Starting phenix.real_space_refine on Sat Aug 23 09:32:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce1_16597/08_2025/8ce1_16597.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce1_16597/08_2025/8ce1_16597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ce1_16597/08_2025/8ce1_16597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce1_16597/08_2025/8ce1_16597.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ce1_16597/08_2025/8ce1_16597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce1_16597/08_2025/8ce1_16597.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.110 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 58 5.16 5 C 7496 2.51 5 N 1974 2.21 5 O 1910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11438 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "c" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1930 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "d" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "A" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "C" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1930 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "D" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Time building chain proxies: 2.31, per 1000 atoms: 0.20 Number of scatterers: 11438 At special positions: 0 Unit cell: (83.52, 120.93, 107.88, 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 58 16.00 O 1910 8.00 N 1974 7.00 C 7496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 419.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 5 sheets defined 73.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'a' and resid 42 through 50 Processing helix chain 'a' and resid 70 through 75 Processing helix chain 'a' and resid 92 through 100 removed outlier: 3.931A pdb=" N TYR a 100 " --> pdb=" O ASN a 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 116 removed outlier: 3.720A pdb=" N ALA a 116 " --> pdb=" O ALA a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 129 Processing helix chain 'a' and resid 130 through 141 removed outlier: 3.830A pdb=" N VAL a 137 " --> pdb=" O GLN a 133 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA a 138 " --> pdb=" O GLN a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 144 No H-bonds generated for 'chain 'a' and resid 142 through 144' Processing helix chain 'a' and resid 160 through 177 removed outlier: 3.874A pdb=" N GLN a 177 " --> pdb=" O GLN a 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 17 removed outlier: 3.662A pdb=" N PHE b 7 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS b 17 " --> pdb=" O VAL b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 20 No H-bonds generated for 'chain 'b' and resid 18 through 20' Processing helix chain 'b' and resid 21 through 40 removed outlier: 4.396A pdb=" N LEU b 25 " --> pdb=" O ILE b 21 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE b 35 " --> pdb=" O VAL b 31 " (cutoff:3.500A) Proline residue: b 36 - end of helix Processing helix chain 'b' and resid 42 through 66 Proline residue: b 51 - end of helix Processing helix chain 'b' and resid 66 through 77 removed outlier: 4.330A pdb=" N PHE b 70 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP b 72 " --> pdb=" O ARG b 68 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP b 73 " --> pdb=" O LEU b 69 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU b 74 " --> pdb=" O PHE b 70 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN b 75 " --> pdb=" O ARG b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 84 removed outlier: 3.920A pdb=" N GLN b 81 " --> pdb=" O GLY b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 119 removed outlier: 3.587A pdb=" N VAL b 92 " --> pdb=" O PRO b 88 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU b 106 " --> pdb=" O MET b 102 " (cutoff:3.500A) Proline residue: b 107 - end of helix Proline residue: b 113 - end of helix removed outlier: 3.503A pdb=" N LEU b 119 " --> pdb=" O VAL b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 151 Proline residue: b 138 - end of helix Proline residue: b 146 - end of helix Processing helix chain 'b' and resid 159 through 169 Proline residue: b 167 - end of helix Processing helix chain 'b' and resid 169 through 185 removed outlier: 3.594A pdb=" N MET b 185 " --> pdb=" O ASP b 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 220 Proline residue: b 208 - end of helix removed outlier: 4.405A pdb=" N ALA b 213 " --> pdb=" O PHE b 209 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 9 Processing helix chain 'c' and resid 10 through 41 Proline residue: c 23 - end of helix Processing helix chain 'c' and resid 50 through 54 removed outlier: 3.592A pdb=" N SER c 53 " --> pdb=" O GLN c 50 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR c 54 " --> pdb=" O GLY c 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 