Starting phenix.real_space_refine on Thu Mar 13 07:21:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejk_28185/03_2025/8ejk_28185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejk_28185/03_2025/8ejk_28185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejk_28185/03_2025/8ejk_28185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejk_28185/03_2025/8ejk_28185.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejk_28185/03_2025/8ejk_28185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejk_28185/03_2025/8ejk_28185.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 51 5.16 5 C 5462 2.51 5 N 1483 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8594 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1869 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2556 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 420 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1768 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1944 Classifications: {'peptide': 267} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 248} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'2YB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.64 Number of scatterers: 8594 At special positions: 0 Unit cell: (97.37, 116.63, 132.68, 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 51 16.00 O 1598 8.00 N 1483 7.00 C 5462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 37.3% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.921A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.780A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.879A pdb=" N GLN A 90 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 93 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.558A pdb=" N ASP A 154 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 175 through 195 Processing helix chain 'A' and resid 215 through 235 Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.554A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.597A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'R' and resid 5 through 35 Proline residue: R 21 - end of helix Processing helix chain 'R' and resid 39 through 69 Proline residue: R 60 - end of helix Processing helix chain 'R' and resid 75 through 77 No H-bonds generated for 'chain 'R' and resid 75 through 77' Processing helix chain 'R' and resid 78 through 110 removed outlier: 3.529A pdb=" N VAL R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Proline residue: R 89 - end of helix removed outlier: 4.090A pdb=" N GLY R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA R 98 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 118 Processing helix chain 'R' and resid 119 through 146 removed outlier: 3.624A pdb=" N SER R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL R 141 " --> pdb=" O HIS R 137 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU R 145 " --> pdb=" O VAL R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 191 Proline residue: R 181 - end of helix removed outlier: 3.740A pdb=" N LEU R 186 " --> pdb=" O ALA R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 212 Processing helix chain 'R' and resid 215 through 227 Processing helix chain 'R' and resid 227 through 236 removed outlier: 3.512A pdb=" N CYS R 236 " --> pdb=" O THR R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 250 removed outlier: 3.786A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 267 removed outlier: 4.374A pdb=" N ARG R 258 " --> pdb=" O GLY R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 272 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 4.677A pdb=" N VAL A 78 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG A 35 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE A 99 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 37 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 101 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 39 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ASP A 103 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 98 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 134 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A 100 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN A 136 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 102 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 131 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N HIS A 206 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 133 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.345A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.797A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.031A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.953A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.643A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.732A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.628A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.651A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.706A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 3.722A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1206 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: 2.50 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2808 1.34 - 1.47: 2189 1.47 - 1.59: 3717 1.59 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 