Starting phenix.real_space_refine on Wed May 21 15:49:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ae1_15378/05_2025/8ae1_15378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ae1_15378/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ae1_15378/05_2025/8ae1_15378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ae1_15378/05_2025/8ae1_15378.map" model { file = "/net/cci-nas-00/data/ceres_data/8ae1_15378/05_2025/8ae1_15378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ae1_15378/05_2025/8ae1_15378.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.70, per 1000 atoms: 0.64 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: 5.87 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 4.31 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: 11.01 Time building geometry restraints manager: 6.70 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: 0.07 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 56.320 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.820 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (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 TRP 0.001 0.000 TRP A 538 HIS 0.003 0.001 HIS B 939 PHE 0.024 0.001 PHE A 512 TYR 0.010 0.001 TYR A 890 ARG 0.009 0.000 ARG A 891 Details of bonding type rmsd hydrogen bonds : bond 0.24560 ( 963) hydrogen bonds : angle 9.05413 ( 3597) SS BOND : bond 0.00038 ( 3) SS BOND : angle 0.45750 ( 6) covalent geometry : bond 0.00234 (21912) covalent geometry : angle 0.46936 (29781) *********************** 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 : 2.310 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: 0.3539 time to fit residues: 40.4992 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 : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.2980 chunk 216 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1136 GLN B 400 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.071477 restraints weight = 33997.852| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.02 r_work: 0.2795 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21915 Z= 0.244 Angle : 0.596 5.861 29787 Z= 0.336 Chirality : 0.048 0.169 3222 Planarity : 0.004 0.050 4044 Dihedral : 4.454 19.997 3207 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.23 % Allowed : 4.51 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2853 helix: 0.36 (0.42), residues: 168 sheet: -0.10 (0.15), residues: 1179 loop : -0.73 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 538 HIS 0.006 0.002 HIS A 939 PHE 0.026 0.002 PHE A 512 TYR 0.017 0.002 TYR C1053 ARG 0.005 0.000 ARG A 891 Details of bonding type rmsd hydrogen bonds : bond 0.05431 ( 963) hydrogen bonds : angle 5.48070 ( 3597) SS BOND : bond 0.00068 ( 3) SS BOND : angle 0.49657 ( 6) covalent geometry : bond 0.00572 (21912) covalent geometry : angle 0.59552 (29781) *********************** 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 56 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 2.318 Fit side-chains REVERT: C 1094 ASP cc_start: 0.8055 (t0) cc_final: 0.7844 (t0) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.3658 time to fit residues: 32.5595 Evaluate side-chains 45 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 2.277 ------------------------------------------------------------------------------- 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 76 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 195 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 400 GLN B 810 ASN C 810 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.091952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.072924 restraints weight = 33694.842| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.01 r_work: 0.2818 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21915 Z= 0.156 Angle : 0.523 5.643 29787 Z= 0.293 Chirality : 0.046 0.166 3222 Planarity : 0.004 0.045 4044 Dihedral : 4.295 18.584 3207 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.36 % Allowed : 7.79 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2853 helix: 0.64 (0.42), residues: 168 sheet: -0.03 (0.15), residues: 1179 loop : -0.69 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.005 0.001 HIS A 939 PHE 0.022 0.001 PHE A 512 TYR 0.013 0.001 TYR A 837 ARG 0.004 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 963) hydrogen bonds : angle 4.88269 ( 3597) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.16973 ( 6) covalent geometry : bond 0.00355 (21912) covalent geometry : angle 0.52271 (29781) *********************** 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 59 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 2.413 Fit side-chains REVERT: A 585 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: B 1074 THR cc_start: 0.8936 (m) cc_final: 0.8662 (p) REVERT: C 1094 ASP cc_start: 0.8047 (t0) cc_final: 0.7797 (t0) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 0.4393 time to fit residues: 41.7749 Evaluate side-chains 49 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 2.402 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 162 optimal weight: 0.5980 chunk 203 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3168 