50 through 54' Processing helix chain 'c' and resid 55 through 83 removed outlier: 3.986A pdb=" N LEU c 59 " --> pdb=" O ARG c 55 " (cutoff:3.500A) Proline residue: c 62 - end of helix removed outlier: 3.853A pdb=" N SER c 67 " --> pdb=" O ALA c 63 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR c 71 " --> pdb=" O SER c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 86 through 120 removed outlier: 3.698A pdb=" N ASN c 90 " --> pdb=" O MET c 86 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA c 94 " --> pdb=" O ASN c 90 " (cutoff:3.500A) Proline residue: c 98 - end of helix Proline residue: c 117 - end of helix Processing helix chain 'c' and resid 126 through 149 removed outlier: 3.568A pdb=" N PHE c 149 " --> pdb=" O LEU c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 151 through 184 Proline residue: c 171 - end of helix Processing helix chain 'c' and resid 198 through 229 removed outlier: 3.882A pdb=" N LEU c 202 " --> pdb=" O MET c 198 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 242 removed outlier: 3.846A pdb=" N SER c 236 " --> pdb=" O ARG c 232 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 12 removed outlier: 3.911A pdb=" N PHE d 12 " --> pdb=" O TRP d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 69 removed outlier: 4.292A pdb=" N VAL d 21 " --> pdb=" O TYR d 17 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP d 22 " --> pdb=" O ALA d 18 " (cutoff:3.500A) Proline residue: d 31 - end of helix Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.926A pdb=" N TYR A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.616A pdb=" N ALA A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.817A pdb=" N VAL A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 removed outlier: 3.504A pdb=" N THR A 145 " --> pdb=" O LEU A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.790A pdb=" N GLN A 177 " --> pdb=" O GLN A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 17 removed outlier: 3.598A pdb=" N PHE B 7 " --> pdb=" O PHE B 3 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 21 Processing helix chain 'B' and resid 22 through 40 removed outlier: 3.880A pdb=" N PHE B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 42 through 66 Proline residue: B 51 - end of helix Processing helix chain 'B' and resid 66 through 77 removed outlier: 4.263A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.656A pdb=" N GLN B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 120 removed outlier: 3.544A pdb=" N VAL B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Proline residue: B 113 - end of helix removed outlier: 3.563A pdb=" N GLY B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 151 Proline residue: B 138 - end of helix Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 158 through 185 removed outlier: 4.101A pdb=" N SER B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Proline residue: B 167 - end of helix Proline residue: B 171 - end of helix removed outlier: 3.616A pdb=" N MET B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 220 Proline residue: B 208 - end of helix removed outlier: 4.120A pdb=" N ALA B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 10 through 41 Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.645A pdb=" N SER C 53 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 50 through 54' Processing helix chain 'C' and resid 55 through 83 removed outlier: 4.094A pdb=" N LEU C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 3.788A pdb=" N SER C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 120 removed outlier: 3.740A pdb=" N ASN C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 126 through 149 removed outlier: 3.645A pdb=" N PHE C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 181 Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 199 through 229 removed outlier: 3.806A pdb=" N ARG C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 removed outlier: 3.734A pdb=" N SER C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.885A pdb=" N PHE D 12 " --> pdb=" O TRP D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 69 Proline residue: D 31 - end of helix removed outlier: 3.742A pdb=" N HIS D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 17 through 26 removed outlier: 6.864A pdb=" N LEU a 18 " --> pdb=" O GLU a 12 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLU a 12 " --> pdb=" O LEU a 18 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER a 20 " --> pdb=" O LEU a 10 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU a 10 " --> pdb=" O SER a 20 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU a 22 " --> pdb=" O GLU a 8 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU a 4 " --> pdb=" O LEU a 26 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU a 9 " --> pdb=" O