Starting phenix.real_space_refine on Wed Jun 18 20:12:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ae1_15378/06_2025/8ae1_15378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ae1_15378/06_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_15378/06_2025/8ae1_15378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ae1_15378/06_2025/8ae1_15378.map" model { file = "/net/cci-nas-00/data/ceres_data/8ae1_15378/06_2025/8ae1_15378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ae1_15378/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.69, per 1000 atoms: 0.59 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: 4.98 Conformation dependent library (CDL) restraints added in 2.8 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: 3.70 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: 10.55 Time building geometry restraints manager: 5.93 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: 2.290 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: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 52.140 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.670 ------------------------------------------------------------------------------- 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 : 2.458 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: 0.3584 time to fit residues: 41.4084 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 : 2.561 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.071479 restraints weight = 33997.774| |-----------------------------------------------------------------------------| 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 : 0.595 5.861 29787 Z= 0.336 Chirality : 0.048 0.169 3222 Planarity : 0.004 0.050 4044 Dihedral : 4.454 19.996 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 5.48083 ( 3597) SS BOND : bond 0.00068 ( 3) SS BOND : angle 0.49662 ( 6) covalent geometry : bond 0.00572 (21912) covalent geometry : angle 0.59551 (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 : 2.674 Fit side-chains REVERT: C 1094 ASP cc_start: 0.8057 (t0) cc_final: 0.7847 (t0) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.3895 time to fit residues: 35.3980 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 : 2.308 ------------------------------------------------------------------------------- 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: 0.9990 chunk 245 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 51 optimal weight: 0.0970 chunk 111 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3202 r_free = 0.3202 target = 0.092191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.072980 restraints weight = 33518.408| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.04 r_work: 0.2834 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21915 Z= 0.120 Angle : 0.500 5.611 29787 Z= 0.280 Chirality : 0.045 0.163 3222 Planarity : 0.003 0.043 4044 Dihedral : 4.140 17.884 3207 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.32 % Allowed : 7.56 % Favored : 92.12 % 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: 0.75 (0.43), residues: 168 sheet: 0.01 (0.15), residues: 1179 loop : -0.66 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 538 HIS 0.004 0.001 HIS A 939 PHE 0.019 0.001 PHE A 512 TYR 0.012 0.001 TYR A 933 ARG 0.003 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 963) hydrogen bonds : angle 4.81030 ( 3597) SS BOND : bond 0.00047 ( 3) SS BOND : angle 0.21615 ( 6) covalent geometry : bond 0.00262 (21912) covalent geometry : angle 0.49984 (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 62 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 2.216 Fit side-chains REVERT: A 585 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: A 891 ARG cc_start: 0.8759 (mtt-85) cc_final: 0.8474 (mtt-85) REVERT: B 1074 THR cc_start: 0.8909 (m) cc_final: 0.8649 (p) REVERT: C 1094 ASP cc_start: 0.8030 (t0) cc_final: 0.7776 (t0) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 0.4059 time to fit residues: 39.7574 Evaluate side-chains 50 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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: 4.9990 chunk 203 optimal weight: 0.0870 chunk 236 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.070310 restraints weight = 34408.543| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.03 r_work: 0.2784 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21915 Z= 0.254 Angle : 0.578 5.554 29787 Z= 0.323 Chirality : 0.048 0.163 3222 Planarity : 0.004 0.054 4044 Dihedral : 4.542 20.662 3207 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.68 % Allowed : 9.56 % Favored : 89.75 % 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: -0.61 (0.16), residues: 2853 helix: 0.61 (0.42), residues: 168 sheet: -0.11 (0.15), residues: 1191 loop : -0.70 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 538 HIS 0.007 0.002 HIS A 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 0.04490 ( 963) hydrogen bonds : angle 4.78546 ( 3597) SS BOND : bond 0.00029 ( 3) SS BOND : angle 0.26450 ( 6) covalent geometry : bond 0.00606 (21912) covalent geometry : angle 0.57787 (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 61 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 2.292 Fit side-chains REVERT: A 585 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: C 1094 ASP cc_start: 0.8081 (t0) cc_final: 0.7845 (t0) outliers start: 15 outliers final: 4 residues processed: 60 average time/residue: 0.3669 time to fit residues: 35.7560 Evaluate side-chains 50 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 990 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 9 optimal weight: 3.9990 chunk 277 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.090186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.071068 restraints weight = 34107.137| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.03 r_work: 0.2798 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21915 Z= 0.190 Angle : 0.534 5.041 29787 Z= 0.299 Chirality : 0.046 0.159 3222 Planarity : 0.004 0.050 4044 Dihedral : 4.442 19.466 3207 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.23 % Allowed : 10.15 % Favored : 88.62 % 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: -0.59 (0.16), residues: 2853 helix: 0.68 (0.42), residues: 168 sheet: -0.08 (0.15), residues: 1191 loop : -0.71 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.005 