8784 Sorted by residual: bond pdb=" C27 2YB R 401 " pdb=" C28 2YB R 401 " ideal model delta sigma weight residual 1.505 1.392 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C1 2YB R 401 " pdb=" C2 2YB R 401 " ideal model delta sigma weight residual 1.503 1.392 0.111 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C14 2YB R 401 " pdb=" C15 2YB R 401 " ideal model delta sigma weight residual 1.502 1.392 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C21 2YB R 401 " pdb=" C22 2YB R 401 " ideal model delta sigma weight residual 1.498 1.395 0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C16 2YB R 401 " pdb=" C17 2YB R 401 " ideal model delta sigma weight residual 1.485 1.395 0.090 2.00e-02 2.50e+03 2.04e+01 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11718 1.92 - 3.83: 174 3.83 - 5.75: 29 5.75 - 7.66: 12 7.66 - 9.58: 2 Bond angle restraints: 11935 Sorted by residual: angle pdb=" N ASN E 194 " pdb=" CA ASN E 194 " pdb=" C ASN E 194 " ideal model delta sigma weight residual 108.60 115.15 -6.55 1.46e+00 4.69e-01 2.01e+01 angle pdb=" N SER E 193 " pdb=" CA SER E 193 " pdb=" C SER E 193 " ideal model delta sigma weight residual 111.36 115.78 -4.42 1.09e+00 8.42e-01 1.64e+01 angle pdb=" CA CYS R 79 " pdb=" C CYS R 79 " pdb=" N PRO R 80 " ideal model delta sigma weight residual 120.81 117.35 3.46 8.60e-01 1.35e+00 1.62e+01 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 113.28 107.55 5.73 1.57e+00 4.06e-01 1.33e+01 angle pdb=" N ARG E 191 " pdb=" CA ARG E 191 " pdb=" C ARG E 191 " ideal model delta sigma weight residual 113.72 108.47 5.25 1.52e+00 4.33e-01 1.19e+01 ... (remaining 11930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 4835 23.80 - 47.61: 304 47.61 - 71.41: 23 71.41 - 95.21: 6 95.21 - 119.02: 1 Dihedral angle restraints: 5169 sinusoidal: 1948 harmonic: 3221 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 157.95 -64.95 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" C8 2YB R 401 " pdb=" C6 2YB R 401 " pdb=" C7 2YB R 401 " pdb=" O5 2YB R 401 " ideal model delta sinusoidal sigma weight residual 180.08 61.06 119.02 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C GLN B 17 " pdb=" N GLN B 17 " pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " ideal model delta harmonic sigma weight residual -122.60 -132.37 9.77 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 5166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1212 0.074 - 0.149: 126 0.149 - 0.223: 5 0.223 - 0.297: 0 0.297 - 0.372: 1 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CA GLN B 17 " pdb=" N GLN B 17 " pdb=" C GLN B 17 " pdb=" CB GLN B 17 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA ASN R 272 " pdb=" N ASN R 272 " pdb=" C ASN R 272 " pdb=" CB ASN R 272 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CB ILE R 263 " pdb=" CA ILE R 263 " pdb=" CG1 ILE R 263 " pdb=" CG2 ILE R 263 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 1341 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.050 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO C 49 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 88 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO R 89 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO R 89 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 89 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 38 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C MET C 38 " -0.041 2.00e-02 2.50e+03 pdb=" O MET C 38 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 39 " 0.014 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 232 2.70 - 3.25: 8474 3.25 - 3.80: 13612 3.80 - 4.35: 17100 4.35 - 4.90: 29678 Nonbonded interactions: 69096 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASP B 27 " pdb=" NZ LYS C 29 " model vdw 2.187 3.120 nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.235 3.040 ... (remaining 69091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.860 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.004 0.113 8784 Z= 0.261 Angle : 0.613 9.576 11935 Z= 0.320 Chirality : 0.045 0.372 1344 Planarity : 0.005 0.077 1526 Dihedral : 14.172 119.016 3095 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.66 % Cbeta Deviations : 0.10 % 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: 0.74 (0.26), residues: 1106 helix: 1.71 (0.27), residues: 369 sheet: 0.44 (0.32), residues: 302 loop : -0.47 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 PHE 0.016 0.001 PHE A 66 TYR 0.027 0.001 TYR B 59 ARG 0.004 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 11 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7554 (tm-30) REVERT: E 73 ASP cc_start: 0.7513 (t0) cc_final: 0.7283 (t0) REVERT: E 82 GLN cc_start: 0.8001 (tp40) cc_final: 0.7754 (mm110) REVERT: R 135 LEU cc_start: 0.9295 (mt) cc_final: 0.8892 (pp) REVERT: R 241 ASN cc_start: 0.9094 (m110) cc_final: 0.8617 (m-40) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1983 time to fit residues: 43.0008 Evaluate side-chains 132 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN E 167 HIS ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.085854 restraints weight = 16682.761| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.62 r_work: 0.2988 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8784 Z= 0.178 