r_free = 0.3168 target = 0.090150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.071013 restraints weight = 34237.474| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.03 r_work: 0.2796 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21915 Z= 0.198 Angle : 0.543 5.339 29787 Z= 0.304 Chirality : 0.046 0.164 3222 Planarity : 0.004 0.049 4044 Dihedral : 4.432 19.835 3207 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.59 % Allowed : 9.84 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2853 helix: 0.68 (0.42), residues: 168 sheet: -0.07 (0.15), residues: 1191 loop : -0.69 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 538 HIS 0.006 0.002 HIS A 939 PHE 0.022 0.002 PHE A 512 TYR 0.015 0.001 TYR A 837 ARG 0.004 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 963) hydrogen bonds : angle 4.73327 ( 3597) SS BOND : bond 0.00016 ( 3) SS BOND : angle 0.18993 ( 6) covalent geometry : bond 0.00467 (21912) covalent geometry : angle 0.54347 (29781) *********************** 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 59 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 2.251 Fit side-chains REVERT: A 585 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: C 1094 ASP cc_start: 0.8064 (t0) cc_final: 0.7834 (t0) outliers start: 13 outliers final: 5 residues processed: 59 average time/residue: 0.3871 time to fit residues: 37.3649 Evaluate side-chains 50 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 2.759 ------------------------------------------------------------------------------- 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 777 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 1001 THR 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 9 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.088926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.069837 restraints weight = 34400.612| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.03 r_work: 0.2775 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21915 Z= 0.265 Angle : 0.583 5.744 29787 Z= 0.326 Chirality : 0.048 0.163 3222 Planarity : 0.004 0.052 4044 Dihedral : 4.667 21.272 3207 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.28 % Allowed : 10.70 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2853 helix: 0.49 (0.42), residues: 168 sheet: -0.15 (0.15), residues: 1191 loop : -0.76 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 538 HIS 0.007 0.002 HIS B 939 PHE 0.024 0.002 PHE A 512 TYR 0.018 0.002 TYR A 837 ARG 0.005 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 963) hydrogen bonds : angle 4.76214 ( 3597) SS BOND : bond 0.00037 ( 3) SS BOND : angle 0.24638 ( 6) covalent geometry : bond 0.00631 (21912) covalent geometry : angle 0.58309 (29781) *********************** 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 77 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 49 time to evaluate : 2.593 Fit side-chains REVERT: A 585 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: C 813 ASP cc_start: 0.8732 (m-30) cc_final: 0.8521 (m-30) REVERT: C 1094 ASP cc_start: 0.8073 (t0) cc_final: 0.7574 (p0) outliers start: 28 outliers final: 16 residues processed: 77 average time/residue: 0.3607 time to fit residues: 44.7663 Evaluate side-chains 63 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 2.542 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 53 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 110 optimal weight: 0.0170 chunk 215 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 270 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 282 optimal weight: 0.6980 overall best weight: 1.2620 ------------------------------------------------------------------------------- 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** C1112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.091465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.072284 restraints weight = 33860.038| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.05 r_work: 0.2821 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21915 Z= 0.123 Angle : 0.497 4.883 29787 Z= 0.279 Chirality : 0.045 0.199 3222 Planarity : 0.003 0.048 4044 Dihedral : 4.255 17.714 3207 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.14 % Allowed : 11.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2853 helix: 0.85 (0.43), residues: 168 sheet: 0.01 (0.15), residues: 1179 loop : -0.70 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 538 HIS 0.003 0.001 HIS A 939 PHE 0.016 0.001 PHE A 512 TYR 0.011 0.001 TYR A 837 ARG 0.005 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 963) hydrogen bonds : angle 4.50133 ( 3597) SS BOND : bond 0.00026 ( 3) SS BOND : angle 0.13951 ( 6) covalent geometry : bond 0.00275 (21912) covalent geometry : angle 0.49702 (29781) *********************** 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 77 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 2.569 Fit side-chains REVERT: A 585 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: B 1074 THR cc_start: 0.8946 (m) cc_final: 0.8670 (p) REVERT: C 434 ASP cc_start: 0.7980 (t0) cc_final: 0.7772 (t0) REVERT: C 813 ASP cc_start: 0.8609 (m-30) cc_final: 