Starting phenix.real_space_refine on Thu Jun 5 19:07:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5i_37293/06_2025/8w5i_37293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5i_37293/06_2025/8w5i_37293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5i_37293/06_2025/8w5i_37293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5i_37293/06_2025/8w5i_37293.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5i_37293/06_2025/8w5i_37293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5i_37293/06_2025/8w5i_37293.cif" } resolution = 3.6 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= 0.005 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 4158 2.51 5 N 1161 2.21 5 O 1328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6664 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 926 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "A" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 993 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "B" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 993 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 993 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "D" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 993 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 993 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Time building chain proxies: 4.26, per 1000 atoms: 0.64 Number of scatterers: 6664 At special positions: 0 Unit cell: (127.84, 116.96, 112.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 1328 8.00 N 1161 7.00 C 4158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS D 74 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 846.6 milliseconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 21 sheets defined 15.3% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.816A pdb=" N ARG A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.718A pdb=" N GLN A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.816A pdb=" N ARG B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.716A pdb=" N GLN B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.816A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.716A pdb=" N GLN C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 116 removed outlier: 3.816A pdb=" N ARG D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.717A pdb=" N GLN D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 116 removed outlier: 3.816A pdb=" N ARG E 105 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 128 removed outlier: 3.718A pdb=" N GLN E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.518A pdb=" N GLN H 8 " --> pdb=" O LYS H 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 22 through 24 removed outlier: 3.512A pdb=" N THR H 81 " --> pdb=" O GLU H 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 60 through 63 removed outlier: 4.250A pdb=" N ASN H 60 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP H 39 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE H 37 " --> pdb=" O ARG H 53 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP H 102 " --> pdb=" O TYR H 36 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA H 100 " --> pdb=" O ASN H 38 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR H 111 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 60 through 63 removed outlier: 4.250A pdb=" N ASN H 60 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP H 39 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE H 37 " --> pdb=" O ARG H 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 21 through 27 removed outlier: 3.684A pdb=" N SER L 76 " --> pdb=" O SER L 69 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER L 67 " --> pdb=" O THR L 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 57 through 58 removed outlier: 3.839A pdb=" N ASN L 57 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR L 53 " --> pdb=" O ASN L 57 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP L 39 " --> pdb=" O TRP L 51 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR L 53 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU L 37 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN L 93 " --> pdb=" O HIS L 38 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN L 94 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR L 101 " --> pdb=" O GLN L 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 7 through 11 removed outlier: 5.253A pdb=" N GLY A 9 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 19 " --> pdb=" O GLY A 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.509A pdb=" N ARG A 24 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N SER A 34 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 50 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 47 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 65 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 86 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.509A pdb=" N ARG A 24 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N SER A 34 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 50 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 47 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 65 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 7 through 11 removed outlier: 5.254A pdb=" N GLY B 9 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 19 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.508A pdb=" N ARG B 24 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER B 34 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 50 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 47 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 65 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 72 through 74 removed outlier: 4.355A pdb=" N ARG B 86 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N CYS B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL B 84 " --> pdb=" O CYS B 74 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 7 through 11 removed outlier: 5.253A pdb=" N GLY C 9 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU C 19 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 22 through 26 removed outlier: 3.508A pdb=" N ARG C 24 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 50 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 47 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 65 