Angle : 0.558 11.146 11935 Z= 0.287 Chirality : 0.044 0.241 1344 Planarity : 0.004 0.058 1526 Dihedral : 5.718 88.359 1239 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.79 % Allowed : 8.72 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1106 helix: 2.06 (0.26), residues: 376 sheet: 0.48 (0.32), residues: 294 loop : -0.37 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 PHE 0.019 0.001 PHE R 9 TYR 0.019 0.001 TYR B 59 ARG 0.003 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8992 (m-30) cc_final: 0.8772 (m-30) REVERT: A 235 TYR cc_start: 0.9336 (m-80) cc_final: 0.9002 (m-80) REVERT: B 20 ASP cc_start: 0.8304 (m-30) cc_final: 0.7918 (m-30) REVERT: B 45 MET cc_start: 0.9096 (mmm) cc_final: 0.8847 (mtp) REVERT: C 11 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7767 (tm-30) REVERT: C 42 GLU cc_start: 0.8323 (mp0) cc_final: 0.7775 (mp0) REVERT: E 73 ASP cc_start: 0.8016 (t0) cc_final: 0.7594 (t0) REVERT: E 82 GLN cc_start: 0.8271 (tp40) cc_final: 0.7992 (mm110) REVERT: R 241 ASN cc_start: 0.9159 (m110) cc_final: 0.8750 (m110) outliers start: 16 outliers final: 9 residues processed: 153 average time/residue: 0.1937 time to fit residues: 41.4592 Evaluate side-chains 144 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 216 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 52 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 142 GLN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 47 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.082348 restraints weight = 16917.378| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.68 r_work: 0.2929 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8784 Z= 0.261 Angle : 0.572 9.822 11935 Z= 0.297 Chirality : 0.045 0.261 1344 Planarity : 0.004 0.060 1526 Dihedral : 5.911 87.835 1239 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.46 % Allowed : 12.19 % Favored : 85.35 % 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 (0.26), residues: 1106 helix: 2.05 (0.27), residues: 376 sheet: 0.49 (0.32), residues: 285 loop : -0.37 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 PHE 0.015 0.001 PHE A 66 TYR 0.013 0.001 TYR B 59 ARG 0.002 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9048 (m-30) cc_final: 0.8774 (m-30) REVERT: A 235 TYR cc_start: 0.9325 (m-80) cc_final: 0.8701 (m-80) REVERT: B 19 ARG cc_start: 0.8435 (mmt90) cc_final: 0.8151 (mmt90) REVERT: B 20 ASP cc_start: 0.8397 (m-30) cc_final: 0.8036 (m-30) REVERT: B 258 ASP cc_start: 0.7335 (t0) cc_final: 0.7068 (t0) REVERT: B 291 ASP cc_start: 0.8582 (m-30) cc_final: 0.7861 (m-30) REVERT: C 11 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 15 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8052 (mp) REVERT: C 42 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: E 73 ASP cc_start: 0.8124 (t0) cc_final: 0.7606 (t0) REVERT: E 82 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7892 (mm110) REVERT: E 246 GLU cc_start: 0.6562 (mp0) cc_final: 0.6304 (mp0) REVERT: R 259 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9108 (ttpt) outliers start: 22 outliers final: 11 residues processed: 149 average time/residue: 0.1908 time to fit residues: 39.8736 Evaluate side-chains 144 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 0.0020 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085392 restraints weight = 16784.382| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.73 r_work: 0.2976 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8784 Z= 0.150 Angle : 0.517 9.667 11935 Z= 0.267 Chirality : 0.042 0.222 1344 Planarity : 0.004 0.051 1526 Dihedral : 5.664 87.836 1239 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.35 % Allowed : 15.10 % Favored : 82.55 % 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: 1.09 (0.26), residues: 1106 helix: 2.16 (0.27), residues: 373 sheet: 0.61 (0.32), residues: 284 loop : -0.40 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS R 137 PHE 0.020 0.001 PHE R 9 TYR 0.016 0.001 TYR A 107 ARG 0.002 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8749 (m-30) cc_final: 0.8466 (m-30) REVERT: A 235 TYR cc_start: 0.9221 (m-80) cc_final: 0.8675 (m-80) REVERT: B 19 ARG cc_start: 0.8320 (mmt90) cc_final: 0.8067 (mmt90) REVERT: B 20 ASP cc_start: 0.8261 (m-30) cc_final: 0.7892 (m-30) REVERT: C 9 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7709 (tp) REVERT: C 11 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 42 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: E 73 ASP cc_start: 0.7911 (t0) cc_final: 0.7580 (t0) REVERT: R 259 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9077 (ttpt) outliers start: 21 outliers final: 8 residues processed: 162 average time/residue: 0.2000 time to fit residues: 45.2516 Evaluate side-chains 145 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.0470 chunk 83 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 0.0270 chunk 6 optimal weight: 0.7980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085387 restraints weight = 16790.687| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.72 r_work: 0.2982 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8784 Z= 0.158 Angle : 0.523 8.775 11935 Z= 0.270 Chirality : 0.042 0.261 1344 Planarity : 0.004 0.055 1526 Dihedral : 5.572 87.256 1239 