0.002 HIS A 939 PHE 0.020 0.001 PHE A 512 TYR 0.015 0.001 TYR A 837 ARG 0.005 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 963) hydrogen bonds : angle 4.64242 ( 3597) SS BOND : bond 0.00026 ( 3) SS BOND : angle 0.12910 ( 6) covalent geometry : bond 0.00445 (21912) covalent geometry : angle 0.53437 (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: 27 poor density : 50 time to evaluate : 5.245 Fit side-chains REVERT: A 585 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: C 434 ASP cc_start: 0.7969 (t0) cc_final: 0.7666 (t0) REVERT: C 813 ASP cc_start: 0.8656 (m-30) cc_final: 0.8453 (m-30) REVERT: C 1022 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7998 (mtm-85) REVERT: C 1094 ASP cc_start: 0.8049 (t0) cc_final: 0.7582 (p0) outliers start: 27 outliers final: 16 residues processed: 76 average time/residue: 0.4317 time to fit residues: 53.1525 Evaluate side-chains 65 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 2.627 ------------------------------------------------------------------------------- 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 590 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 53 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 270 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 400 GLN C1112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.090992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.071802 restraints weight = 33934.591| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.05 r_work: 0.2811 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 0.034 21915 Z= 0.151 Angle : 0.509 4.867 29787 Z= 0.285 Chirality : 0.045 0.204 3222 Planarity : 0.004 0.049 4044 Dihedral : 4.290 18.148 3207 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.23 % Allowed : 11.29 % Favored : 87.48 % 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: -0.52 (0.16), residues: 2853 helix: 0.84 (0.43), residues: 168 sheet: -0.04 (0.15), residues: 1191 loop : -0.68 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.004 0.001 HIS A 939 PHE 0.018 0.001 PHE A 512 TYR 0.012 0.001 TYR A 933 ARG 0.006 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 963) hydrogen bonds : angle 4.50187 ( 3597) SS BOND : bond 0.00023 ( 3) SS BOND : angle 0.11827 ( 6) covalent geometry : bond 0.00350 (21912) covalent geometry : angle 0.50891 (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 78 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 2.326 Fit side-chains REVERT: A 585 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: B 1074 THR cc_start: 0.8961 (m) cc_final: 0.8672 (p) REVERT: C 434 ASP cc_start: 0.7975 (t0) cc_final: 0.7766 (t0) REVERT: C 1094 ASP cc_start: 0.8059 (t0) cc_final: 0.7552 (p0) outliers start: 27 outliers final: 15 residues processed: 76 average time/residue: 0.4039 time to fit residues: 50.4754 Evaluate side-chains 62 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 2.322 ------------------------------------------------------------------------------- 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 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 777 THR 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 766 LEU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 236 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 172 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 400 GLN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.092160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.072958 restraints weight = 33730.492| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.05 r_work: 0.2832 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1432 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= 0.120 Angle : 0.487 4.760 29787 Z= 0.272 Chirality : 0.044 0.181 3222 Planarity : 0.003 0.046 4044 Dihedral : 4.088 16.144 3207 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.50 % Allowed : 11.89 % Favored : 86.61 % 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: -0.40 (0.16), residues: 2853 helix: 1.03 (0.43), residues: 168 sheet: 0.08 (0.15), residues: 1179 loop : -0.65 (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 0.014 0.001 TYR A1060 ARG 0.006 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 963) hydrogen bonds : angle 4.35548 ( 3597) SS BOND : bond 0.00025 ( 3) SS BOND : angle 0.13110 ( 6) covalent geometry : bond 0.00270 (21912) covalent geometry : angle 0.48671 (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 86 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 2.502 Fit side-chains REVERT: A 585 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: A 785 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8333 (t0) REVERT: B 1074 THR cc_start: 0.8961 (m) cc_final: 0.8659 (p) REVERT: C 434 ASP cc_start: 0.7962 (t0) cc_final: 0.7762 (t0) REVERT: C 1094 ASP cc_start: 0.8043 (t0) cc_final: 0.7558 (p0) outliers start: 33 outliers final: 17 residues processed: 84 average time/residue: 0.3577 time to fit residues: 48.8079 Evaluate side-chains 68 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain B residue 269 THR 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 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 988 VAL Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 224 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 280 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 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 = 0.3200 r_free = 0.3200 target = 0.092062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.072892 restraints weight = 33921.338| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.05 r_work: 0.2831 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1469 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= 0.127 Angle : 0.495 4.811 29787 Z= 0.276 Chirality : 0.045 0.193 3222 Planarity : 0.003 0.046 4044 Dihedral : 4.086 18.032 3207 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.23 % Allowed : 12.07 % Favored : 86.70 % 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: -0.39 (0.16), residues: 2853 helix: 1.07 (0.43), residues: 168 sheet: 0.09 (0.15), residues: 1185 loop : -0.65 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 538 HIS 0.004 0.001 HIS A 939 PHE 0.017 0.001 PHE A 512 TYR 0.011 0.001 TYR A 837 ARG 0.008 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 963) hydrogen bonds : angle 4.32737 ( 