 0.205 3222 Planarity : 0.003 0.041 4044 Dihedral : 12.787 85.014 7674 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -1.01 (0.16), residues: 2853 helix: -0.65 (0.39), residues: 183 sheet: -0.39 (0.15), residues: 1236 loop : -0.83 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 891 TYR 0.010 0.001 TYR A 890 PHE 0.024 0.001 PHE A 512 TRP 0.001 0.000 TRP A 538 HIS 0.003 0.001 HIS B 939 Details of bonding type rmsd covalent geometry : bond 0.00234 (21912) covalent geometry : angle 0.46936 (29781) SS BOND : bond 0.00038 ( 3) SS BOND : angle 0.45750 ( 6) hydrogen bonds : bond 0.24560 ( 963) hydrogen bonds : angle 9.05413 ( 3597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.814 Fit side-chains REVERT: A 789 MET cc_start: 0.9144 (ttp) cc_final: 0.8938 (ttt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1458 time to fit residues: 16.6002 Evaluate side-chains 44 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.090960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.071793 restraints weight = 33902.815| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.03 r_work: 0.2812 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21915 Z= 0.192 Angle : 0.569 5.805 29787 Z= 0.321 Chirality : 0.047 0.167 3222 Planarity : 0.004 0.045 4044 Dihedral : 4.314 19.545 3207 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.23 % Allowed : 4.14 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.59 (0.16), residues: 2853 helix: 0.43 (0.42), residues: 168 sheet: -0.05 (0.15), residues: 1179 loop : -0.70 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 519 TYR 0.016 0.001 TYR C1053 PHE 0.023 0.002 PHE A 512 TRP 0.003 0.001 TRP C 538 HIS 0.005 0.002 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00441 (21912) covalent geometry : angle 0.56879 (29781) SS BOND : bond 0.00066 ( 3) SS BOND : angle 0.51193 ( 6) hydrogen bonds : bond 0.04943 ( 963) hydrogen bonds : angle 5.40441 ( 3597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.716 Fit side-chains REVERT: B 1074 THR cc_start: 0.8930 (m) cc_final: 0.8710 (p) REVERT: C 1094 ASP cc_start: 0.8043 (t0) cc_final: 0.7833 (t0) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.1658 time to fit residues: 14.5623 Evaluate side-chains 47 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain B residue 990 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 176 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 260 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 273 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 ASN C 810 ASN C1112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.090389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.071220 restraints weight = 34244.628| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.04 r_work: 0.2801 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21915 Z= 0.195 Angle : 0.546 5.653 29787 Z= 0.306 Chirality : 0.046 0.167 3222 Planarity : 0.004 0.047 4044 Dihedral : 4.404 19.863 3207 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.41 % Allowed : 7.56 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.57 (0.16), residues: 2853 helix: 0.60 (0.42), residues: 168 sheet: -0.06 (0.15), residues: 1191 loop : -0.69 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 869 TYR 0.015 0.001 TYR A 837 PHE 0.025 0.002 PHE A 512 TRP 0.003 0.001 TRP A 538 HIS 0.006 0.002 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00458 (21912) covalent geometry : angle 0.54620 (29781) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.20766 ( 6) hydrogen bonds : bond 0.04558 ( 963) hydrogen bonds : angle 4.90877 ( 3597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.871 Fit side-chains REVERT: A 585 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: B 585 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8691 (tt0) REVERT: C 585 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: C 1094 ASP cc_start: 0.8072 (t0) cc_final: 0.7823 (t0) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 0.1582 time to fit residues: 14.8135 Evaluate side-chains 50 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain C residue 585 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 271 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.090850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.071704 restraints weight = 34033.387| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.04 