ALA a 57 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA a 57 " --> pdb=" O LEU a 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 32 through 34 Processing sheet with id=AA3, first strand: chain 'a' and resid 78 through 81 removed outlier: 6.211A pdb=" N LEU a 79 " --> pdb=" O ILE a 151 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASP a 153 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE a 81 " --> pdb=" O ASP a 153 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N TRP a 150 " --> pdb=" O ILE a 182 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N THR a 184 " --> pdb=" O TRP a 150 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU a 152 " --> pdb=" O THR a 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 16 through 25 removed outlier: 6.787A pdb=" N LEU A 18 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU A 12 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER A 20 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 10 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 22 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 9 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 57 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.214A pdb=" N LEU A 79 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASP A 153 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 81 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 32 " --> pdb=" O VAL A 181 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2136 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: 1.65 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2570 1.33 - 1.45: 2490 1.45 - 1.57: 6560 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 11730 Sorted by residual: bond pdb=" CA MET C 198 " pdb=" C MET C 198 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.61e-02 3.86e+03 9.24e+00 bond pdb=" CA ALA C 197 " pdb=" C ALA C 197 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.33e-02 5.65e+03 6.92e+00 bond pdb=" CB TRP C 39 " pdb=" CG TRP C 39 " ideal model delta sigma weight residual 1.498 1.570 -0.072 3.10e-02 1.04e+03 5.33e+00 bond pdb=" C ILE c 22 " pdb=" N PRO c 23 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.97e+00 bond pdb=" N MET C 198 " pdb=" CA MET C 198 " ideal model delta sigma weight residual 1.460 1.428 0.032 1.45e-02 4.76e+03 4.89e+00 ... (remaining 11725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 15550 2.91 - 5.83: 379 5.83 - 8.74: 64 8.74 - 11.66: 10 11.66 - 14.57: 3 Bond angle restraints: 16006 Sorted by residual: angle pdb=" N MET C 198 " pdb=" CA MET C 198 " pdb=" C MET C 198 " ideal model delta sigma weight residual 110.44 96.70 13.74 1.20e+00 6.94e-01 1.31e+02 angle pdb=" N GLN c 16 " pdb=" CA GLN c 16 " pdb=" CB GLN c 16 " ideal model delta sigma weight residual 110.30 118.21 -7.91 1.54e+00 4.22e-01 2.64e+01 angle pdb=" CA TRP C 39 " pdb=" CB TRP C 39 " pdb=" CG TRP C 39 " ideal model delta sigma weight residual 113.60 122.59 -8.99 1.90e+00 2.77e-01 2.24e+01 angle pdb=" N GLN C 16 " pdb=" CA GLN C 16 " pdb=" CB GLN C 16 " ideal model delta sigma weight residual 110.30 117.56 -7.26 1.54e+00 4.22e-01 2.22e+01 angle pdb=" N ALA C 197 " pdb=" CA ALA C 197 " pdb=" C ALA C 197 " ideal model delta sigma weight residual 113.56 107.21 6.35 1.39e+00 5.18e-01 2.09e+01 ... (remaining 16001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 5888 16.10 - 32.21: 729 32.21 - 48.31: 193 48.31 - 64.41: 25 64.41 - 80.51: 7 Dihedral angle restraints: 6842 sinusoidal: 2660 harmonic: 4182 Sorted by residual: dihedral pdb=" CA ASN C 181 " pdb=" C ASN C 181 " pdb=" N THR C 182 " pdb=" CA THR C 182 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA THR C 182 " pdb=" C THR C 182 " pdb=" N LEU C 183 " pdb=" CA LEU C 183 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU A 110 " pdb=" C LEU A 110 " pdb=" N GLU A 111 " pdb=" CA GLU A 111 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 6839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1357 0.057 - 0.114: 401 0.114 - 0.171: 96 0.171 - 0.228: 12 0.228 - 0.285: 4 Chirality restraints: 1870 Sorted by residual: chirality pdb=" CB VAL a 70 " pdb=" CA VAL a 70 " pdb=" CG1 VAL a 70 " pdb=" CG2 VAL a 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA TRP b 55 " pdb=" N TRP b 55 " pdb=" C TRP b 55 " pdb=" CB TRP b 55 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1867 not shown) Planarity restraints: 1978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE b 35 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO b 36 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO b 36 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO b 36 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 89 " 0.063 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO B 90 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU b 89 " -0.061 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO b 90 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO b 90 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO b 90 " -0.050 5.00e-02 4.00e+02 ... (remaining 1975 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 515 2.73 - 3.27: 11691 3.27 - 3.82: 19175 3.82 - 4.36: 22688 4.36 - 4.90: 38499 Nonbonded interactions: 92568 Sorted by model distance: nonbonded pdb=" OH TYR c 54 " pdb=" O SER c 193 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR C 54 " pdb=" O SER C 193 " model vdw 2.227 3.040 nonbonded pdb=" O VAL B 159 " pdb=" OG SER B 162 " model vdw 2.294 3.040 nonbonded pdb=" OE2 GLU B 10 " pdb=" NH2 ARG B 68 " model vdw 2.319 3.120 nonbonded pdb=" O VAL b 159 " pdb=" OG SER b 162 " model vdw 2.349 3.040 ... (remaining 92563 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.180 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.006 0.072 11730 Z= 0.252 Angle : 1.081 14.571 16006 Z= 0.548 Chirality : 0.058 0.285 1870 Planarity : 0.010 0.110 1978 Dihedral : 15.030 80.514 4138 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 0.42 % Allowed : 7.36 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.21), residues: 1446 helix: -0.03 (0.16), residues: 962 sheet: -0.84 (0.83), residues: 48 loop : -1.09 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 90 TYR 0.021 0.003 TYR C 54 PHE 0.022 0.002 PHE B 142 TRP 0.055 0.003 TRP c 20 HIS 0.012 0.002 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00586 (11730) covalent geometry : angle 1.08077 (16006) hydrogen bonds : bond 0.11540 ( 720) hydrogen bonds : angle 6.43138 ( 2136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 194 ILE cc_start: 0.7607 (mt) cc_final: 0.7387 (mm) outliers start: 5 outliers final: 4 residues processed: 151 average time/residue: 0.1164 time to fit residues: 24.9647 Evaluate side-chains 130 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 198 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 169 ASN A 174 HIS B 17 HIS B 100 HIS ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.179474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.154568 restraints weight = 13658.536| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.74 r_work: 0.3660 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11730 Z= 0.161 Angle : 0.685 9.663 16006 Z= 0.337 Chirality : 0.042 0.160 1870 Planarity : 0.007 0.088 1978 Dihedral : 5.454 58.337 1580 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.37 % Allowed : 9.73 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.22), residues: 1446 helix: 0.90 (0.16), residues: 976 sheet: 1.45 (1.24), residues: 24 loop : -0.92 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 59 TYR 0.011 0.001 TYR A 100 PHE 0.013 0.001 PHE b 7 TRP 0.032 0.002 TRP b 55 HIS 0.005 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00401 (11730) covalent geometry : angle 0.68487 (16006) hydrogen bonds : bond 0.03984 ( 720) hydrogen bonds : angle 4.78241 ( 2136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.394 Fit side-chains REVERT: a 59 GLU cc_start: 0.7567 (pm20) cc_final: 0.7215 (pm20) REVERT: C 38 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8248 (tp) REVERT: C 198 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8557 (tmm) outliers start: 28 outliers final: 20 residues processed: 143 average time/residue: 0.1107 time to fit residues: 22.7869 Evaluate side-chains 145 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 104 THR Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 198 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 109 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 73 optimal weight: 0.0570 chunk 129 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.182282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157981 restraints weight = 13776.229| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.80 r_work: 0.3676 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11730 Z= 0.124 Angle : 0.613 9.391 16006 Z= 0.297 Chirality : 0.040 0.152 1870 Planarity : 0.006 0.076 1978 Dihedral : 5.068 58.040 1577 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.03 % Allowed : 12.52 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.23), residues: 1446 helix: 1.44 (0.17), residues: 970 sheet: -0.46 (0.88), residues: 48 loop : -0.50 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 90 TYR 0.009 0.001 TYR C 58 PHE 0.012 0.001 PHE b 7 TRP 0.025 0.001 TRP b 55 HIS 0.002 0.001 HIS a 186 Details of bonding type rmsd covalent geometry : bond 0.00300 (11730) covalent geometry : angle 0.61312 (16006) hydrogen bonds : bond 0.03465 ( 720) hydrogen bonds : angle 4.41235 ( 2136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.452 Fit side-chains REVERT: a 59 GLU cc_start: 0.7694 (pm20) cc_final: 0.7306 (pm20) REVERT: c 230 LYS cc_start: 0.8313 (pttp) cc_final: 0.7825 (ttpt) REVERT: A 154 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7031 (pt0) REVERT: C 198 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8301 (tmm) outliers start: 24 outliers final: 11 residues processed: 140 average time/residue: 0.1086 time to fit residues: 22.2986 Evaluate side-chains 138 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 198 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 118 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 28 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 81 GLN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.176929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.151930 restraints weight = 13826.899| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.74 r_work: 0.3606 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11730 Z= 0.152 Angle : 0.621 9.044 16006 Z= 0.301 Chirality : 0.042 0.155 1870 Planarity : 0.006 0.074 1978 Dihedral : 4.676 52.842 1575 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.54 % Allowed : 14.13 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.23), residues: 1446 helix: 1.57 (0.17), residues: 982 sheet: -1.27 (0.68), residues: 68 loop : -0.26 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.010 0.001 TYR A 100 PHE 0.010 0.001 PHE b 7 TRP 0.023 0.001 TRP c 20 HIS 0.003 0.001 HIS a 174 Details of bonding type rmsd covalent geometry : bond 0.00382 (11730) covalent geometry : angle 0.62058 (16006) hydrogen bonds : bond 0.03557 ( 720) hydrogen bonds : angle 4.29498 ( 2136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.340 Fit side-chains REVERT: a 160 ASP cc_start: 0.8523 (p0) cc_final: 0.8289 (p0) REVERT: b 156 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7828 (mtm-85) REVERT: c 80 ILE cc_start: 0.9220 (mm) cc_final: 0.8958 (mt) REVERT: c 230 LYS cc_start: 0.8320 (pttp) cc_final: 0.7991 (ttpt) REVERT: A 1 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6620 (ptp) REVERT: A 154 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7070 (pt0) REVERT: C 198 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8292 (tmm) outliers start: 30 outliers final: 22 residues processed: 146 average time/residue: 0.1103 time to fit residues: 23.2282 Evaluate side-chains 151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142549 restraints weight = 14021.125| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.66 r_work: 0.3542 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11730 Z= 0.168 Angle : 0.627 9.130 16006 Z= 0.303 Chirality : 0.042 0.154 1870 Planarity : 0.006 0.072 1978 Dihedral : 4.560 44.219 1575 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.45 % Allowed : 14.81 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.23), residues: 1446 helix: 1.65 (0.17), residues: 978 sheet: -0.51 (1.02), residues: 36 loop : -0.60 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 54 TYR 0.011 0.001 TYR A 100 PHE 0.009 0.001 PHE D 5 TRP 0.020 0.001 TRP c 20 HIS 0.004 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00427 (11730) covalent geometry : angle 0.62695 (16006) hydrogen bonds : bond 0.03637 ( 720) hydrogen bonds : angle 4.24636 ( 2136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.458 Fit side-chains REVERT: a 1 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6877 (ptp) REVERT: b 156 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7731 (mtm-85) REVERT: c 80 ILE cc_start: 0.9194 (mm) cc_final: 0.8943 (mt) REVERT: c 204 TRP cc_start: 0.8312 (m100) cc_final: 0.7993 (m100) REVERT: c 230 LYS cc_start: 0.8415 (pttp) cc_final: 0.8032 (ttpt) REVERT: A 154 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7116 (pt0) REVERT: C 80 ILE cc_start: 0.9251 (mm) cc_final: 0.9025 (mt) REVERT: C 198 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8135 (ttt) outliers start: 29 outliers final: 18 residues processed: 149 average time/residue: 0.1174 time to fit residues: 25.1491 Evaluate side-chains 151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.171112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144804 restraints weight = 13957.016| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.68 r_work: 0.3555 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11730 Z= 0.147 Angle : 0.602 9.453 16006 Z= 0.289 Chirality : 0.041 0.152 1870 Planarity : 0.005 0.071 1978 Dihedral : 4.422 35.151 1575 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.28 % Allowed : 15.91 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.23), residues: 1446 helix: 1.76 (0.17), residues: 982 sheet: -0.59 (1.01), residues: 36 loop : -0.60 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 54 TYR 0.009 0.001 TYR A 100 PHE 0.009 0.001 PHE b 7 TRP 0.021 0.001 TRP c 20 HIS 0.003 0.001 HIS c 174 Details of bonding type rmsd covalent