Starting phenix.real_space_refine on Wed May 14 00:34:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce1_16597/05_2025/8ce1_16597.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce1_16597/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ce1_16597/05_2025/8ce1_16597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce1_16597/05_2025/8ce1_16597.map" model { file = "/net/cci-nas-00/data/ceres_data/8ce1_16597/05_2025/8ce1_16597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce1_16597/05_2025/8ce1_16597.cif" } resolution = 3.47 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= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.76, per 1000 atoms: 0.59 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: 2.46 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.99 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: 3.16 Time building geometry restraints manager: 2.92 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: 0.02 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.910 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (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 TRP 0.055 0.003 TRP c 20 HIS 0.012 0.002 HIS A 174 PHE 0.022 0.002 PHE B 142 TYR 0.021 0.003 TYR C 54 ARG 0.015 0.001 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.11540 ( 720) hydrogen bonds : angle 6.43138 ( 2136) covalent geometry : bond 0.00586 (11730) covalent geometry : angle 1.08077 (16006) *********************** 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 : 1.182 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: 0.2455 time to fit residues: 52.6330 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 : 1.100 ------------------------------------------------------------------------------- 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 119 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.181887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.157425 restraints weight = 13558.090| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.66 r_work: 0.3721 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1208 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= 0.141 Angle : 0.653 9.102 16006 Z= 0.322 Chirality : 0.042 0.156 1870 Planarity : 0.007 0.085 1978 Dihedral : 5.380 59.016 1580 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.20 % Allowed : 10.15 % Favored : 87.65 % 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: 0.64 (0.22), residues: 1446 helix: 1.03 (0.16), residues: 974 sheet: -0.08 (0.92), residues: 44 loop : -0.80 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP b 55 HIS 0.006 0.001 HIS D 38 PHE 0.013 0.001 PHE b 7 TYR 0.009 0.001 TYR A 100 ARG 0.005 0.000 ARG d 59 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 720) hydrogen bonds : angle 4.64835 ( 2136) covalent geometry : bond 0.00347 (11730) covalent geometry : angle 0.65311 (16006) *********************** 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 157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.154 Fit side-chains REVERT: a 59 GLU cc_start: 0.7605 (pm20) cc_final: 0.7190 (pm20) REVERT: C 59 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8112 (mp) REVERT: C 198 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8532 (tmm) outliers start: 26 outliers final: 17 residues processed: 142 average time/residue: 0.2244 time to fit residues: 46.3943 Evaluate side-chains 142 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 2 MET 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 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 59 LEU 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 136 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 81 GLN d 38 HIS ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140064 restraints weight = 13971.817| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.69 r_work: 0.3483 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 11730 Z= 0.314 Angle : 0.820 9.413 16006 Z= 0.401 Chirality : 0.049 0.194 1870 Planarity : 0.007 0.079 1978 Dihedral : 5.449 55.922 1577 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.55 % Allowed : 11.76 % Favored : 84.69 % 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: 0.39 (0.22), residues: 1446 helix: 0.78 (0.17), residues: 972 sheet: -0.62 (1.08), residues: 36 loop : -0.67 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP c 20 HIS 0.007 0.001 HIS C 174 PHE 0.018 0.002 PHE B 70 TYR 0.017 0.002 TYR A 100 ARG 0.006 0.001 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 720) hydrogen bonds : angle 4.86690 ( 2136) covalent geometry : bond 0.00795 (11730) covalent geometry : angle 0.81973 (16006) *********************** 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 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.291 Fit side-chains REVERT: c 80 ILE cc_start: 0.9285 (mm) cc_final: 0.9017 (mt) REVERT: c 204 TRP cc_start: 0.8371 (m100) cc_final: 0.8121 (m100) REVERT: A 61 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8017 (mt) REVERT: A 154 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7139 (pt0) REVERT: C 38 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8355 (tp) REVERT: C 204 TRP cc_start: 0.8264 (m100) cc_final: 0.7955 (m100) REVERT: D 54 ARG cc_start: 0.7730 (mmt90) cc_final: 0.7514 (mpt-90) outliers start: 42 outliers final: 27 residues processed: 155 average time/residue: 0.2211 time to fit residues: 50.3720 Evaluate side-chains 153 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 104 THR Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 185 MET Chi-restraints excluded: chain b residue 205 THR 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 182 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 106 LEU 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 B residue 190 ASP Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 181 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 6 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.170820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144901 restraints weight = 13917.082| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.63 r_work: 0.3558 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11730 Z= 0.138 Angle : 0.627 9.350 16006 Z= 0.304 Chirality : 0.041 0.161 1870 Planarity : 0.006 0.073 1978 Dihedral : 4.647 22.481 1572 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.54 % Allowed : 14.21 % Favored : 83.25 % 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: 0.96 (0.23), residues: 1446 helix: 1.27 (0.17), residues: 986 sheet: -0.78 (1.02), residues: 36 loop : -0.64 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 55 HIS 0.003 0.001 HIS c 174 PHE 0.009 0.001 PHE b 7 TYR 0.009 0.001 TYR A 100 ARG 0.003 0.000 ARG D 59 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 720) hydrogen bonds : angle 4.40679 ( 2136) covalent geometry : bond 0.00345 (11730) covalent geometry : angle 0.62708 (16006) *********************** 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 : 1.137 Fit side-chains REVERT: a 1 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6969 (ptp) REVERT: b 156 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7727 (mtm-85) REVERT: c 80 ILE cc_start: 0.9175 (mm) cc_final: 0.8935 (mt) REVERT: c 204 TRP cc_start: 0.8305 (m100) cc_final: 0.8003 (m100) REVERT: A 61 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 154 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7091 (pt0) REVERT: C 80 ILE cc_start: 0.9237 (mm) cc_final: 0.9000 (mt) REVERT: C 198 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7392 (tmt) REVERT: C 204 TRP cc_start: 0.8111 (m100) cc_final: 0.7807 (m100) outliers start: 30 outliers final: 17 residues processed: 146 average time/residue: 0.2271 time to fit residues: 47.9008 Evaluate side-chains 149 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 185 MET Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 140 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 84 optimal weight: 10.0000 chunk 41 optimal weight: 0.0270 chunk 99 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.169171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143812 restraints weight = 13855.052| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.72 r_work: 0.3525 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11730 Z= 0.159 Angle : 0.626 9.346 16006 Z= 0.303 Chirality : 0.042 0.159 1870 Planarity : 0.005 0.071 1978 Dihedral : 4.471 21.808 1572 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.79 % Allowed : 14.81 % Favored : 82.40 % 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: 1.23 (0.23), residues: 1446 helix: 1.51 (0.17), residues: 986 sheet: -0.94 (1.01), residues: 36 loop : -0.59 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 20 HIS 0.003 0.001 HIS C 174 PHE 0.009 0.001 PHE b 28 TYR 0.010 0.001 TYR A 100 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 720) hydrogen bonds : angle 4.28892 ( 2136) covalent geometry : bond 0.00401 (11730) covalent geometry : angle 0.62637 (16006) *********************** 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 161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.147 Fit side-chains REVERT: a 1 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6969 (ptp) REVERT: b 156 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7736 (mtm-85) REVERT: c 80 ILE cc_start: 0.9202 (mm) cc_final: 0.8963 (mt) REVERT: c 204 TRP cc_start: 0.8354 (m100) cc_final: 0.8043 (m-10) REVERT: A 1 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6669 (ptp) REVERT: A 61 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7699 (mt) REVERT: A 154 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7120 (pt0) REVERT: C 80 ILE cc_start: 0.9231 (mm) cc_final: 0.9019 (mt) REVERT: C 198 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.7402 (tmt) REVERT: C 204 TRP cc_start: 0.8215 (m100) cc_final: 0.7884 (m100) outliers start: 33 outliers final: 20 residues processed: 144 average time/residue: 0.2273 time to fit residues: 47.3474 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 : 1.125 ------------------------------------------------------------------------------- 