0.8402 (m-30) REVERT: C 1094 ASP cc_start: 0.8050 (t0) cc_final: 0.7549 (p0) outliers start: 25 outliers final: 12 residues processed: 76 average time/residue: 0.3532 time to fit residues: 43.2391 Evaluate side-chains 64 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain B residue 512 PHE 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 B residue 1139 LEU Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 766 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 236 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.091174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.071985 restraints weight = 33900.167| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.05 r_work: 0.2814 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21915 Z= 0.148 Angle : 0.509 4.791 29787 Z= 0.285 Chirality : 0.045 0.191 3222 Planarity : 0.004 0.048 4044 Dihedral : 4.242 18.081 3207 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.41 % Allowed : 12.11 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2853 helix: 0.91 (0.43), residues: 168 sheet: 0.01 (0.15), residues: 1191 loop : -0.68 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 538 HIS 0.004 0.001 HIS A 939 PHE 0.018 0.001 PHE A 512 TYR 0.013 0.001 TYR A1060 ARG 0.007 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 963) hydrogen bonds : angle 4.44910 ( 3597) SS BOND : bond 0.00021 ( 3) SS BOND : angle 0.12140 ( 6) covalent geometry : bond 0.00342 (21912) covalent geometry : angle 0.50942 (29781) *********************** 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 83 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 2.467 Fit side-chains REVERT: A 585 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8432 (tt0) REVERT: A 785 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8371 (t0) REVERT: B 1074 THR cc_start: 0.8972 (m) cc_final: 0.8671 (p) REVERT: C 434 ASP cc_start: 0.7968 (t0) cc_final: 0.7755 (t0) REVERT: C 813 ASP cc_start: 0.8625 (m-30) cc_final: 0.8421 (m-30) REVERT: C 1094 ASP cc_start: 0.8062 (t0) cc_final: 0.7559 (p0) outliers start: 31 outliers final: 20 residues processed: 83 average time/residue: 0.3387 time to fit residues: 45.7017 Evaluate side-chains 70 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 2.387 ------------------------------------------------------------------------------- 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 785 ASN Chi-restraints excluded: chain A residue 882 GLU 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 990 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain C residue 490 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 224 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 230 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 = 0.091629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.072412 restraints weight = 34007.639| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.05 r_work: 0.2823 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21915 Z= 0.137 Angle : 0.503 4.755 29787 Z= 0.281 Chirality : 0.045 0.200 3222 Planarity : 0.003 0.047 4044 Dihedral : 4.178 16.794 3207 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.41 % Allowed : 12.43 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2853 helix: 1.00 (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 TRP 0.002 0.000 TRP C 538 HIS 0.004 0.001 HIS A 939 PHE 0.017 0.001 PHE A 512 TYR 0.012 0.001 TYR A 933 ARG 0.008 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 963) hydrogen bonds : angle 4.38400 ( 3597) SS BOND : bond 0.00023 ( 3) SS BOND : angle 0.12714 ( 6) covalent geometry : bond 0.00314 (21912) covalent geometry : angle 0.50257 (29781) *********************** 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 82 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 51 time to evaluate : 2.355 Fit side-chains REVERT: A 585 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: A 785 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8358 (t0) REVERT: B 1074 THR cc_start: 0.8964 (m) cc_final: 0.8670 (p) REVERT: C 434 ASP cc_start: 0.7960 (t0) cc_final: 0.7756 (t0) REVERT: C 813 ASP cc_start: 0.8591 (m-30) cc_final: 0.8384 (m-30) REVERT: C 1094 ASP cc_start: 0.8069 (t0) cc_final: 0.7575 (p0) outliers start: 31 outliers final: 24 residues processed: 81 average time/residue: 0.3391 time to fit residues: 44.3883 Evaluate side-chains 73 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 2.305 ------------------------------------------------------------------------------- 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 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 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 490 VAL 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 59 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 109 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 207 optimal weight: 0.2980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.092131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.072949 restraints weight = 33754.873| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.04 r_work: 0.2834 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21915 