3597) SS BOND : bond 0.00020 ( 3) SS BOND : angle 0.10491 ( 6) covalent geometry : bond 0.00290 (21912) covalent geometry : angle 0.49483 (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 77 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 2.732 Fit side-chains REVERT: A 585 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: A 785 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8321 (t0) REVERT: B 337 TYR cc_start: 0.8620 (m-80) cc_final: 0.8281 (m-80) REVERT: B 1074 THR cc_start: 0.8965 (m) cc_final: 0.8676 (p) REVERT: C 1094 ASP cc_start: 0.8051 (t0) cc_final: 0.7569 (p0) outliers start: 27 outliers final: 22 residues processed: 77 average time/residue: 0.4354 time to fit residues: 54.1457 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 : 2.400 ------------------------------------------------------------------------------- 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 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 988 VAL Chi-restraints excluded: chain B residue 990 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 1069 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 59 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.071457 restraints weight = 34051.638| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.04 r_work: 0.2806 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1474 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= 0.192 Angle : 0.535 5.125 29787 Z= 0.299 Chirality : 0.046 0.185 3222 Planarity : 0.004 0.048 4044 Dihedral : 4.337 17.807 3207 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.23 % Allowed : 12.07 % Favored : 86.70 % 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: -0.52 (0.16), residues: 2853 helix: 0.47 (0.40), residues: 186 sheet: 0.03 (0.15), residues: 1191 loop : -0.70 (0.16), residues: 1476 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 0.021 0.001 PHE A 512 TYR 0.015 0.001 TYR A 837 ARG 0.008 0.000 ARG A 415 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 963) hydrogen bonds : angle 4.44467 ( 3597) SS BOND : bond 0.00029 ( 3) SS BOND : angle 0.15504 ( 6) covalent geometry : bond 0.00454 (21912) covalent geometry : angle 0.53553 (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 77 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 2.378 Fit side-chains REVERT: A 585 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8523 (tt0) REVERT: A 785 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8360 (t0) REVERT: B 337 TYR cc_start: 0.8678 (m-80) cc_final: 0.8382 (m-80) REVERT: B 1074 THR cc_start: 0.9001 (m) cc_final: 0.8697 (p) REVERT: C 1094 ASP cc_start: 0.8076 (t0) cc_final: 0.7570 (p0) outliers start: 27 outliers final: 23 residues processed: 77 average time/residue: 0.3612 time to fit residues: 45.2959 Evaluate side-chains 73 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 2.390 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 265 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 227 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 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 = 0.3200 r_free = 0.3200 target = 0.092085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.072886 restraints weight = 33930.851| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.05 r_work: 0.2832 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1513 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= 0.124 Angle : 0.496 4.683 29787 Z= 0.277 Chirality : 0.045 0.199 3222 Planarity : 0.003 0.046 4044 Dihedral : 4.130 16.313 3207 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.14 % Allowed : 12.30 % Favored : 86.57 % 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: -0.38 (0.16), residues: 2853 helix: 1.07 (0.43), residues: 168 sheet: 0.13 (0.15), residues: 1179 loop : -0.66 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 538 HIS 0.003 0.001 HIS B 939 PHE 0.017 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 0.03360 ( 963) hydrogen bonds : angle 4.31918 ( 3597) SS BOND : bond 0.00030 ( 3) SS BOND : angle 0.11005 ( 6) covalent geometry : bond 0.00280 (21912) covalent geometry : angle 0.49577 (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 74 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 2.418 Fit side-chains REVERT: A 585 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: A 671 PHE cc_start: 0.6992 (m-10) cc_final: 0.6096 (t80) REVERT: A 785 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8313 (t0) REVERT: B 337 TYR cc_start: 0.8651 (m-80) cc_final: 0.8299 (m-80) REVERT: B 1074 THR cc_start: 0.8967 (m) cc_final: 0.8674 (p) REVERT: C 1094 ASP cc_start: 0.8049 (t0) cc_final: 0.7588 (p0) outliers start: 25 outliers final: 23 residues processed: 74 average time/residue: 0.3628 time to fit residues: 43.1411 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 : 2.437 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 106 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 chunk 277 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 114 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 273 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 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 = 0.3215 r_free = 0.3215 target = 0.093002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.073849 restraints weight = 33660.943| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.04 r_work: 0.2852 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21915 Z= 0.107 Angle : 0.481 4.665 29787 Z= 0.268 Chirality : 0.044 0.219 3222 Planarity : 0.003 0.046 4044 Dihedral : 3.950 16.091 3207 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.09 % Allowed : 12.39 % Favored : 86.52 % 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: -0.32 (0.16), residues: 2853 helix: 1.20 (0.43), residues: 168 sheet: 0.16 (0.15), residues: 1185 loop : -0.63 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 538 HIS 0.002 0.001 HIS C 612 PHE 0.015 0.001 PHE A 512 TYR 0.014 0.001 TYR A1060 ARG 0.010 0.000 ARG C 415 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 963) hydrogen bonds : angle 4.19652 ( 3597) SS BOND : bond 0.00020 ( 3) SS BOND : angle 0.14534 ( 6) covalent geometry : bond 0.00236 (21912) covalent geometry : angle 0.48066 (29781) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9534.05 seconds wall clock time: 168 minutes 15.70 seconds (10095.70 seconds total)