r_work: 0.2810 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21915 Z= 0.163 Angle : 0.522 5.253 29787 Z= 0.292 Chirality : 0.045 0.160 3222 Planarity : 0.004 0.047 4044 Dihedral : 4.320 18.814 3207 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.55 % Allowed : 9.65 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.52 (0.16), residues: 2853 helix: 0.72 (0.42), residues: 168 sheet: -0.02 (0.15), residues: 1191 loop : -0.67 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 415 TYR 0.013 0.001 TYR A 837 PHE 0.019 0.001 PHE A 512 TRP 0.002 0.001 TRP C 538 HIS 0.005 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00379 (21912) covalent geometry : angle 0.52161 (29781) SS BOND : bond 0.00037 ( 3) SS BOND : angle 0.17207 ( 6) hydrogen bonds : bond 0.04008 ( 963) hydrogen bonds : angle 4.68768 ( 3597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.659 Fit side-chains REVERT: A 585 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: B 1074 THR cc_start: 0.8964 (m) cc_final: 0.8684 (p) REVERT: C 434 ASP cc_start: 0.8033 (t0) cc_final: 0.7826 (t0) REVERT: C 1094 ASP cc_start: 0.8054 (t0) cc_final: 0.7821 (t0) outliers start: 12 outliers final: 3 residues processed: 62 average time/residue: 0.1575 time to fit residues: 15.4956 Evaluate side-chains 52 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain B residue 990 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 254 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 271 optimal weight: 0.0060 chunk 25 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.072681 restraints weight = 33782.146| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.05 r_work: 0.2827 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21915 Z= 0.127 Angle : 0.495 5.003 29787 Z= 0.277 Chirality : 0.045 0.159 3222 Planarity : 0.003 0.046 4044 Dihedral : 4.148 17.245 3207 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.96 % Allowed : 10.06 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.43 (0.16), residues: 2853 helix: 0.91 (0.43), residues: 168 sheet: 0.06 (0.15), residues: 1179 loop : -0.65 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 415 TYR 0.012 0.001 TYR A 837 PHE 0.015 0.001 PHE A 512 TRP 0.002 0.000 TRP C 538 HIS 0.004 0.001 HIS B 939 Details of bonding type rmsd covalent geometry : bond 0.00288 (21912) covalent geometry : angle 0.49550 (29781) SS BOND : bond 0.00020 ( 3) SS BOND : angle 0.09869 ( 6) hydrogen bonds : bond 0.03636 ( 963) hydrogen bonds : angle 4.50248 ( 3597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.842 Fit side-chains REVERT: B 1074 THR cc_start: 0.8949 (m) cc_final: 0.8682 (p) REVERT: C 434 ASP cc_start: 0.7945 (t0) cc_final: 0.7671 (t0) REVERT: C 1094 ASP cc_start: 0.8034 (t0) cc_final: 0.7814 (t0) outliers start: 21 outliers final: 8 residues processed: 72 average time/residue: 0.1541 time to fit residues: 17.9841 Evaluate side-chains 57 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 766 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 75 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 205 optimal weight: 0.0970 chunk 253 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.090287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.071132 restraints weight = 34128.694| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.04 r_work: 0.2800 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21915 Z= 0.208 Angle : 0.539 4.889 29787 Z= 0.302 Chirality : 0.047 0.194 3222 Planarity : 0.004 0.050 4044 Dihedral : 4.372 18.861 3207 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.00 % Allowed : 11.02 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.52 (0.16), residues: 2853 helix: 0.77 (0.42), residues: 168 sheet: -0.02 (0.15), residues: 1191 loop : -0.69 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 415 TYR 0.016 0.001 TYR A 837 PHE 0.020 0.002 PHE A 512 TRP 0.003 0.001 TRP A 538 HIS 0.006 0.002 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00493 (21912) covalent geometry : angle 0.53937 (29781) SS BOND : bond 0.00022 ( 3) SS BOND : angle 0.17222 ( 6) hydrogen bonds : bond 0.04011 ( 963) hydrogen bonds : angle 4.55972 ( 3597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.697 Fit side-chains REVERT: A 585 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: A 785 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8342 (t0) REVERT: C 434 ASP cc_start: 0.7965 (t0) cc_final: 0.7656 (t0) REVERT: C 1022 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7984 (mtm-85) REVERT: C 1094 ASP cc_start: 0.8064 (t0) cc_final: 0.7557 (p0) outliers start: 22 outliers final: 15 residues processed: 72 average time/residue: 0.1394 time to fit residues: 16.1959 Evaluate side-chains 65 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 119 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 75 optimal weight: 0.0670 chunk 278 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 271 optimal weight: 0.5980 chunk 253 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.091574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.072376 restraints weight = 33801.709| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.05 r_work: 0.2822 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21915 Z= 0.133 Angle : 0.499 4.785 29787 Z= 0.279 Chirality : 0.045 0.186 3222 Planarity : 0.003 0.048 4044 Dihedral : 4.196 17.145 3207 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.41 % Allowed : 11.43 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.42 (0.16), residues: 2853 helix: 0.96 (0.43), residues: 168 sheet: 0.08 (0.15), residues: 1179 loop : -0.66 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 415 TYR 0.012 0.001 TYR A 933 PHE 0.017 0.001 PHE A 512 TRP 0.001 0.000 TRP C 538 HIS 0.004 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00303 (21912) covalent geometry : angle 0.49877 (29781) SS BOND : bond 0.00026 ( 3) SS BOND : angle 0.10195 ( 6) hydrogen bonds : bond 0.03556 ( 963) hydrogen bonds : angle 4.43450 ( 3597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 51 time to evaluate : 0.766 Fit side-chains REVERT: A 585 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: A 785 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8302 (t0) REVERT: B 1074 THR cc_start: 0.8971 (m) cc_final: 0.8671 (p) REVERT: C 434 ASP cc_start: 0.7983 (t0) cc_final: 0.7774 (t0) REVERT: C 1094 ASP cc_start: 0.8061 (t0) cc_final: 0.7558 (p0) outliers start: 31 outliers final: 18 residues processed: 82 average time/residue: 0.1606 time to fit residues: 21.0215 Evaluate side-chains 67 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 198 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.091719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.072513 restraints weight = 33801.237| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.05 r_work: 0.2823 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21915 Z= 0.138 Angle : 0.498 4.869 29787 Z= 0.278 Chirality : 0.045 0.187 3222 Planarity : 0.003 0.047 4044 Dihedral : 4.155 16.350 3207 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.55 % Allowed : 11.66 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.40 (0.16), residues: 2853 helix: 1.02 (0.43), residues: 168 sheet: 0.08 (0.15), residues: 1185 loop : -0.65 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 415 TYR 0.014 0.001 TYR A1060 PHE 0.018 0.001 PHE A 512 TRP 0.001 0.001 TRP B 538 HIS 0.004 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00319 (21912) covalent geometry : angle 0.49843 (29781) SS BOND : bond 0.00020 ( 3) SS BOND : angle 0.11696 ( 6) hydrogen bonds : bond 0.03504 ( 963) hydrogen bonds : angle 4.37731 ( 3597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 51 time to evaluate : 0.807 Fit side-chains REVERT: A 585 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: A 785 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8314 (t0) REVERT: B 1074 THR cc_start: 0.8971 (m) cc_final: 0.8671 (p) REVERT: C 434 ASP cc_start: 0.7975 (t0) cc_final: 0.7772 (t0) REVERT: C 1094 ASP cc_start: 0.8084 (t0) cc_final: 0.7588 (p0) outliers start: 34 outliers final: 23 residues processed: 82 average time/residue: 0.1388 time to fit residues: 18.2734 Evaluate side-chains 75 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 79 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.073179 restraints weight = 33665.422| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.04 r_work: 0.2837 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21915 Z= 0.118 Angle : 0.488 4.785 29787 Z= 0.273 Chirality : 0.044 0.193 3222 Planarity : 0.003 0.046 4044 Dihedral : 4.057 17.460 3207 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.28 % Allowed : 11.84 