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.57 % Allowed : 15.88 % Favored : 81.54 % 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: 1.12 (0.26), residues: 1106 helix: 2.25 (0.27), residues: 373 sheet: 0.56 (0.32), residues: 284 loop : -0.39 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 PHE 0.019 0.001 PHE R 9 TYR 0.016 0.001 TYR A 107 ARG 0.002 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8750 (m-30) cc_final: 0.8473 (m-30) REVERT: A 235 TYR cc_start: 0.9213 (m-80) cc_final: 0.8776 (m-80) REVERT: B 19 ARG cc_start: 0.8382 (mmt90) cc_final: 0.8153 (mmt90) REVERT: B 20 ASP cc_start: 0.8259 (m-30) cc_final: 0.7908 (m-30) REVERT: C 11 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7836 (tm-30) REVERT: E 246 GLU cc_start: 0.6416 (mp0) cc_final: 0.6202 (mp0) REVERT: R 59 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8528 (mt) REVERT: R 259 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9147 (ttpt) outliers start: 23 outliers final: 14 residues processed: 156 average time/residue: 0.2193 time to fit residues: 49.2338 Evaluate side-chains 150 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 41 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.086273 restraints weight = 16750.324| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.73 r_work: 0.2999 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8784 Z= 0.146 Angle : 0.532 11.397 11935 Z= 0.268 Chirality : 0.042 0.300 1344 Planarity : 0.004 0.053 1526 Dihedral : 5.451 84.995 1239 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.35 % Allowed : 17.11 % Favored : 80.54 % 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: 1.19 (0.26), residues: 1106 helix: 2.37 (0.27), residues: 372 sheet: 0.56 (0.32), residues: 284 loop : -0.38 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 PHE 0.020 0.001 PHE R 9 TYR 0.016 0.001 TYR A 107 ARG 0.004 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8711 (m-30) cc_final: 0.8418 (m-30) REVERT: A 235 TYR cc_start: 0.9196 (m-80) cc_final: 0.8790 (m-80) REVERT: B 19 ARG cc_start: 0.8348 (mmt90) cc_final: 0.8123 (mmt90) REVERT: B 20 ASP cc_start: 0.8226 (m-30) cc_final: 0.7874 (m-30) REVERT: C 11 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7900 (tm-30) REVERT: C 15 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8119 (mp) REVERT: E 82 GLN cc_start: 0.8182 (tp40) cc_final: 0.7913 (mm110) REVERT: E 246 GLU cc_start: 0.6426 (mp0) cc_final: 0.6168 (mp0) REVERT: R 59 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8545 (mt) REVERT: R 259 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9107 (ttpt) outliers start: 21 outliers final: 12 residues processed: 162 average time/residue: 0.1868 time to fit residues: 42.6104 Evaluate side-chains 154 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 142 GLN R 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086297 restraints weight = 16866.136| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.66 r_work: 0.3000 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8784 Z= 0.167 Angle : 0.541 10.191 11935 Z= 0.276 Chirality : 0.043 0.326 1344 Planarity : 0.004 0.053 1526 Dihedral : 5.451 84.444 1239 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.80 % Allowed : 17.67 % 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: 1.24 (0.27), residues: 1106 helix: 2.40 (0.27), residues: 373 sheet: 0.60 (0.32), residues: 279 loop : -0.34 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 266 PHE 0.021 0.001 PHE R 9 TYR 0.017 0.001 TYR A 107 ARG 0.005 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8952 (m-30) cc_final: 0.8662 (m-30) REVERT: A 235 TYR cc_start: 0.9262 (m-80) cc_final: 0.8849 (m-80) REVERT: B 19 ARG cc_start: 0.8382 (mmt90) cc_final: 0.8148 (mmt90) REVERT: B 20 ASP cc_start: 0.8322 (m-30) cc_final: 0.7979 (m-30) REVERT: C 11 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 15 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7826 (mp) REVERT: E 82 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7959 (mm110) REVERT: R 59 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8566 (mt) REVERT: R 241 ASN cc_start: 0.9237 (m110) cc_final: 0.8717 (m-40) REVERT: R 259 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9063 (ttpt) outliers start: 25 outliers final: 13 residues processed: 157 average time/residue: 0.1963 time to fit residues: 43.4399 Evaluate side-chains 150 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.083281 restraints weight = 17032.532| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.68 r_work: 0.2948 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8784 Z= 0.246 Angle : 0.585 9.154 11935 Z= 0.301 Chirality : 0.045 0.357 1344 Planarity : 0.004 0.052 1526 Dihedral : 5.683 86.334 1239 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.35 % Allowed : 18.23 % Favored : 79.42 % 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 (0.26), residues: 1106 helix: 2.32 (0.27), residues: 376 sheet: 0.43 (0.31), residues: 289 loop : -0.37 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 PHE 0.021 0.001 PHE R 9 TYR 0.017 0.001 TYR A 107 ARG 0.006 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9024 (m-30) cc_final: 0.8731 (m-30) REVERT: A 24 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7927 (mtp85) REVERT: A 235 TYR