Z= 0.122 Angle : 0.494 4.737 29787 Z= 0.276 Chirality : 0.045 0.193 3222 Planarity : 0.003 0.046 4044 Dihedral : 4.089 16.365 3207 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.14 % Allowed : 12.89 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 2853 helix: 1.07 (0.43), residues: 168 sheet: 0.12 (0.15), residues: 1179 loop : -0.65 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 538 HIS 0.003 0.001 HIS B 939 PHE 0.016 0.001 PHE A 512 TYR 0.014 0.001 TYR A1060 ARG 0.008 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 963) hydrogen bonds : angle 4.31192 ( 3597) SS BOND : bond 0.00025 ( 3) SS BOND : angle 0.13602 ( 6) covalent geometry : bond 0.00276 (21912) covalent geometry : angle 0.49416 (29781) *********************** 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 74 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 2.288 Fit side-chains REVERT: A 585 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: A 785 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8299 (t0) REVERT: B 337 TYR cc_start: 0.8646 (m-80) cc_final: 0.8297 (m-80) REVERT: B 1074 THR cc_start: 0.8958 (m) cc_final: 0.8678 (p) REVERT: C 813 ASP cc_start: 0.8573 (m-30) cc_final: 0.8358 (m-30) REVERT: C 1094 ASP cc_start: 0.8067 (t0) cc_final: 0.7581 (p0) outliers start: 25 outliers final: 22 residues processed: 72 average time/residue: 0.3536 time to fit residues: 40.6878 Evaluate side-chains 72 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 2.283 ------------------------------------------------------------------------------- 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 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 B residue 1139 LEU 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 243 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.090812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.071669 restraints weight = 34158.156| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.04 r_work: 0.2810 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21915 Z= 0.177 Angle : 0.527 4.776 29787 Z= 0.294 Chirality : 0.046 0.198 3222 Planarity : 0.004 0.048 4044 Dihedral : 4.280 17.554 3207 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.32 % Allowed : 12.93 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2853 helix: 0.92 (0.42), residues: 168 sheet: 0.04 (0.15), residues: 1197 loop : -0.69 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 538 HIS 0.005 0.002 HIS A 939 PHE 0.020 0.001 PHE A 512 TYR 0.014 0.001 TYR A 837 ARG 0.009 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 963) hydrogen bonds : angle 4.39498 ( 3597) SS BOND : bond 0.00021 ( 3) SS BOND : angle 0.13057 ( 6) covalent geometry : bond 0.00416 (21912) covalent geometry : angle 0.52696 (29781) ********************** 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 78 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 49 time to evaluate : 2.214 Fit side-chains REVERT: A 585 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: A 590 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7623 (ptm) REVERT: A 671 PHE cc_start: 0.7037 (m-10) cc_final: 0.6097 (t80) REVERT: A 785 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8330 (t0) REVERT: B 337 TYR cc_start: 0.8662 (m-80) cc_final: 0.8362 (m-80) REVERT: B 1074 THR cc_start: 0.8979 (m) cc_final: 0.8691 (p) REVERT: C 813 ASP cc_start: 0.8640 (m-30) cc_final: 0.8433 (m-30) REVERT: C 1094 ASP cc_start: 0.8084 (t0) cc_final: 0.7598 (p0) outliers start: 29 outliers final: 24 residues processed: 76 average time/residue: 0.3500 time to fit residues: 42.5365 Evaluate side-chains 75 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 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 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 B residue 1139 LEU Chi-restraints excluded: chain C residue 490 VAL 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 235 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 277 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 273 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.073179 restraints weight = 33723.333| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.04 r_work: 0.2837 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1532 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= 0.117 Angle : 0.492 4.701 29787 Z= 0.274 Chirality : 0.045 0.215 3222 Planarity : 0.003 0.046 4044 Dihedral : 4.078 16.292 3207 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.28 % Allowed : 12.89 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2853 helix: 1.11 (0.43), residues: 168 sheet: 0.14 (0.15), residues: 1185 loop : -0.64 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 538 HIS 0.003 0.001 HIS B 939 PHE 0.016 0.001 PHE A 512 TYR 0.013 0.001 TYR A1060 ARG 0.008 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 963) hydrogen bonds : angle 4.27514 ( 3597) SS BOND : bond 0.00022 ( 3) SS BOND : angle 0.12276 ( 6) covalent geometry : bond 0.00261 (21912) covalent geometry : angle 0.49206 (29781) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8737.30 seconds wall clock time: 152 minutes 32.81 seconds (9152.81 seconds total)