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 b residue 219 ILE Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain c residue 228 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 106 LEU 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 38 ILE 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 140 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.165604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139698 restraints weight = 14095.283| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.75 r_work: 0.3507 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11730 Z= 0.206 Angle : 0.660 9.303 16006 Z= 0.320 Chirality : 0.044 0.164 1870 Planarity : 0.006 0.071 1978 Dihedral : 4.514 21.425 1572 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.71 % Allowed : 15.99 % Favored : 81.30 % 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: 1.13 (0.23), residues: 1446 helix: 1.44 (0.17), residues: 986 sheet: -1.15 (1.01), residues: 36 loop : -0.61 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 20 HIS 0.005 0.001 HIS C 174 PHE 0.010 0.001 PHE D 5 TYR 0.013 0.001 TYR A 100 ARG 0.008 0.000 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 720) hydrogen bonds : angle 4.38458 ( 2136) covalent geometry : bond 0.00522 (11730) covalent geometry : angle 0.66042 (16006) *********************** 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 166 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.203 Fit side-chains REVERT: a 1 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7074 (ptp) REVERT: b 156 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.7809 (mtm-85) REVERT: c 80 ILE cc_start: 0.9204 (mm) cc_final: 0.8967 (mt) REVERT: c 91 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7784 (mp) REVERT: c 204 TRP cc_start: 0.8398 (m100) cc_final: 0.8088 (m100) REVERT: c 230 LYS cc_start: 0.8396 (pttp) cc_final: 0.8015 (ttpt) REVERT: A 30 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: A 61 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7672 (mt) REVERT: A 154 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7184 (pt0) REVERT: C 80 ILE cc_start: 0.9250 (mm) cc_final: 0.9029 (mt) REVERT: C 198 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7356 (tmt) REVERT: C 204 TRP cc_start: 0.8311 (m100) cc_final: 0.7964 (m100) outliers start: 32 outliers final: 24 residues processed: 151 average time/residue: 0.2274 time to fit residues: 50.1782 Evaluate side-chains 158 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 b residue 205 THR Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 38 ILE Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 182 THR 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 61 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 106 LEU 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 162 LEU Chi-restraints excluded: chain C residue 198 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 65 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.168078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142331 restraints weight = 14160.211| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.76 r_work: 0.3516 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11730 Z= 0.156 Angle : 0.623 12.157 16006 Z= 0.299 Chirality : 0.042 0.157 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.381 21.176 1572 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.71 % Allowed : 16.67 % Favored : 80.63 % 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: 1.38 (0.23), residues: 1446 helix: 1.63 (0.17), residues: 986 sheet: -1.05 (1.00), residues: 36 loop : -0.53 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 55 HIS 0.003 0.001 HIS C 174 PHE 0.009 0.001 PHE B 28 TYR 0.010 0.001 TYR A 100 ARG 0.004 0.000 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 720) hydrogen bonds : angle 4.24064 ( 2136) covalent geometry : bond 0.00395 (11730) covalent geometry : angle 0.62289 (16006) *********************** 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 165 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.147 Fit side-chains REVERT: a 1 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6973 (ptp) REVERT: a 52 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8788 (mp) REVERT: b 156 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7775 (mtm-85) REVERT: c 80 ILE cc_start: 0.9182 (mm) cc_final: 0.8936 (mt) REVERT: c 91 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7884 (mp) REVERT: c 204 TRP cc_start: 0.8355 (m100) cc_final: 0.8077 (m100) REVERT: c 230 LYS cc_start: 0.8373 (pttp) cc_final: 0.7999 (ttpt) REVERT: d 54 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8066 (mpt180) REVERT: A 1 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6483 (ptp) REVERT: A 30 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: A 61 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7684 (mt) REVERT: A 154 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7214 (pt0) REVERT: C 7 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8209 (mm-40) REVERT: C 