cc_start: 0.9301 (m-80) cc_final: 0.8682 (m-80) REVERT: B 16 ASN cc_start: 0.7686 (t0) cc_final: 0.7233 (t0) REVERT: B 19 ARG cc_start: 0.8387 (mmt90) cc_final: 0.8135 (mmt90) REVERT: B 20 ASP cc_start: 0.8384 (m-30) cc_final: 0.8001 (m-30) REVERT: C 11 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 15 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8023 (mp) REVERT: R 59 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8652 (mt) REVERT: R 241 ASN cc_start: 0.9237 (m110) cc_final: 0.8797 (m-40) REVERT: R 259 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9024 (ttpt) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 0.2017 time to fit residues: 43.9429 Evaluate side-chains 151 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 131 TRP Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.0020 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.084618 restraints weight = 16893.729| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.74 r_work: 0.2970 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8784 Z= 0.181 Angle : 0.575 9.213 11935 Z= 0.292 Chirality : 0.043 0.236 1344 Planarity : 0.004 0.052 1526 Dihedral : 5.556 84.005 1239 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 18.68 % Favored : 78.75 % 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: 1.07 (0.26), residues: 1106 helix: 2.24 (0.27), residues: 373 sheet: 0.39 (0.31), residues: 284 loop : -0.34 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS E 232 PHE 0.024 0.001 PHE R 9 TYR 0.016 0.001 TYR A 107 ARG 0.006 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8725 (m-30) cc_final: 0.8428 (m-30) REVERT: B 16 ASN cc_start: 0.7635 (t0) cc_final: 0.7182 (t0) REVERT: B 19 ARG cc_start: 0.8387 (mmt90) cc_final: 0.8165 (mmt90) REVERT: B 20 ASP cc_start: 0.8245 (m-30) cc_final: 0.7864 (m-30) REVERT: B 45 MET cc_start: 0.8660 (mmm) cc_final: 0.8458 (mtp) REVERT: C 11 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7844 (tm-30) REVERT: C 15 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7931 (mp) REVERT: E 39 GLN cc_start: 0.7894 (tt0) cc_final: 0.7563 (tt0) REVERT: E 82 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7899 (mm110) REVERT: R 59 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8651 (mt) REVERT: R 241 ASN cc_start: 0.9133 (m110) cc_final: 0.8665 (m-40) REVERT: R 259 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9034 (ttpt) outliers start: 23 outliers final: 15 residues processed: 156 average time/residue: 0.1912 time to fit residues: 42.0121 Evaluate side-chains 155 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 131 TRP Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 0.0170 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.085289 restraints weight = 16738.005| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.72 r_work: 0.2953 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8784 Z= 0.173 Angle : 0.584 15.096 11935 Z= 0.292 Chirality : 0.044 0.437 1344 Planarity : 0.004 0.052 1526 Dihedral : 5.424 82.170 1239 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.24 % Allowed : 19.13 % Favored : 78.64 % 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: 1.02 (0.26), residues: 1106 helix: 2.19 (0.27), residues: 373 sheet: 0.35 (0.31), residues: 286 loop : -0.34 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 PHE 0.023 0.001 PHE R 9 TYR 0.015 0.001 TYR A 107 ARG 0.006 0.000 ARG A 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8723 (m-30) cc_final: 0.8413 (m-30) REVERT: A 235 TYR cc_start: 0.9241 (m-80) cc_final: 0.8847 (m-80) REVERT: B 16 ASN cc_start: 0.7644 (t0) cc_final: 0.7182 (t0) REVERT: B 19 ARG cc_start: 0.8353 (mmt90) cc_final: 0.8129 (mmt90) REVERT: B 20 ASP cc_start: 0.8212 (m-30) cc_final: 0.7839 (m-30) REVERT: C 11 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7866 (tm-30) REVERT: E 39 GLN cc_start: 0.7826 (tt0) cc_final: 0.7492 (tt0) REVERT: E 82 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7885 (mm110) REVERT: R 59 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8646 (mt) REVERT: R 241 ASN cc_start: 0.9182 (m110) cc_final: 0.8668 (m-40) REVERT: R 259 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8938 (ttpt) outliers start: 20 outliers final: 15 residues processed: 154 average time/residue: 0.1902 time to fit residues: 41.6219 Evaluate side-chains 154 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 131 TRP Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.084155 restraints weight = 16947.774| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.67 r_work: 0.2956 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8784 Z= 0.215 Angle : 0.599 15.404 11935 Z= 0.302 Chirality : 0.045 0.410 1344 Planarity : 0.004 0.050 1526 Dihedral : 5.510 82.913 1239 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.24 % Allowed : 18.68 % Favored : 79.08 % 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: 1.01 (0.26), residues: 1106 helix: 2.18 (0.27), residues: 376 sheet: 0.25 (0.31), residues: 296 loop : -0.31 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 PHE 0.021 0.001 PHE R 142 TYR 0.015 0.001 TYR A 204 ARG 0.006 0.000 ARG A 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4871.53 seconds wall clock time: 85 minutes 45.52 seconds (5145.52 seconds total)