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.34 (0.16), residues: 2853 helix: 1.11 (0.43), residues: 168 sheet: 0.14 (0.15), residues: 1185 loop : -0.63 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 415 TYR 0.012 0.001 TYR A1060 PHE 0.016 0.001 PHE A 512 TRP 0.001 0.000 TRP C 538 HIS 0.003 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00267 (21912) covalent geometry : angle 0.48834 (29781) SS BOND : bond 0.00022 ( 3) SS BOND : angle 0.11970 ( 6) hydrogen bonds : bond 0.03326 ( 963) hydrogen bonds : angle 4.30338 ( 3597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.690 Fit side-chains REVERT: A 585 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: A 590 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7679 (ptm) REVERT: A 785 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8358 (t0) REVERT: B 337 TYR cc_start: 0.8625 (m-80) cc_final: 0.8287 (m-80) REVERT: B 1074 THR cc_start: 0.8962 (m) cc_final: 0.8677 (p) REVERT: C 1094 ASP cc_start: 0.8073 (t0) cc_final: 0.7611 (p0) outliers start: 28 outliers final: 22 residues processed: 77 average time/residue: 0.1481 time to fit residues: 18.0617 Evaluate side-chains 74 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 132 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 164 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 205 optimal weight: 0.0170 chunk 171 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 ASN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.093936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.074775 restraints weight = 33556.075| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.05 r_work: 0.2868 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21915 Z= 0.092 Angle : 0.469 4.807 29787 Z= 0.261 Chirality : 0.044 0.192 3222 Planarity : 0.003 0.045 4044 Dihedral : 3.832 17.342 3207 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.91 % Allowed : 12.43 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.22 (0.16), residues: 2853 helix: 1.31 (0.44), residues: 168 sheet: 0.24 (0.15), residues: 1185 loop : -0.58 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 415 TYR 0.010 0.001 TYR A 645 PHE 0.013 0.001 PHE A 512 TRP 0.002 0.000 TRP C 538 HIS 0.002 0.001 HIS B 939 Details of bonding type rmsd covalent geometry : bond 0.00195 (21912) covalent geometry : angle 0.46893 (29781) SS BOND : bond 0.00015 ( 3) SS BOND : angle 0.16758 ( 6) hydrogen bonds : bond 0.02977 ( 963) hydrogen bonds : angle 4.13826 ( 3597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.689 Fit side-chains REVERT: A 585 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: A 590 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7750 (ptm) REVERT: A 1074 THR cc_start: 0.9040 (m) cc_final: 0.8725 (p) REVERT: B 337 TYR cc_start: 0.8632 (m-80) cc_final: 0.8198 (m-80) REVERT: B 1074 THR cc_start: 0.8944 (m) cc_final: 0.8674 (p) REVERT: C 1094 ASP cc_start: 0.8065 (t0) cc_final: 0.7593 (p0) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.1368 time to fit residues: 16.6999 Evaluate side-chains 66 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 988 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 228 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 278 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.074657 restraints weight = 33618.174| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.05 r_work: 0.2866 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 21915 Z= 0.139 Angle : 0.665 59.194 29787 Z= 0.394 Chirality : 0.044 0.185 3222 Planarity : 0.003 0.051 4044 Dihedral : 3.840 17.229 3207 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.91 % Allowed : 12.30 % Favored : 86.79 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: -0.22 (0.16), residues: 2853 helix: 1.31 (0.43), residues: 168 sheet: 0.24 (0.15), residues: 1185 loop : -0.58 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 415 TYR 0.010 0.001 TYR A 837 PHE 0.013 0.001 PHE A 512 TRP 0.002 0.001 TRP C 538 HIS 0.002 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00281 (21912) covalent geometry : angle 0.66509 (29781) SS BOND : bond 0.00004 ( 3) SS BOND : angle 0.13494 ( 6) hydrogen bonds : bond 0.03071 ( 963) hydrogen bonds : angle 4.14709 ( 3597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.29 seconds wall clock time: 71 minutes 6.44 seconds (4266.44 seconds total)