geometry : bond 0.00372 (11730) covalent geometry : angle 0.60164 (16006) hydrogen bonds : bond 0.03473 ( 720) hydrogen bonds : angle 4.15146 ( 2136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.469 Fit side-chains REVERT: b 156 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7858 (mtm-85) REVERT: c 80 ILE cc_start: 0.9170 (mm) cc_final: 0.8930 (mt) REVERT: c 204 TRP cc_start: 0.8277 (m100) cc_final: 0.7980 (m-10) REVERT: c 230 LYS cc_start: 0.8429 (pttp) cc_final: 0.8048 (ttpt) REVERT: d 54 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.8162 (mpt180) REVERT: A 154 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7101 (pt0) REVERT: C 80 ILE cc_start: 0.9238 (mm) cc_final: 0.9015 (mt) outliers start: 27 outliers final: 20 residues processed: 145 average time/residue: 0.1129 time to fit residues: 23.5740 Evaluate side-chains 148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 228 MET Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 141 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 130 optimal weight: 0.0670 chunk 30 optimal weight: 0.8980 chunk 107 optimal weight: 0.0970 chunk 132 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.1918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134154 restraints weight = 13798.371| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.57 r_work: 0.3373 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11730 Z= 0.136 Angle : 0.601 12.031 16006 Z= 0.286 Chirality : 0.041 0.149 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.214 19.400 1572 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.20 % Allowed : 16.41 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.23), residues: 1446 helix: 1.87 (0.17), residues: 982 sheet: -0.21 (0.88), residues: 46 loop : -0.47 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 54 TYR 0.009 0.001 TYR A 100 PHE 0.009 0.001 PHE b 7 TRP 0.019 0.001 TRP c 20 HIS 0.003 0.001 HIS c 174 Details of bonding type rmsd covalent geometry : bond 0.00341 (11730) covalent geometry : angle 0.60125 (16006) hydrogen bonds : bond 0.03370 ( 720) hydrogen bonds : angle 4.07378 ( 2136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.461 Fit side-chains REVERT: a 1 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6787 (ptp) REVERT: b 156 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7837 (mtm-85) REVERT: c 80 ILE cc_start: 0.9189 (mm) cc_final: 0.8941 (mt) REVERT: c 204 TRP cc_start: 0.8307 (m100) cc_final: 0.8047 (m-10) REVERT: c 230 LYS cc_start: 0.8406 (pttp) cc_final: 0.8096 (ttpt) REVERT: d 54 ARG cc_start: 0.8413 (tpp-160) cc_final: 0.8161 (mpt180) REVERT: A 30 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: A 154 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7216 (pt0) REVERT: C 80 ILE cc_start: 0.9233 (mm) cc_final: 0.9023 (mt) outliers start: 26 outliers final: 21 residues processed: 142 average time/residue: 0.1188 time to fit residues: 23.8147 Evaluate side-chains 151 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 228 MET Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 73 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128019 restraints weight = 13930.764| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.70 r_work: 0.3295 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11730 Z= 0.244 Angle : 0.691 11.279 16006 Z= 0.333 Chirality : 0.045 0.165 1870 Planarity : 0.006 0.070 1978 Dihedral : 4.411 20.096 1572 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.37 % Allowed : 16.67 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.23), residues: 1446 helix: 1.56 (0.17), residues: 970 sheet: -0.74 (1.01), residues: 36 loop : -0.53 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 54 TYR 0.014 0.002 TYR A 100 PHE 0.012 0.002 PHE D 5 TRP 0.021 0.002 TRP c 20 HIS 0.005 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00619 (11730) covalent geometry : angle 0.69147 (16006) hydrogen bonds : bond 0.04085 ( 720) hydrogen bonds : angle 4.33354 ( 2136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6899 (ptp) REVERT: b 156 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7769 (mtm-85) REVERT: c 80 ILE cc_start: 0.9237 (mm) cc_final: 0.8980 (mt) REVERT: c 204 TRP cc_start: 0.8413 (m100) cc_final: 0.8152 (m100) REVERT: c 230 LYS cc_start: 0.8527 (pttp) cc_final: 0.8211 (ttpt) REVERT: A 30 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: A 154 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7300 (pt0) REVERT: C 80 ILE cc_start: 0.9304 (mm) cc_final: 0.9060 (mt) REVERT: C 204 TRP cc_start: 0.8288 (m100) cc_final: 0.8001 (m100) outliers start: 28 outliers final: 25 residues processed: 150 average time/residue: 0.1043 time to fit residues: 22.7760 Evaluate side-chains 162 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 228 MET Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130785 