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 68 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 74 removed outlier: 7.326A pdb=" N THR C 72 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR C 85 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS C 74 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 83 " --> pdb=" O CYS C 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 7 through 11 removed outlier: 5.253A pdb=" N GLY D 9 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU D 19 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 22 through 26 removed outlier: 3.509A pdb=" N ARG D 24 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER D 34 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 50 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 47 " --> pdb=" O GLN D 69 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN D 65 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 68 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 72 through 74 removed outlier: 6.982A pdb=" N THR D 72 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 83 " --> pdb=" O CYS D 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 7 through 11 removed outlier: 5.253A pdb=" N GLY E 9 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU E 19 " --> pdb=" O GLY E 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 22 through 26 removed outlier: 3.509A pdb=" N ARG E 24 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER E 34 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL E 50 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG E 47 " --> pdb=" O GLN E 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN E 65 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 68 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 72 through 74 removed outlier: 6.956A pdb=" N THR E 72 " --> pdb=" O THR E 85 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 549 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: 1.44 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 972 1.24 - 1.38: 1636 1.38 - 1.52: 3207 1.52 - 1.66: 944 1.66 - 1.80: 20 Bond restraints: 6779 Sorted by residual: bond pdb=" C ILE H 54 " pdb=" O ILE H 54 " ideal model delta sigma weight residual 1.235 1.097 0.138 9.90e-03 1.02e+04 1.94e+02 bond pdb=" C PRO B 71 " pdb=" N THR B 72 " ideal model delta sigma weight residual 1.331 1.497 -0.166 1.44e-02 4.82e+03 1.32e+02 bond pdb=" C ALA A 88 " pdb=" O ALA A 88 " ideal model delta sigma weight residual 1.236 1.132 0.104 1.14e-02 7.69e+03 8.28e+01 bond pdb=" C ALA H 52 " pdb=" O ALA H 52 " ideal model delta sigma weight residual 1.234 1.122 0.111 1.25e-02 6.40e+03 7.90e+01 bond pdb=" CA THR H 33 " pdb=" C THR H 33 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.04e-02 9.25e+03 7.00e+01 ... (remaining 6774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 9102 5.15 - 10.29: 114 10.29 - 15.44: 9 15.44 - 20.59: 7 20.59 - 25.73: 2 Bond angle restraints: 9234 Sorted by residual: angle pdb=" C ASP C 81 " pdb=" N PRO C 82 " pdb=" CA PRO C 82 " ideal model delta sigma weight residual 119.89 137.42 -17.53 1.02e+00 9.61e-01 2.96e+02 angle pdb=" C ASP E 81 " pdb=" N PRO E 82 " pdb=" CA PRO E 82 " ideal model delta sigma weight residual 119.84 139.55 -19.71 1.25e+00 6.40e-01 2.49e+02 angle pdb=" N VAL H 104 " pdb=" CA VAL H 104 " pdb=" C VAL H 104 " ideal model delta sigma weight residual 109.34 131.97 -22.63 2.08e+00 2.31e-01 1.18e+02 angle pdb=" N TYR B 89 " pdb=" CA TYR B 89 " pdb=" C TYR B 89 " ideal model delta sigma weight residual 109.60 125.14 -15.54 1.53e+00 4.27e-01 1.03e+02 angle pdb=" C ASP A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 119.89 129.04 -9.15 1.02e+00 9.61e-01 8.05e+01 ... (remaining 9229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 3978 16.52 - 33.04: 119 33.04 - 49.56: 31 49.56 - 66.08: 10 66.08 - 82.60: 6 Dihedral angle restraints: 4144 sinusoidal: 1581 harmonic: 2563 Sorted by residual: dihedral pdb=" N TYR L 98 " pdb=" C TYR L 98 " pdb=" CA TYR L 98 " pdb=" CB TYR L 98 " ideal model delta harmonic sigma weight residual 122.80 144.70 -21.90 0 2.50e+00 1.60e-01 7.67e+01 dihedral pdb=" C TYR L 98 " pdb=" N TYR L 98 " pdb=" CA TYR L 98 " pdb=" CB TYR L 98 " ideal model delta harmonic sigma weight residual -122.60 -142.02 19.42 0 2.50e+00 1.60e-01 6.04e+01 dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 146.69 -53.69 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 4141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.229: 1056 0.229 - 0.457: 22 0.457 - 0.686: 3 0.686 - 0.915: 0 0.915 - 1.144: 1 Chirality restraints: 1082 Sorted by residual: chirality pdb=" CA TYR L 98 " pdb=" N TYR L 98 " pdb=" C TYR L 98 " pdb=" CB TYR L 98 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.14 2.00e-01 2.50e+01 3.27e+01 chirality pdb=" CA VAL H 104 " pdb=" N VAL H 104 " pdb=" C VAL H 104 " pdb=" CB VAL H 104 " both_signs ideal model delta sigma weight residual False 2.44 1.77 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA TYR H 105 " pdb=" N TYR H 105 " pdb=" C TYR H 105 " pdb=" CB TYR H 105 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.44e+00 ... (remaining 1079 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP H 102 " 0.028 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C ASP H 102 " -0.097 2.00e-02 2.50e+03 pdb=" O ASP H 102 " 0.037 2.00e-02 2.50e+03 pdb=" N ASP H 103 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 107 " 0.056 2.00e-02 2.50e+03 3.47e-02 2.11e+01 pdb=" CG PHE H 107 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE H 107 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE H 107 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE H 107 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE H 107 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 107 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 105 " 0.047 2.00e-02 2.50e+03 3.00e-02 1.80e+01 pdb=" CG TYR H 105 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR H 105 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR H 105 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 105 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR H 105 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 105 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 105 " 0.008 2.00e-02 2.50e+03 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 101 2.61 - 3.18: 5549 3.18 - 3.76: 8801 3.76 - 4.33: 10986 4.33 - 4.90: 18971 Nonbonded interactions: 44408 Sorted by model distance: nonbonded pdb=" O VAL H 104 " pdb=" CG1 VAL H 104 " model vdw 2.039 3.460 nonbonded pdb=" N ASP C 81 " pdb=" OD1 ASP C 81 " model vdw 2.154 3.120 nonbonded pdb=" N GLN L 94 " pdb=" OE1 GLN L 94 " model vdw 2.170 3.120 nonbonded pdb=" O THR C 72 " pdb=" OG1 THR C 72 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP H 34 " pdb=" OG1 THR B 75 " model vdw 2.238 3.040 ... (remaining 44403 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.730 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.015 0.212 6783 Z= 0.973 Angle : 1.551 38.496 9240 Z= 0.921 Chirality : 0.093 1.144 1082 Planarity : 0.008 0.065 1208 Dihedral : 10.131 82.596 2485 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.16 % Favored : 92.38 % Rotamer: Outliers : 1.91 % Allowed : 6.82 % Favored : 91.27 % Cbeta Deviations : 1.09 % Peptide Plane: Cis-proline : 0.00 % 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: -4.13 (0.23), residues: 866 helix: -2.00 (0.43), residues: 120 sheet: -2.50 (0.24), residues: 341 loop : -3.13 (0.23), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 112 HIS 0.003 0.002 HIS L 38 PHE 0.059 0.004 PHE H 107 TYR 0.069 0.004 TYR H 105 ARG 0.005 0.001 ARG L 27 Details of bonding type rmsd hydrogen bonds : bond 0.25847 ( 196) hydrogen bonds : angle 9.41836 ( 549) SS BOND : bond 0.00718 ( 3) SS BOND : angle 18.57499 ( 6) covalent geometry : bond 0.01521 ( 6779) covalent geometry : angle 1.47712 ( 9234) Misc. bond : bond 0.21234 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 286 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 TYR cc_start: 0.9273 (m-80) cc_final: 0.8819 (m-80) REVERT: H 46 GLN cc_start: 0.8616 (mp10) cc_final: 0.8308 (mp10) REVERT: H 54 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9007 (pp) REVERT: H 89 LEU cc_start: 0.9037 (mm) cc_final: 0.8709 (mm) REVERT: H 102 ASP cc_start: 0.9079 (p0) cc_final: 0.8761 (p0) REVERT: H 111 TYR cc_start: 0.9029 (m-10) cc_final: 0.8671 (m-80) REVERT: L 13 ILE cc_start: 0.9022 (pt) cc_final: 0.8820 (mm) REVERT: L 101 THR cc_start: 0.8828 (p) cc_final: 0.8581 (p) REVERT: A 2 LYS cc_start: 0.8343 (tttp) cc_final: 0.7210 (mmtt) REVERT: A 24 ARG cc_start: 0.8788 (mtp180) cc_final: 0.8438 (mtp-110) REVERT: A 47 ARG cc_start: 0.8541 (ptp-170) cc_final: 0.8292 (ptp-110) REVERT: A 63 LYS cc_start: 0.8571 (tttt) cc_final: 0.8222 (ttmm) REVERT: A 67 LYS cc_start: 0.8758 (mttt) cc_final: 0.8455 (mttp) REVERT: A 69 GLN cc_start: 0.8432 (pt0) cc_final: 0.8139 (pt0) REVERT: A 103 GLU cc_start: 0.8090 (mp0) cc_final: 0.7886 (mp0) REVERT: A 127 GLN cc_start: 0.8952 (mm110) cc_final: 0.8675 (mm-40) REVERT: B 2 LYS cc_start: 0.9157 (tttp) cc_final: 0.8593 (tppt) REVERT: B 27 ASN cc_start: 0.8403 (t0) cc_final: 0.7719 (t0) REVERT: B 47 ARG cc_start: 0.8537 (ptp-170) cc_final: 0.7977 (ptp90) REVERT: B 69 GLN cc_start: 0.8285 (pt0) cc_final: 0.8039 (pt0) REVERT: B 77 ASN cc_start: 0.9575 (t0) cc_final: 0.9087 (t0) REVERT: B 102 ASP cc_start: 0.8158 (p0) cc_final: 0.7822 (t70) REVERT: C 2 LYS cc_start: 0.8645 (tttp) cc_final: 0.8436 (mmtt) REVERT: C 11 ILE cc_start: 0.9150 (mt) cc_final: 0.8886 (tp) REVERT: C 41 VAL cc_start: 0.8778 (t) cc_final: 0.8528 (m) REVERT: C 47 ARG cc_start: 0.8812 (ptp-170) cc_final: 0.8551 (mtm-85) REVERT: C 102 ASP cc_start: 0.8464 (p0) cc_final: 0.8073 (t70) REVERT: D 41 VAL cc_start: 0.8672 (t) cc_final: 0.8417 (t) REVERT: D 47 ARG cc_start: 0.8752 (ptp-170) cc_final: 0.8061 (ptp-110) REVERT: D 57 ARG cc_start: 0.7660 (ptt180) cc_final: 0.7456 (ttp80) REVERT: D 61 ASN cc_start: 0.8727 (m110) cc_final: 0.8520 (m-40) REVERT: D 63 LYS cc_start: 0.8389 (tttt) cc_final: 0.7947 (ttpp) REVERT: D 86 ARG cc_start: 0.8138 (ptt-90) cc_final: 0.6868 (mtp180) REVERT: D 122 ILE cc_start: 0.8710 (pp) cc_final: 0.8070 (mm) REVERT: D 123 ASP cc_start: 0.7774 (t0) cc_final: 0.7081 (t0) REVERT: D 127 GLN cc_start: 0.9202 (mm110) cc_final: 0.8470 (mm110) REVERT: E 2 LYS cc_start: 0.8704 (tttp) cc_final: 0.7699 (mmtt) REVERT: E 11 ILE cc_start: 0.8630 (mt) cc_final: 0.8376 (mt) REVERT: E 14 ASP cc_start: 0.8586 (p0) cc_final: 0.8260 (p0) REVERT: E 17 GLN cc_start: 0.8364 (mt0) cc_final: 0.8163 (mp10) REVERT: E 63 LYS cc_start: 0.8482 (tttt) cc_final: 0.8084 (ttmm) REVERT: E 87 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8379 (mm110) REVERT: E 127 GLN cc_start: 0.9011 (mm110) cc_final: 0.8745 (mm-40) REVERT: E 129 ASN cc_start: 0.8737 (m-40) cc_final: 0.8436 (t0) outliers start: 14 outliers final: 5 residues processed: 298 average time/residue: 0.2474 time to fit residues: 91.1188 Evaluate side-chains 222 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain E residue 82 PRO Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 87 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 0.0030 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN L 4 GLN C 10 ASN D 65 GLN E 69 GLN E 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.083542 restraints weight = 12778.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.086536 restraints weight = 6312.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.088559 restraints weight = 4118.183| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6783 Z= 0.123 Angle : 0.653 8.871 9240 Z= 0.347 Chirality : 0.046 0.162 1082 Planarity : 0.004 0.041 1208 Dihedral : 7.045 56.302 974 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.96 % Allowed : 14.32 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.24 (0.25), residues: 866 helix: -0.43 (0.48), residues: 120 sheet: -1.92 (0.25), residues: 339 loop : -2.87 (0.24), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 112 HIS 0.001 0.001 HIS L 38 PHE 0.008 0.001 PHE H 109 TYR 0.022 0.001 TYR H 30 ARG 0.006 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 196) hydrogen bonds : angle 5.96904 ( 549) SS BOND : bond 0.00259 ( 3) SS BOND : angle 1.06443 ( 6) covalent geometry : bond 0.00264 ( 6779) covalent geometry : angle 0.65275 ( 9234) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 TYR cc_start: 0.9317 (m-80) cc_final: 0.8923 (m-80) REVERT: H 89 LEU cc_start: 0.9121 (mm) cc_final: 0.8907 (mm) REVERT: H 104 VAL cc_start: 0.9033 (t) cc_final: 0.8434 (t) REVERT: H 107 PHE cc_start: 0.8192 (m-80) cc_final: 0.7920 (m-80) REVERT: L 13 ILE cc_start: 0.8876 (pt) cc_final: 0.8614 (mm) REVERT: L 53 TYR cc_start: 0.9083 (p90) cc_final: 0.8796 (p90) REVERT: L 95 TYR cc_start: 0.9478 (t80) cc_final: 0.8989 (t80) REVERT: A 2 LYS cc_start: 0.8316 (tttp) cc_final: 0.7317 (mmtt) REVERT: A 63 LYS cc_start: 0.8670 (tttt) cc_final: 0.8425 (ttmm) REVERT: A 103 GLU cc_start: 0.7804 (mp0) cc_final: 0.7531 (mp0) REVERT: B 2 LYS cc_start: 0.9124 (tttp) cc_final: 0.8653 (tppt) REVERT: B 14 ASP cc_start: 0.9079 (p0) cc_final: 0.8754 (p0) REVERT: B 27 ASN cc_start: 0.8651 (t0) cc_final: 0.7940 (t0) REVERT: B 77 ASN cc_start: 0.9404 (t0) cc_final: 0.8943 (t0) REVERT: B 79 SER cc_start: 0.9562 (t) cc_final: 0.8994 (p) REVERT: B 102 ASP cc_start: 0.8099 (p0) cc_final: 0.7749 (t70) REVERT: C 102 ASP cc_start: 0.8548 (p0) cc_final: 0.8233 (t70) REVERT: D 47 ARG cc_start: 0.8298 (ptp-170) cc_final: 0.8075 (ptp-110) REVERT: D 61 ASN cc_start: 0.8621 (m110) cc_final: 0.8099 (m-40) REVERT: D 81 ASP cc_start: 0.8608 (m-30) cc_final: 0.8252 (t0) REVERT: D 86 ARG cc_start: 0.8616 (ptt-90) cc_final: 0.6831 (ttt180) REVERT: D 98 GLN cc_start: 0.8763 (tt0) cc_final: 0.8056 (tm-30) REVERT: D 122 ILE cc_start: 0.8652 (pp) cc_final: 0.8281 (mm) REVERT: D 123 ASP cc_start: 0.7954 (t0) cc_final: 0.7286 (t0) REVERT: D 127 GLN cc_start: 0.8961 (mm110) cc_final: 0.8459 (mm110) REVERT: E 2 LYS cc_start: 0.8577 (tttp) cc_final: 0.7830 (mmtt) REVERT: E 63 LYS cc_start: 0.8546 (tttt) cc_final: 0.8108 (ttmm) REVERT: E 81 ASP cc_start: 0.8740 (m-30) cc_final: 0.8343 (m-30) REVERT: E 83 SER cc_start: 0.8393 (m) cc_final: 0.8055 (t) REVERT: E 104 GLU cc_start: 0.7735 (mp0) cc_final: 0.7398 (mp0) outliers start: 29 outliers final: 16 residues processed: 256 average time/residue: 0.2269 time to fit residues: 71.9603 Evaluate side-chains 230 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 111 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 44 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 overall best weight: 2.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN C 10 ASN D 37 GLN E 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.081495 restraints weight = 12940.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.084325 restraints weight = 6594.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.086222 restraints weight = 4387.473| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6783 Z= 0.152 Angle : 0.648 11.395 9240 Z= 0.338 Chirality : 0.047 0.163 1082 Planarity : 0.004 0.037 1208 Dihedral : 6.102 55.776 965 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.46 % Allowed : 16.78 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.71 (0.26), residues: 866 helix: 0.49 (0.49), residues: 120 sheet: -1.67 (0.25), residues: 353 loop : -2.61 (0.26), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 112 HIS 0.002 0.001 HIS L 38 PHE 0.009 0.001 PHE H 67 TYR 0.023 0.001 TYR H 105 ARG 0.004 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 196) hydrogen bonds : angle 5.51681 ( 549) SS BOND : bond 0.00303 ( 3) SS BOND : angle 1.01352 ( 6) covalent geometry : bond 0.00343 ( 6779) covalent geometry : angle 0.64790 ( 9234) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 TYR cc_start: 0.9192 (m-80) cc_final: 0.8953 (m-80) REVERT: H 70 LYS cc_start: 0.9064 (tppp) cc_final: 0.8405 (tppt) REVERT: H 89 LEU cc_start: 0.9156 (mm) cc_final: 0.8868 (mm) REVERT: H 107 PHE cc_start: 0.8198 (m-80) cc_final: 0.7873 (m-80) REVERT: H 110 ASP cc_start: 0.8009 (t0) cc_final: 0.7312 (t0) REVERT: H 111 TYR cc_start: 0.8640 (m-10) cc_final: 0.8118 (m-80) REVERT: L 13 ILE cc_start: 0.8844 (pt) cc_final: 0.8540 (mm) REVERT: L 21 LYS cc_start: 0.9263 (ttmm) cc_final: 0.9019 (ttmm) REVERT: L 53 TYR cc_start: 0.9059 (p90) cc_final: 0.8742 (p90) REVERT: L 95 TYR cc_start: 0.9521 (t80) cc_final: 0.8428 (t80) REVERT: A 2 LYS cc_start: 0.8586 (tttp) cc_final: 0.7542 (mmtt) REVERT: A 60 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8119 (pttm) REVERT: A 63 LYS cc_start: 0.8753 (tttt) cc_final: 0.8491 (ttmm) REVERT: A 81 ASP cc_start: 0.8640 (p0) cc_final: 0.8393 (p0) REVERT: A 103 GLU cc_start: 0.7847 (mp0) cc_final: 0.7618 (mp0) REVERT: B 2 LYS cc_start: 0.9260 (tttp) cc_final: 0.8157 (mmtt) REVERT: B 14 ASP cc_start: 0.9180 (p0) cc_final: 0.8773 (p0) REVERT: B 27 ASN cc_start: 0.8476 (t0) cc_final: 0.7742 (t0) REVERT: B 77 ASN cc_start: 0.9411 (t0) cc_final: 0.8475 (t0) REVERT: B 81 ASP cc_start: 0.8976 (t0) cc_final: 0.8010 (p0) REVERT: B 98 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 102 ASP cc_start: 0.8180 (p0) cc_final: 0.7626 (t70) REVERT: B 132 TYR cc_start: 0.7643 (t80) cc_final: 0.7404 (t80) REVERT: C 102 ASP cc_start: 0.8577 (p0) cc_final: 0.8200 (t70) REVERT: C 123 ASP cc_start: 0.8317 (t0) cc_final: 0.8046 (t0) REVERT: D 2 LYS cc_start: 0.8592 (tttp) cc_final: 0.6352 (mmtt) REVERT: D 47 ARG cc_start: 0.8518 (ptp-170) cc_final: 0.8232 (ptp-110) REVERT: D 61 ASN cc_start: 0.8667 (m110) cc_final: 0.8169 (m-40) REVERT: D 63 LYS cc_start: 0.8539 (tttt) cc_final: 0.8242 (ttpp) REVERT: D 98 GLN cc_start: 0.8790 (tt0) cc_final: 0.8089 (tm-30) REVERT: D 122 ILE cc_start: 0.8766 (pp) cc_final: 0.8472 (mm) REVERT: D 123 ASP cc_start: 0.8031 (t0) cc_final: 0.7425 (t0) REVERT: D 127 GLN cc_start: 0.9047 (mm110) cc_final: 0.8513 (mm110) REVERT: E 2 LYS cc_start: 0.8539 (tttp) cc_final: 0.7925 (mmtt) REVERT: E 61 ASN cc_start: 0.8513 (m110) cc_final: 0.8237 (m-40) REVERT: E 63 LYS cc_start: 0.8616 (tttt) cc_final: 0.8153 (ttmm) REVERT: E 81 ASP cc_start: 0.8756 (m-30) cc_final: 0.8469 (m-30) REVERT: E 83 SER cc_start: 0.8627 (m) cc_final: 0.8160 (t) REVERT: E 104 GLU cc_start: 0.7762 (mp0) cc_final: 0.7311 (mp0) outliers start: 40 outliers final: 23 residues processed: 253 average time/residue: 0.2400 time to fit residues: 74.7612 Evaluate side-chains 243 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 111 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 ASN E 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.080154 restraints weight = 13152.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.083005 restraints weight = 6641.