80 ILE cc_start: 0.9240 (mm) cc_final: 0.9018 (mt) REVERT: C 198 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7455 (tmt) REVERT: C 204 TRP cc_start: 0.8276 (m100) cc_final: 0.7968 (m100) outliers start: 32 outliers final: 23 residues processed: 151 average time/residue: 0.2303 time to fit residues: 49.7499 Evaluate side-chains 161 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 52 LEU 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 b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 91 LEU 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 30 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 106 LEU 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 30 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 198 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.163635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137698 restraints weight = 14109.782| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.76 r_work: 0.3472 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11730 Z= 0.254 Angle : 0.703 11.112 16006 Z= 0.339 Chirality : 0.045 0.169 1870 Planarity : 0.006 0.070 1978 Dihedral : 4.553 21.300 1572 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.21 % Allowed : 16.58 % Favored : 80.20 % 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: 1.00 (0.23), residues: 1446 helix: 1.33 (0.17), residues: 994 sheet: -1.09 (1.02), residues: 36 loop : -0.70 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 20 HIS 0.006 0.001 HIS C 174 PHE 0.011 0.002 PHE D 5 TYR 0.014 0.002 TYR A 100 ARG 0.006 0.000 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 720) hydrogen bonds : angle 4.44520 ( 2136) covalent geometry : bond 0.00639 (11730) covalent geometry : angle 0.70321 (16006) *********************** 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 172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: a 1 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7193 (ptp) REVERT: a 160 ASP cc_start: 0.8636 (p0) cc_final: 0.8364 (p0) REVERT: b 156 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.8009 (mtm-85) REVERT: c 16 GLN cc_start: 0.8448 (mt0) cc_final: 0.7786 (mp10) REVERT: c 80 ILE cc_start: 0.9217 (mm) cc_final: 0.8974 (mt) REVERT: c 91 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7868 (mp) REVERT: c 204 TRP cc_start: 0.8378 (m100) cc_final: 0.8089 (m100) REVERT: c 230 LYS cc_start: 0.8495 (pttp) cc_final: 0.8087 (ttpt) REVERT: d 54 ARG cc_start: 0.8368 (tpp-160) cc_final: 0.8146 (mpt180) REVERT: A 1 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6651 (ptp) REVERT: A 30 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: A 154 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7184 (pt0) REVERT: C 80 ILE cc_start: 0.9274 (mm) cc_final: 0.9037 (mt) REVERT: C 198 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7178 (tmt) REVERT: C 204 TRP cc_start: 0.8326 (m100) cc_final: 0.8012 (m100) outliers start: 38 outliers final: 27 residues processed: 155 average time/residue: 0.2201 time to fit residues: 49.1596 Evaluate side-chains 164 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 b residue 205 THR 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 91 LEU Chi-restraints excluded: chain c residue 182 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 140 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.157293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131363 restraints weight = 13930.609| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.60 r_work: 0.3338 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11730 Z= 0.134 Angle : 0.606 10.602 16006 Z= 0.292 Chirality : 0.041 0.155 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.339 21.042 1572 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.54 % Allowed : 17.68 % Favored : 79.78 % 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: 1.44 (0.23), residues: 1446 helix: 1.70 (0.17), residues: 982 sheet: -0.90 (1.02), residues: 36 loop : -0.57 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 55 HIS 0.002 0.000 HIS c 174 PHE 0.008 0.001 PHE B 28 TYR 0.008 0.001 TYR A 100 ARG 0.005 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 720) hydrogen bonds : angle 4.20281 ( 2136) covalent geometry : bond 0.00336 (11730) covalent geometry : angle 0.60625 (16006) *********************** 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 155 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.217 Fit side-chains REVERT: a 1 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7060 (ptp) REVERT: b 156 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7949 (mtm-85) REVERT: b 217 ILE cc_start: 0.8705 (mt) cc_final: 0.8423 (mt) REVERT: c 80 ILE cc_start: 0.9196 (mm) cc_final: 0.8947 (mt) REVERT: c 204 TRP cc_start: 0.8386 (m100) cc_final: 0.8124 (m100) REVERT: c 229 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7290 (mm-30) REVERT: c 230 LYS cc_start: 0.8434 (pttp) cc_final: 0.8164 (ttpt) REVERT: A 1 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6438 (ptp) REVERT: A 30 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: A 61 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 154 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7287 (pt0) REVERT: C 80 ILE cc_start: 0.9217 (mm) cc_final: 0.8990 (mt) REVERT: C 198 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7281 (tmt) REVERT: C 204 TRP cc_start: 0.8290 (m100) cc_final: 0.7999 (m100) outliers start: 30 outliers final: 22 residues processed: 142 average time/residue: 0.2305 time to fit residues: 47.2890 Evaluate side-chains 149 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 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 30 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 140 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 38 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 198 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 10.0000 chunk 106 optimal weight: 0.0870 chunk 15 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 112 optimal weight: 0.0050 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.2178 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.154244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128645 restraints weight = 13956.387| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.66 r_work: 0.3307 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11730 Z= 0.197 Angle : 0.649 10.351 16006 Z= 0.313 Chirality : 0.043 0.162 1870 Planarity : 0.005 0.070 1978 Dihedral : 4.388 21.083 1572 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.54 % Allowed : 17.94 % Favored : 79.53 % 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: 1.25 (0.23), residues: 1446 helix: 1.53 (0.17), residues: 994 sheet: -0.98 (1.02), residues: 36 loop : -0.65 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 55 HIS 0.004 0.001 HIS C 174 PHE 0.010 0.001 PHE B 175 TYR 0.012 0.001 TYR A 100 ARG 0.008 0.000 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 720) hydrogen bonds : angle 4.29727 ( 2136) covalent geometry : bond 0.00499 (11730) covalent geometry : angle 0.64881 (16006) ********************** 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 158 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 1 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7109 (ptp) REVERT: a 160 ASP cc_start: 0.8581 (p0) cc_final: 0.8325 (p0) REVERT: b 156 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7961 (mtm-85) REVERT: c 80 ILE cc_start: 0.9205 (mm) cc_final: 0.8955 (mt) REVERT: c 91 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7936 (mp) REVERT: c 204 TRP cc_start: 0.8417 (m100) cc_final: 0.8150 (m100) REVERT: c 230 LYS cc_start: 0.8417 (pttp) cc_final: 0.8094 (ttpt) REVERT: d 54 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7809 (mpt180) REVERT: A 1 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6485 (ptp) REVERT: A 30 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: A 61 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7926 (mt) REVERT: A 154 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7295 (pt0) REVERT: C 7 GLN cc_start: 0.8536 (mm-40) cc_final: 0.7847 (mm-40) REVERT: C 80 ILE cc_start: 0.9273 (mm) cc_final: 0.9037 (mt) REVERT: C 198 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7173 (tmt) REVERT: C 204 TRP cc_start: 0.8305 (m100) cc_final: 0.8036 (m100) outliers start: 30 outliers final: 24 residues processed: 144 average time/residue: 0.2267 time to fit residues: 46.8533 Evaluate side-chains 158 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 b residue 219 ILE Chi-restraints excluded: chain c residue 21 PHE Chi-restraints excluded: chain c residue 91 LEU 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 30 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 140 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 38 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 198 MET 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 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 131 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.160131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134533 restraints weight = 13673.981| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.61 r_work: 0.3384 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11730 Z= 0.115 Angle : 0.584 10.404 16006 Z= 0.282 Chirality : 0.040 0.154 1870 Planarity : 0.005 0.071 1978 Dihedral : 4.212 20.704 1572 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.28 % Allowed : 18.44 % Favored : 79.27 % 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: 1.65 (0.23), residues: 1446 helix: 1.90 (0.17), residues: 982 sheet: -0.76 (1.02), residues: 36 loop : -0.61 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 55 HIS 0.002 0.000 HIS a 186 PHE 0.008 0.001 PHE b 28 TYR 0.007 0.001 TYR C 58 ARG 0.008 0.000 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 720) hydrogen bonds : angle 4.05376 ( 2136) covalent geometry : bond 0.00271 (11730) covalent geometry : angle 0.58415 (16006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4981.03 seconds wall clock time: 86 minutes 52.68 seconds (5212.68 seconds total)