restraints weight = 13803.448| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.66 r_work: 0.3338 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11730 Z= 0.164 Angle : 0.632 10.842 16006 Z= 0.305 Chirality : 0.042 0.225 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.318 19.554 1572 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.45 % Allowed : 16.58 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.23), residues: 1446 helix: 1.65 (0.17), residues: 982 sheet: -0.82 (0.99), residues: 36 loop : -0.60 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 54 TYR 0.010 0.001 TYR A 100 PHE 0.009 0.001 PHE D 5 TRP 0.021 0.001 TRP c 20 HIS 0.004 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00415 (11730) covalent geometry : angle 0.63164 (16006) hydrogen bonds : bond 0.03666 ( 720) hydrogen bonds : angle 4.20170 ( 2136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.454 Fit side-chains REVERT: a 1 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6850 (ptp) REVERT: b 156 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7812 (mtm-85) REVERT: c 80 ILE cc_start: 0.9198 (mm) cc_final: 0.8945 (mt) REVERT: c 204 TRP cc_start: 0.8361 (m100) cc_final: 0.8130 (m100) REVERT: c 230 LYS cc_start: 0.8477 (pttp) cc_final: 0.8221 (ttpt) REVERT: A 30 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: A 154 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7285 (pt0) REVERT: C 80 ILE cc_start: 0.9269 (mm) cc_final: 0.9031 (mt) REVERT: C 204 TRP cc_start: 0.8274 (m100) cc_final: 0.8005 (m100) outliers start: 29 outliers final: 22 residues processed: 145 average time/residue: 0.1147 time to fit residues: 24.0703 Evaluate side-chains 156 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 135 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.160725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135182 restraints weight = 13792.570| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.57 r_work: 0.3390 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11730 Z= 0.117 Angle : 0.591 10.322 16006 Z= 0.283 Chirality : 0.040 0.154 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.155 19.296 1572 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.03 % Allowed : 17.26 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.23), residues: 1446 helix: 1.95 (0.17), residues: 978 sheet: -0.29 (0.87), residues: 46 loop : -0.51 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 54 TYR 0.006 0.001 TYR A 100 PHE 0.008 0.001 PHE b 7 TRP 0.018 0.001 TRP c 20 HIS 0.003 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00283 (11730) covalent geometry : angle 0.59060 (16006) hydrogen bonds : bond 0.03295 ( 720) hydrogen bonds : angle 4.02752 ( 2136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.448 Fit side-chains REVERT: a 1 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6960 (ptp) REVERT: b 156 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7836 (mtm-85) REVERT: c 80 ILE cc_start: 0.9176 (mm) cc_final: 0.8932 (mt) REVERT: c 204 TRP cc_start: 0.8340 (m100) cc_final: 0.8082 (m-10) REVERT: c 229 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7207 (mm-30) REVERT: c 230 LYS cc_start: 0.8386 (pttp) cc_final: 0.8085 (ttpt) REVERT: d 54 ARG cc_start: 0.8196 (tpp-160) cc_final: 0.7826 (mpt180) REVERT: A 30 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: A 154 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7277 (pt0) REVERT: C 80 ILE cc_start: 0.9218 (mm) cc_final: 0.8983 (mt) REVERT: C 204 TRP cc_start: 0.8239 (m100) cc_final: 0.7973 (m100) outliers start: 24 outliers final: 18 residues processed: 147 average time/residue: 0.1181 time to fit residues: 24.8179 Evaluate side-chains 150 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 20 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134619 restraints weight = 13649.133| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.63 r_work: 0.3382 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11730 Z= 0.134 Angle : 0.599 10.008 16006 Z= 0.288 Chirality : 0.041 0.172 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.142 19.180 1572 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.20 % Allowed : 17.09 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.23), residues: 1446 helix: 1.89 (0.17), residues: 990 sheet: -0.20 (0.88), residues: 46 loop : -0.56 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 54 TYR 0.008 0.001 TYR A 100 PHE 0.008 0.001 PHE b 7 TRP 0.016 0.001 TRP B 55 HIS 0.002 0.001 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00331 (11730) covalent geometry : angle 0.59913 (16006) hydrogen bonds : bond 0.03383 ( 720) hydrogen bonds : angle 4.03178 ( 2136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2586.52 seconds wall clock time: 45 minutes 2.69 seconds (2702.69 seconds total)