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.084942 restraints weight = 4382.792| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6783 Z= 0.173 Angle : 0.652 7.248 9240 Z= 0.340 Chirality : 0.047 0.162 1082 Planarity : 0.004 0.037 1208 Dihedral : 5.626 55.770 962 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.00 % Allowed : 17.87 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.43 (0.27), residues: 866 helix: 0.94 (0.49), residues: 120 sheet: -1.53 (0.26), residues: 366 loop : -2.49 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 112 HIS 0.002 0.001 HIS L 38 PHE 0.007 0.001 PHE H 98 TYR 0.033 0.002 TYR H 105 ARG 0.007 0.001 ARG C 47 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 196) hydrogen bonds : angle 5.39956 ( 549) SS BOND : bond 0.00242 ( 3) SS BOND : angle 1.02155 ( 6) covalent geometry : bond 0.00399 ( 6779) covalent geometry : angle 0.65123 ( 9234) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLN cc_start: 0.8963 (mp10) cc_final: 0.8733 (mp10) REVERT: H 70 LYS cc_start: 0.9093 (tppp) cc_final: 0.8456 (tppt) REVERT: H 89 LEU cc_start: 0.9196 (mm) cc_final: 0.8903 (mm) REVERT: H 103 ASP cc_start: 0.8721 (t0) cc_final: 0.8386 (t0) REVERT: H 110 ASP cc_start: 0.8185 (t0) cc_final: 0.7491 (t0) REVERT: H 111 TYR cc_start: 0.8576 (m-10) cc_final: 0.8168 (m-80) REVERT: L 13 ILE cc_start: 0.8921 (pt) cc_final: 0.8622 (mm) REVERT: L 53 TYR cc_start: 0.8989 (p90) cc_final: 0.8736 (p90) REVERT: L 95 TYR cc_start: 0.9453 (t80) cc_final: 0.8851 (t80) REVERT: A 2 LYS cc_start: 0.8560 (tttp) cc_final: 0.7584 (mmtt) REVERT: A 60 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8381 (pttm) REVERT: A 63 LYS cc_start: 0.8872 (tttt) cc_final: 0.8636 (ttmm) REVERT: B 2 LYS cc_start: 0.9207 (tttp) cc_final: 0.8088 (mmtt) REVERT: B 14 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8857 (p0) REVERT: B 27 ASN cc_start: 0.8535 (t0) cc_final: 0.7875 (t0) REVERT: B 77 ASN cc_start: 0.9381 (t0) cc_final: 0.8316 (t0) REVERT: B 81 ASP cc_start: 0.8905 (t0) cc_final: 0.8295 (p0) REVERT: B 98 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8471 (tm-30) REVERT: B 102 ASP cc_start: 0.8322 (p0) cc_final: 0.7531 (t70) REVERT: C 47 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.7924 (mtp85) REVERT: C 89 TYR cc_start: 0.9100 (m-80) cc_final: 0.8876 (m-80) REVERT: C 102 ASP cc_start: 0.8591 (p0) cc_final: 0.8177 (t70) REVERT: C 123 ASP cc_start: 0.8366 (t0) cc_final: 0.8047 (t0) REVERT: D 2 LYS cc_start: 0.8031 (tttp) cc_final: 0.7345 (mmtt) REVERT: D 24 ARG cc_start: 0.8948 (ttm-80) cc_final: 0.8660 (mmm-85) REVERT: D 47 ARG cc_start: 0.8428 (ptp-170) cc_final: 0.8196 (ptp-110) REVERT: D 61 ASN cc_start: 0.8681 (m110) cc_final: 0.8209 (m-40) REVERT: D 63 LYS cc_start: 0.8563 (tttt) cc_final: 0.8341 (ttpp) REVERT: D 98 GLN cc_start: 0.8838 (tt0) cc_final: 0.8111 (tm-30) REVERT: D 102 ASP cc_start: 0.8058 (p0) cc_final: 0.7527 (p0) REVERT: D 122 ILE cc_start: 0.8713 (pp) cc_final: 0.8461 (mm) REVERT: D 123 ASP cc_start: 0.8094 (t0) cc_final: 0.7630 (t0) REVERT: D 127 GLN cc_start: 0.9039 (mm110) cc_final: 0.8486 (mm110) REVERT: E 2 LYS cc_start: 0.8483 (tttp) cc_final: 0.7909 (mmtt) REVERT: E 34 SER cc_start: 0.8607 (m) cc_final: 0.8345 (t) REVERT: E 61 ASN cc_start: 0.8525 (m110) cc_final: 0.8294 (m-40) REVERT: E 63 LYS cc_start: 0.8674 (tttt) cc_final: 0.8291 (ttmm) REVERT: E 83 SER cc_start: 0.8628 (m) cc_final: 0.8147 (t) REVERT: E 104 GLU cc_start: 0.8073 (mp0) cc_final: 0.7806 (mp0) REVERT: E 129 ASN cc_start: 0.9032 (m-40) cc_final: 0.8439 (t0) outliers start: 44 outliers final: 37 residues processed: 247 average time/residue: 0.2254 time to fit residues: 68.9076 Evaluate side-chains 250 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 121 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 58 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN C 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.080274 restraints weight = 12887.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.083095 restraints weight = 6522.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.085043 restraints weight = 4319.764| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6783 Z= 0.154 Angle : 0.624 8.380 9240 Z= 0.327 Chirality : 0.046 0.156 1082 Planarity : 0.004 0.036 1208 Dihedral : 5.365 54.228 962 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 6.00 % Allowed : 18.01 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.27), residues: 866 helix: 1.13 (0.49), residues: 120 sheet: -1.31 (0.26), residues: 359 loop : -2.36 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS L 38 PHE 0.006 0.001 PHE H 98 TYR 0.021 0.002 TYR H 30 ARG 0.005 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 196) hydrogen bonds : angle 5.28794 ( 549) SS BOND : bond 0.00228 ( 3) SS BOND : angle 1.26937 ( 6) covalent geometry : bond 0.00354 ( 6779) covalent geometry : angle 0.62371 ( 9234) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 70 LYS cc_start: 0.9099 (tppp) cc_final: 0.8471 (tppt) REVERT: H 76 GLU cc_start: 0.8068 (mp0) cc_final: 0.7691 (mp0) REVERT: H 89 LEU cc_start: 0.9196 (mm) cc_final: 0.8893 (mm) REVERT: H 110 ASP cc_start: 0.8139 (t0) cc_final: 0.7562 (t0) REVERT: H 111 TYR cc_start: 0.8539 (m-10) cc_final: 0.8104 (m-80) REVERT: L 13 ILE cc_start: 0.8919 (pt) cc_final: 0.8665 (mm) REVERT: L 53 TYR cc_start: 0.8938 (p90) cc_final: 0.8683 (p90) REVERT: L 95 TYR cc_start: 0.9393 (t80) cc_final: 0.8990 (t80) REVERT: A 2 LYS cc_start: 0.8590 (tttp) cc_final: 0.7588 (mmtt) REVERT: A 63 LYS cc_start: 0.8864 (tttt) cc_final: 0.8621 (ttmm) REVERT: B 2 LYS cc_start: 0.9185 (tttp) cc_final: 0.8087 (mmtt) REVERT: B 14 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8723 (p0) REVERT: B 27 ASN cc_start: 0.8540 (t0) cc_final: 0.7856 (t0) REVERT: B 77 ASN cc_start: 0.9301 (t0) cc_final: 0.8183 (t0) REVERT: B 81 ASP cc_start: 0.8893 (t0) cc_final: 0.8386 (p0) REVERT: B 98 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 102 ASP cc_start: 0.8329 (p0) cc_final: 0.7503 (t70) REVERT: C 47 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.8040 (mtp85) REVERT: C 89 TYR cc_start: 0.9094 (m-80) cc_final: 0.8853 (m-80) REVERT: C 102 ASP cc_start: 0.8610 (p0) cc_final: 0.8151 (t70) REVERT: C 123 ASP cc_start: 0.8336 (t0) cc_final: 0.8007 (t0) REVERT: D 2 LYS cc_start: 0.8117 (tttp) cc_final: 0.7803 (mmtt) REVERT: D 47 ARG cc_start: 0.8437 (ptp-170) cc_final: 0.8169 (ptp-110) REVERT: D 60 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8133 (ptpp) REVERT: D 61 ASN cc_start: 0.8598 (m110) cc_final: 0.8135 (m-40) REVERT: D 63 LYS cc_start: 0.8536 (tttt) cc_final: 0.8329 (ttpp) REVERT: D 98 GLN cc_start: 0.8827 (tt0) cc_final: 0.8112 (tm-30) REVERT: D 127 GLN cc_start: 0.9010 (mm110) cc_final: 0.8435 (mm110) REVERT: E 2 LYS cc_start: 0.8387 (tttp) cc_final: 0.7846 (mmtt) REVERT: E 10 ASN cc_start: 0.8826 (m-40) cc_final: 0.8441 (t0) REVERT: E 24 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8474 (mmm-85) REVERT: E 34 SER cc_start: 0.8590 (m) cc_final: 0.8345 (t) REVERT: E 61 ASN cc_start: 0.8525 (m110) cc_final: 0.7512 (p0) REVERT: E 63 LYS cc_start: 0.8651 (tttt) cc_final: 0.8270 (ttmm) REVERT: E 83 SER cc_start: 0.8613 (m) cc_final: 0.8134 (t) REVERT: E 129 ASN cc_start: 0.9069 (m-40) cc_final: 0.8479 (t0) outliers start: 44 outliers final: 36 residues processed: 245 average time/residue: 0.2241 time to fit residues: 67.9546 Evaluate side-chains 251 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 121 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN A 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.080380 restraints weight = 12795.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.083199 restraints weight = 6481.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.085127 restraints weight = 4280.741| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6783 Z= 0.172 Angle : 0.642 8.121 9240 Z= 0.337 Chirality : 0.047 0.156 1082 Planarity : 0.004 0.036 1208 Dihedral : 5.233 53.895 962 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 6.55 % Allowed : 17.46 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.07 (0.27), residues: 866 helix: 1.34 (0.49), residues: 120 sheet: -1.32 (0.26), residues: 364 loop : -2.27 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS L 38 PHE 0.007 0.001 PHE H 98 TYR 0.028 0.002 TYR H 105 ARG 0.006 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 196) hydrogen bonds : angle 5.21007 ( 549) SS BOND : bond 0.00269 ( 3) SS BOND : angle 1.48236 ( 6) covalent geometry : bond 0.00398 ( 6779) covalent geometry : angle 0.64143 ( 9234) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 70 LYS cc_start: 0.9069 (tppp) cc_final: 0.8446 (tppt) REVERT: H 76 GLU cc_start: 0.8076 (mp0) cc_final: 0.7673 (mp0) REVERT: H 89 LEU cc_start: 0.9210 (mm) cc_final: 0.8901 (mm) REVERT: H 110 ASP cc_start: 0.8152 (t0) cc_final: 0.7470 (t0) REVERT: H 111 TYR cc_start: 0.8569 (m-10) cc_final: 0.8012 (m-80) REVERT: L 13 ILE cc_start: 0.8979 (pt) cc_final: 0.8718 (mm) REVERT: L 53 TYR cc_start: 0.8900 (p90) cc_final: 0.8636 (p90) REVERT: L 95 TYR cc_start: 0.9404 (t80) cc_final: 0.9050 (t80) REVERT: A 2 LYS cc_start: 0.8629 (tttp) cc_final: 0.7747 (mmtt) REVERT: A 63 LYS cc_start: 0.8912 (tttt) cc_final: 0.8653 (ttmm) REVERT: A 127 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8358 (mp10) REVERT: B 2 LYS cc_start: 0.9185 (tttp) cc_final: 0.8094 (mmtt) REVERT: B 4 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8165 (mm-30) REVERT: B 27 ASN cc_start: 0.8577 (t0) cc_final: 0.7887 (t0) REVERT: B 77 ASN cc_start: 0.9357 (t0) cc_final: 0.8873 (t0) REVERT: B 98 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 102 ASP cc_start: 0.8443 (p0) cc_final: 0.7993 (p0) REVERT: C 47 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8097 (mtp85) REVERT: C 102 ASP cc_start: 0.8684 (p0) cc_final: 0.8173 (t70) REVERT: C 123 ASP cc_start: 0.8362 (t0) cc_final: 0.8092 (t0) REVERT: D 2 LYS cc_start: 0.8733 (tttp) cc_final: 0.7913 (mmtt) REVERT: D 4 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8123 (mm-30) REVERT: D 13 LYS cc_start: 0.2345 (mttt) cc_final: 0.0971 (mttt) REVERT: D 47 ARG cc_start: 0.8460 (ptp-170) cc_final: 0.8195 (ptp-110) REVERT: D 61 ASN cc_start: 0.8628 (m110) cc_final: 0.8201 (m-40) REVERT: D 63 LYS cc_start: 0.8564 (tttt) cc_final: 0.8347 (ttpp) REVERT: D 98 GLN cc_start: 0.8836 (tt0) cc_final: 0.8123 (tm-30) REVERT: D 127 GLN cc_start: 0.8955 (mm110) cc_final: 0.8349 (mm110) REVERT: E 2 LYS cc_start: 0.8445 (tttp) cc_final: 0.7826 (mmtt) REVERT: E 10 ASN cc_start: 0.8867 (m-40) cc_final: 0.8596 (m-40) REVERT: E 11 ILE cc_start: 0.8491 (mm) cc_final: 0.8279 (mt) REVERT: E 34 SER cc_start: 0.8581 (m) cc_final: 0.8337 (t) REVERT: E 61 ASN cc_start: 0.8510 (m110) cc_final: 0.7631 (p0) REVERT: E 63 LYS cc_start: 0.8657 (tttt) cc_final: 0.8315 (ttmm) REVERT: E 83 SER cc_start: 0.8615 (m) cc_final: 0.8132 (t) REVERT: E 129 ASN cc_start: 0.9066 (m-40) cc_final: 0.8501 (t0) outliers start: 48 outliers final: 39 residues processed: 246 average time/residue: 0.2447 time to fit residues: 74.4009 Evaluate side-chains 255 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 121 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.085009 restraints weight = 13077.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087848 restraints weight = 6260.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089748 restraints weight = 4068.171| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6783 Z= 0.194 Angle : 0.663 8.505 9240 Z= 0.349 Chirality : 0.048 0.158 1082 Planarity : 0.004 0.036 1208 Dihedral : 5.229 54.439 962 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 6.55 % Allowed : 17.74 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.04 (0.27), residues: 866 helix: 1.35 (0.49), residues: 120 sheet: -1.30 (0.26), residues: 364 loop : -2.26 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.001 0.001 HIS L 38 PHE 0.008 0.001 PHE H 98 TYR 0.027 0.002 TYR H 105 ARG 0.004 0.001 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 196) hydrogen bonds : angle 5.22345 ( 549) SS BOND : bond 0.00313 ( 3) SS BOND : angle 1.28767 ( 6) covalent geometry : bond 0.00450 ( 6779) covalent geometry : angle 0.66281 ( 9234) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 70 LYS cc_start: 0.9138 (tppp) cc_final: 0.8541 (tppt) REVERT: H 76 GLU cc_start: 0.8124 (mp0) cc_final: 0.7757 (mp0) REVERT: H 89 LEU cc_start: 0.9153 (mm) cc_final: 0.8916 (mm) REVERT: H 110 ASP cc_start: 0.8124 (t0) cc_final: 0.7583 (t0) REVERT: H 111 TYR cc_start: 0.8562 (m-10) cc_final: 0.8063 (m-80) REVERT: L 21 LYS cc_start: 0.8985 (tppp) cc_final: 0.8766 (mmmm) REVERT: L 53 TYR cc_start: 0.8889 (p90) cc_final: 0.8588 (p90) REVERT: L 95 TYR cc_start: 0.9342 (t80) cc_final: 0.9072 (t80) REVERT: A 2 LYS cc_start: 0.8667 (tttp) cc_final: 0.7804 (mmtt) REVERT: A 127 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8610 (mp10) REVERT: B 2 LYS cc_start: 0.9188 (tttp) cc_final: 0.8215 (mmtt) REVERT: B 27 ASN cc_start: 0.8816 (t0) cc_final: 0.8199 (t0) REVERT: B 77 ASN cc_start: 0.9221 (t0) cc_final: 0.8762 (t0) REVERT: B 98 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8389 (tm-30) REVERT: B 102 ASP cc_start: 0.8329 (p0) cc_final: 0.7926 (p0) REVERT: C 47 ARG cc_start: 0.8625 (mtm-85) cc_final: 0.8089 (mtp85) REVERT: C 123 ASP cc_start: 0.8441 (t0) cc_final: 0.8160 (t0) REVERT: D 2 LYS cc_start: 0.8624 (tttp) cc_final: 0.7796 (mmtt) REVERT: D 13 LYS cc_start: 0.2469 (mttt) cc_final: 0.1047 (ttmt) REVERT: D 47 ARG cc_start: 0.8492 (ptp-170) cc_final: 0.8264 (ptp-110) REVERT: D 61 ASN cc_start: 0.8594 (m110) cc_final: 0.8210 (m-40) REVERT: D 98 GLN cc_start: 0.8723 (tt0) cc_final: 0.8056 (tm-30) REVERT: D 127 GLN cc_start: 0.9043 (mm110) cc_final: 0.8440 (mm110) REVERT: E 2 LYS cc_start: 0.8342 (tttp) cc_final: 0.7916 (mmtt) REVERT: E 61 ASN cc_start: 0.8516 (m110) cc_final: 0.7835 (p0) REVERT: E 63 LYS cc_start: 0.8704 (tttt) cc_final: 0.8439 (ttmm) REVERT: E 83 SER cc_start: 0.8854 (m) cc_final: 0.8354 (t) REVERT: E 102 ASP cc_start: 0.8654 (p0) cc_final: 0.8289 (p0) REVERT: E 129 ASN cc_start: 0.9254 (m-40) cc_final: 0.8757 (t0) outliers start: 48 outliers final: 44 residues processed: 243 average time/residue: 0.3043 time to fit residues: 92.1898 Evaluate side-chains 256 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 121 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 71 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN ** D 65 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.103748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.084667 restraints weight = 13113.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.087579 restraints weight = 6319.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089452 restraints weight = 4127.296| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6783 Z= 0.162 Angle : 0.658 8.545 9240 Z= 0.345 Chirality : 0.047 0.159 1082 Planarity : 0.004 0.035 1208 Dihedral : 5.041 52.690 962 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.14 % Allowed : 19.37 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.01 (0.27), residues: 866 helix: 1.41 (0.49), residues: 120 sheet: -1.20 (0.26), residues: 361 loop : -2.35 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.002 0.001 HIS L 38 PHE 0.007 0.001 PHE H 98 TYR 0.022 0.001 TYR H 30 ARG 0.004 0.001 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 196) hydrogen bonds : angle 5.17111 ( 549) SS BOND : bond 0.00250 ( 3) SS BOND : angle 1.28081 ( 6) covalent geometry : bond 0.00375 ( 6779) covalent geometry : angle 0.65698 ( 9234) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 70 LYS cc_start: 0.9201 (tppp) cc_final: 0.8639 (tppt) REVERT: H 89 LEU cc_start: 0.9122 (mm) cc_final: 0.8898 (mm) REVERT: H 110 ASP cc_start: 0.8073 (t0) cc_final: 0.7519 (t0) REVERT: H 111 TYR cc_start: 0.8527 (m-10) cc_final: 0.8005 (m-80) REVERT: L 21 LYS cc_start: 0.8985 (tppp) cc_final: 0.8752 (mmmm) REVERT: L 53 TYR cc_start: 0.8864 (p90) cc_final: 0.8553 (p90) REVERT: L 95 TYR cc_start: 0.9349 (t80) cc_final: 0.9115 (t80) REVERT: A 2 LYS cc_start: 0.8683 (tttp) cc_final: 0.7879 (mmtt) REVERT: A 127 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8679 (mp10) REVERT: B 2 LYS cc_start: 0.9154 (tttp) cc_final: 0.8231 (mmtt) REVERT: B 27 ASN cc_start: 0.8836 (t0) cc_final: 0.8215 (t0) REVERT: B 77 ASN cc_start: 0.9197 (t0) cc_final: 0.8729 (t0) REVERT: B 102 ASP cc_start: 0.8201 (p0) cc_final: 0.7784 (p0) REVERT: C 2 LYS cc_start: 0.5037 (mmtt) cc_final: 0.4798 (mmmt) REVERT: C 47 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8134 (mtp85) REVERT: C 123 ASP cc_start: 0.8371 (t0) cc_final: 0.8035 (t0) REVERT: D 2 LYS cc_start: 0.8723 (tttp) cc_final: 0.7804 (mmtt) REVERT: D 13 LYS cc_start: 0.2246 (mttt) cc_final: 0.0835 (ttmt) REVERT: D 61 ASN cc_start: 0.8568 (m110) cc_final: 0.8170 (m-40) REVERT: D 98 GLN cc_start: 0.8628 (tt0) cc_final: 0.8189 (tm-30) REVERT: D 127 GLN cc_start: 0.9003 (mm110) cc_final: 0.8369 (mm110) REVERT: E 2 LYS cc_start: 0.8360 (tttp) cc_final: 0.8008 (mmtt) REVERT: E 10 ASN cc_start: 0.8643 (m-40) cc_final: 0.8150 (t0) REVERT: E 13 LYS cc_start: 0.3162 (mttp) cc_final: 0.2086 (ttmt) REVERT: E 61 ASN cc_start: 0.8491 (m110) cc_final: 0.7792 (p0) REVERT: E 63 LYS cc_start: 0.8704 (tttt) cc_final: 0.8435 (ttmm) REVERT: E 83 SER cc_start: 0.8913 (m) cc_final: 0.8422 (t) REVERT: E 102 ASP cc_start: 0.8608 (p0) cc_final: 0.8243 (p0) REVERT: E 129 ASN cc_start: 0.9203 (m-40) cc_final: 0.8795 (t0) outliers start: 45 outliers final: 43 residues processed: 240 average time/residue: 0.2277 time to fit residues: 67.6827 Evaluate side-chains 256 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 121 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 81 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN ** D 65 GLN ** 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 = 0.3338 r_free = 0.3338 target = 0.103274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.084078 restraints weight = 13231.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.086972 restraints weight = 6313.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088890 restraints weight = 4087.919| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6783 Z= 0.219 Angle : 0.727 12.688 9240 Z= 0.378 Chirality : 0.048 0.159 1082 Planarity : 0.004 0.035 1208 Dihedral : 5.163 54.530 962 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 6.28 % Allowed : 19.51 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.12 (0.27), residues: 866 helix: 1.32 (0.48), residues: 120 sheet: -1.31 (0.26), residues: 365 loop : -2.38 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.003 0.002 HIS L 38 PHE 0.009 0.001 PHE H 98 TYR 0.037 0.002 TYR H 105 ARG 0.004 0.001 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 196) hydrogen bonds : angle 5.23222 ( 549) SS BOND : bond 0.00274 ( 3) SS BOND : angle 1.39734 ( 6) covalent geometry : bond 0.00508 ( 6779) covalent geometry : angle 0.72606 ( 9234) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 70 LYS cc_start: 0.9197 (tppp) cc_final: 0.8625 (tppt) REVERT: H 89 LEU cc_start: 0.9194 (mm) cc_final: 0.8944 (mm) REVERT: L 14 MET cc_start: 0.8408 (mmm) cc_final: 0.8128 (mmm) REVERT: L 21 LYS cc_start: 0.8990 (tppp) cc_final: 0.8765 (mmmm) REVERT: L 95 TYR cc_start: 0.9334 (t80) cc_final: 0.9066 (t80) REVERT: A 2 LYS cc_start: 0.8632 (tttp) cc_final: 0.7819 (mmtt) REVERT: A 127 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8630 (mp10) REVERT: B 2 LYS cc_start: 0.9171 (tttp) cc_final: 0.8410 (mmtt) REVERT: B 27 ASN cc_start: 0.8846 (t0) cc_final: 0.8221 (t0) REVERT: B 77 ASN cc_start: 0.9219 (t0) cc_final: 0.8739 (t0) REVERT: B 102 ASP cc_start: 0.8373 (p0) cc_final: 0.7958 (p0) REVERT: C 2 LYS cc_start: 0.5076 (mmtt) cc_final: 0.4588 (mmmt) REVERT: C 47 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.8088 (mtp85) REVERT: C 61 ASN cc_start: 0.8392 (m110) cc_final: 0.8013 (m-40) REVERT: C 123 ASP cc_start: 0.8407 (t0) cc_final: 0.8089 (t0) REVERT: D 2 LYS cc_start: 0.8659 (tttp) cc_final: 0.7666 (mmtt) REVERT: D 13 LYS cc_start: 0.2279 (mttt) cc_final: 0.0789 (ttmt) REVERT: D 61 ASN cc_start: 0.8622 (m110) cc_final: 0.8223 (m-40) REVERT: D 98 GLN cc_start: 0.8711 (tt0) cc_final: 0.8198 (tm-30) REVERT: D 127 GLN cc_start: 0.8967 (mm110) cc_final: 0.8266 (mm110) REVERT: E 2 LYS cc_start: 0.8486 (tttp) cc_final: 0.7966 (mmtt) REVERT: E 10 ASN cc_start: 0.8667 (m-40) cc_final: 0.8175 (t0) REVERT: E 13 LYS cc_start: 0.3343 (mttp) cc_final: 0.2273 (ttmt) REVERT: E 61 ASN cc_start: 0.8534 (m110) cc_final: 0.7859 (p0) REVERT: E 63 LYS cc_start: 0.8735 (tttt) cc_final: 0.8441 (ttmm) REVERT: E 102 ASP cc_start: 0.8711 (p0) cc_final: 0.8347 (p0) REVERT: E 129 ASN cc_start: 0.9214 (m-40) cc_final: 0.8801 (t0) outliers start: 46 outliers final: 44 residues processed: 240 average time/residue: 0.2568 time to fit residues: 76.0059 Evaluate side-chains 256 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 34 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN ** D 65 GLN ** 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 = 0.3246 r_free = 0.3246 target = 0.099491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.079351 restraints weight = 13156.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.082187 restraints weight = 6598.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.084095 restraints weight = 4337.643| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6783 Z= 0.190 Angle : 0.704 11.928 9240 Z= 0.366 Chirality : 0.048 0.158 1082 Planarity : 0.004 0.038 1208 Dihedral : 5.068 53.861 962 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 6.14 % Allowed : 20.60 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.09 (0.27), residues: 866 helix: 1.38 (0.48), residues: 120 sheet: -1.27 (0.26), residues: 365 loop : -2.39 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.002 0.001 HIS L 38 PHE 0.008 0.001 PHE H 98 TYR 0.024 0.002 TYR H 30 ARG 0.004 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 196) hydrogen bonds : angle 5.18817 ( 549) SS BOND : bond 0.00274 ( 3) SS BOND : angle 1.55996 ( 6) covalent geometry : bond 0.00444 ( 6779) covalent geometry : angle 0.70314 ( 9234) Misc. bond : bond 0.00024 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 213 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: H 70 LYS cc_start: 0.9104 (tppp) cc_final: 0.8509 (tppt) REVERT: H 89 LEU cc_start: 0.9260 (mm) cc_final: 0.8939 (mm) REVERT: H 111 TYR cc_start: 0.8396 (m-10) cc_final: 0.8005 (m-80) REVERT: L 14 MET cc_start: 0.8462 (mmm) cc_final: 0.8109 (mmm) REVERT: L 21 LYS cc_start: 0.8987 (tppp) cc_final: 0.8729 (mmmm) REVERT: L 95 TYR cc_start: 0.9415 (t80) cc_final: 0.9182 (t80) REVERT: A 2 LYS cc_start: 0.8676 (tttp) cc_final: 0.7845 (mmtt) REVERT: A 127 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8563 (mp10) REVERT: B 2 LYS cc_start: 0.9128 (tttp) cc_final: 0.8275 (mmtt) REVERT: B 4 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8088 (mm-30) REVERT: B 27 ASN cc_start: 0.8697 (t0) cc_final: 0.8034 (t0) REVERT: B 102 ASP cc_start: 0.8483 (p0) cc_final: 0.8063 (p0) REVERT: C 2 LYS cc_start: 0.5166 (mmtt) cc_final: 0.4687 (mmmt) REVERT: C 47 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.7949 (mtp85) REVERT: C 61 ASN cc_start: 0.8395 (m110) cc_final: 0.7983 (m-40) REVERT: C 98 GLN cc_start: 0.8629 (tt0) cc_final: 0.8319 (tm-30) REVERT: C 123 ASP cc_start: 0.8458 (t0) cc_final: 0.8143 (t0) REVERT: D 2 LYS cc_start: 0.8683 (tttp) cc_final: 0.7631 (mmtt) REVERT: D 13 LYS cc_start: 0.2155 (mttt) cc_final: 0.0687 (ttmt) REVERT: D 61 ASN cc_start: 0.8638 (m110) cc_final: 0.8198 (m-40) REVERT: D 98 GLN cc_start: 0.8864 (tt0) cc_final: 0.8230 (tm-30) REVERT: D 127 GLN cc_start: 0.8920 (mm110) cc_final: 0.8165 (mm110) REVERT: E 2 LYS cc_start: 0.8522 (tttp) cc_final: 0.7841 (mmtt) REVERT: E 10 ASN cc_start: 0.8744 (m-40) cc_final: 0.8195 (t0) REVERT: E 13 LYS cc_start: 0.3202 (mttp) cc_final: 0.2187 (ttmt) REVERT: E 61 ASN cc_start: 0.8562 (m110) cc_final: 0.7742 (p0) REVERT: E 63 LYS cc_start: 0.8717 (tttt) cc_final: 0.8364 (ttmm) REVERT: E 102 ASP cc_start: 0.8792 (p0) cc_final: 0.8374 (p0) REVERT: E 129 ASN cc_start: 0.9110 (m-40) cc_final: 0.8789 (t0) outliers start: 45 outliers final: 44 residues processed: 237 average time/residue: 0.3412 time to fit residues: 100.8396 Evaluate side-chains 255 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 36 TYR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN ** D 65 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.103900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084618 restraints weight = 13093.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.087608 restraints weight = 6172.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.089603 restraints weight = 3987.755| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6783 Z= 0.162 Angle : 0.684 11.390 9240 Z= 0.355 Chirality : 0.047 0.157 1082 Planarity : 0.004 0.039 1208 Dihedral : 4.855 51.826 962 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.41 % Allowed : 20.60 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.99 (0.27), residues: 866 helix: 1.47 (0.48), residues: 120 sheet: -1.19 (0.26), residues: 365 loop : -2.36 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.002 0.001 HIS L 38 PHE 0.007 0.001 PHE H 98 TYR 0.027 0.002 TYR H 105 ARG 0.004 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 196) hydrogen bonds : angle 5.09365 ( 549) SS BOND : bond 0.00263 ( 3) SS BOND : angle 1.91446 ( 6) covalent geometry : bond 0.00376 ( 6779) covalent geometry : angle 0.68272 ( 9234) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3090.18 seconds wall clock time: 55 minutes 52.68 seconds (3352.68 seconds total)