Starting phenix.real_space_refine on Thu Feb 13 04:15:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejc_28177/02_2025/8ejc_28177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejc_28177/02_2025/8ejc_28177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejc_28177/02_2025/8ejc_28177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejc_28177/02_2025/8ejc_28177.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejc_28177/02_2025/8ejc_28177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejc_28177/02_2025/8ejc_28177.cif" } resolution = 3.0 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 50 5.16 5 C 5506 2.51 5 N 1489 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8659 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1877 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2572 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 406 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1983 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 20, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 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: 5.12, per 1000 atoms: 0.59 Number of scatterers: 8659 At special positions: 0 Unit cell: (96.3, 115.56, 129.47, 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 50 16.00 O 1614 8.00 N 1489 7.00 C 5506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 39.0% alpha, 21.8% 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 6 through 33 removed outlier: 4.324A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.918A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.737A 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 156 removed outlier: 3.870A pdb=" N PHE A 156 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 removed outlier: 4.040A pdb=" N ARG A 161 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.620A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 235 Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.915A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 7 through 28 removed outlier: 4.306A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.137A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.582A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 37 Proline residue: R 21 - end of helix removed outlier: 4.197A pdb=" N LEU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG R 37 " --> pdb=" O HIS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 68 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 Proline residue: R 89 - end of helix Processing helix chain 'R' and resid 110 through 117 Processing helix chain 'R' and resid 119 through 144 removed outlier: 3.683A pdb=" N SER R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 212 Proline residue: R 181 - end of helix removed outlier: 4.919A pdb=" N LEU R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) Proline residue: R 194 - end of helix Processing helix chain 'R' and resid 215 through 235 Processing helix chain 'R' and resid 236 through 250 removed outlier: 3.875A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 277 removed outlier: 3.801A pdb=" N LYS R 259 " --> pdb=" O GLY R 255 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 removed outlier: 3.820A pdb=" N ALA A 97 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.179A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.598A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.515A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.535A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.727A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.162A 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: 3.540A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.506A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.695A 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 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.546A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.893A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1284 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: 2.65 Time building geometry restraints manager: 2.54 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: 2831 1.34 - 1.46: 2186 1.46 - 1.58: 3770 1.58 - 1.71: 0 1.71 - 1.83: 68 Bond restraints: 8855 Sorted by residual: bond pdb=" C27 2YB R 401 " pdb=" C28 2YB R 401 " ideal model delta sigma weight residual 1.505 1.384 0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C1 2YB R 401 " pdb=" C2 2YB R 401 " ideal model delta sigma weight residual 1.503 1.391 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C14 2YB R 401 " pdb=" C15 2YB R 401 " ideal model delta sigma weight residual 1.502 1.390 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C21 2YB R 401 " pdb=" C22 2YB R 401 " ideal model delta sigma weight residual 1.498 1.391 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C16 2YB R 401 " pdb=" C17 2YB R 401 " ideal model delta sigma weight residual 1.485 1.394 0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 8850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 11699 1.62 - 3.25: 281 3.25 - 4.87: 42 4.87 - 6.50: 14 6.50 - 8.12: 6 Bond angle restraints: 12042 Sorted by residual: angle pdb=" CA TRP R 131 " pdb=" CB TRP R 131 " pdb=" CG TRP R 131 " ideal model delta sigma weight residual 113.60 119.94 -6.34 1.90e+00 2.77e-01 1.11e+01 angle pdb=" O11 2YB R 401 " pdb=" S9 2YB R 401 " pdb=" O12 2YB R 401 " ideal model delta sigma weight residual 117.70 109.58 8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" N GLU A 171 " pdb=" CA GLU A 171 " pdb=" C GLU A 171 " ideal model delta sigma weight residual 109.81 115.39 -5.58 2.21e+00 2.05e-01 6.37e+00 angle pdb=" C22 2YB R 401 " pdb=" O23 2YB R 401 " pdb=" C24 2YB R 401 " ideal model delta sigma weight residual 118.60 111.15 7.45 3.00e+00 1.11e-01 6.17e+00 angle pdb=" C TYR B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta sigma weight residual 121.85 117.88 3.97 1.77e+00 3.19e-01 5.03e+00 ... (remaining 12037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.52: 4962 24.52 - 49.04: 224 49.04 - 73.56: 18 73.56 - 98.08: 3 98.08 - 122.60: 1 Dihedral angle restraints: 5208 sinusoidal: 1958 harmonic: 3250 Sorted by residual: dihedral pdb=" CA GLY B 141 " pdb=" C GLY B 141 " pdb=" N HIS B 142 " pdb=" CA HIS B 142 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLY B 182 " pdb=" C GLY B 182 " pdb=" N HIS B 183 " pdb=" CA HIS B 183 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+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 57.48 122.60 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 5205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 824 0.034 - 0.068: 367 0.068 - 0.102: 113 0.102 - 0.136: 48 0.136 - 0.170: 4 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CB THR E 172 " pdb=" CA THR E 172 " pdb=" OG1 THR E 172 " pdb=" CG2 THR E 172 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CG LEU R 11 " pdb=" CB LEU R 11 " pdb=" CD1 LEU R 11 " pdb=" CD2 LEU R 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1353 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 238 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO R 239 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 239 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 239 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 131 " 0.014 2.00e-02 2.50e+03 1.07e-02 2.86e+00 pdb=" CG TRP R 131 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP R 131 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP R 131 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 131 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 131 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 131 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 131 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 131 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 131 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO B 236 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.023 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 851 2.74 - 3.28: 8711 3.28 - 3.82: 14578 3.82 - 4.36: 17216 4.36 - 4.90: 29793 Nonbonded interactions: 71149 Sorted by model distance: nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.199 3.120 nonbonded pdb=" OE2 GLU A 234 " pdb=" NH1 ARG R 118 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.232 3.040 nonbonded pdb=" OG SER C 57 " pdb=" OE1 GLU C 58 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.317 3.040 ... (remaining 71144 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: 0.830 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.000 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 0.121 8855 Z= 0.377 Angle : 0.645 8.121 12042 Z= 0.323 Chirality : 0.044 0.170 1356 Planarity : 0.004 0.052 1543 Dihedral : 13.368 122.600 3119 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.20 (0.26), residues: 1118 helix: 2.17 (0.26), residues: 375 sheet: 0.40 (0.32), residues: 294 loop : -0.02 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 131 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.002 PHE B 253 TYR 0.017 0.002 TYR B 105 ARG 0.005 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 32 LYS cc_start: 0.8887 (tttm) cc_final: 0.8540 (tttm) REVERT: E 93 MET cc_start: 0.7848 (tpt) cc_final: 0.7597 (tpt) REVERT: E 201 ASP cc_start: 0.7962 (p0) cc_final: 0.7738 (t70) REVERT: R 137 HIS cc_start: 0.8206 (t-90) cc_final: 0.7843 (t-90) REVERT: R 170 CYS cc_start: 0.7786 (m) cc_final: 0.7584 (m) REVERT: R 240 TYR cc_start: 0.8514 (t80) cc_final: 0.8231 (t80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.3055 time to fit residues: 223.4091 Evaluate side-chains 117 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN B 16 ASN B 36 ASN B 220 GLN E 77 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082579 restraints weight = 15588.444| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.65 r_work: 0.2991 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8855 Z= 0.234 Angle : 0.588 7.438 12042 Z= 0.303 Chirality : 0.043 0.129 1356 Planarity : 0.004 0.051 1543 Dihedral : 5.358 87.375 1249 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.99 % Allowed : 12.07 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.31 (0.25), residues: 1118 helix: 2.27 (0.26), residues: 381 sheet: 0.55 (0.33), residues: 282 loop : -0.06 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 131 HIS 0.004 0.001 HIS B 142 PHE 0.011 0.001 PHE B 234 TYR 0.010 0.001 TYR E 190 ARG 0.007 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: B 16 ASN cc_start: 0.8672 (m-40) cc_final: 0.8238 (m110) REVERT: B 17 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 20 ASP cc_start: 0.8189 (m-30) cc_final: 0.7892 (m-30) REVERT: B 175 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8334 (mp10) REVERT: B 260 GLU cc_start: 0.8473 (tt0) cc_final: 0.8268 (tt0) REVERT: E 93 MET cc_start: 0.8661 (tpt) cc_final: 0.8174 (tpt) REVERT: E 201 ASP cc_start: 0.8563 (p0) cc_final: 0.7953 (t70) REVERT: R 53 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8727 (tp) REVERT: R 137 HIS cc_start: 0.8226 (t-90) cc_final: 0.7744 (t-90) REVERT: R 161 ASN cc_start: 0.8374 (t0) cc_final: 0.8087 (t0) REVERT: R 170 CYS cc_start: 0.8012 (m) cc_final: 0.7753 (m) REVERT: R 221 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6702 (ttm170) REVERT: R 240 TYR cc_start: 0.8716 (t80) cc_final: 0.8311 (t80) outliers start: 18 outliers final: 7 residues processed: 144 average time/residue: 1.2289 time to fit residues: 188.7922 Evaluate side-chains 131 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 221 ARG Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN B 36 ASN C 11 GLN E 77 ASN R 23 ASN R 47 ASN R 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081356 restraints weight = 15826.271| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.64 r_work: 0.2967 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8855 Z= 0.282 Angle : 0.589 7.585 12042 Z= 0.305 Chirality : 0.043 0.129 1356 Planarity : 0.004 0.050 1543 Dihedral : 5.338 75.590 1249 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.32 % Allowed : 13.40 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.21 (0.25), residues: 1118 helix: 2.14 (0.26), residues: 383 sheet: 0.56 (0.33), residues: 279 loop : -0.13 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 131 HIS 0.005 0.001 HIS B 183 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.002 TYR E 190 ARG 0.007 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: B 20 ASP cc_start: 0.8216 (m-30) cc_final: 0.8001 (m-30) REVERT: B 175 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8337 (mp10) REVERT: B 260 GLU cc_start: 0.8569 (tt0) cc_final: 0.8361 (tt0) REVERT: E 19 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8787 (tttm) REVERT: E 51 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8805 (tp) REVERT: E 93 MET cc_start: 0.8612 (tpt) cc_final: 0.8137 (tpt) REVERT: R 23 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8703 (t0) REVERT: R 52 ASP cc_start: 0.8788 (t70) cc_final: 0.8472 (t70) REVERT: R 53 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8819 (tp) REVERT: R 137 HIS cc_start: 0.8194 (t-90) cc_final: 0.7789 (t-90) REVERT: R 161 ASN cc_start: 0.8236 (t0) cc_final: 0.7871 (t0) REVERT: R 170 CYS cc_start: 0.8073 (m) cc_final: 0.7785 (m) REVERT: R 221 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6726 (ttm170) REVERT: R 240 TYR cc_start: 0.8759 (t80) cc_final: 0.8392 (t80) outliers start: 39 outliers final: 17 residues processed: 146 average time/residue: 1.2498 time to fit residues: 194.4942 Evaluate side-chains 141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 221 ARG Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 66 optimal weight: 0.4980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN A 229 GLN B 75 GLN C 44 HIS R 23 ASN R 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080702 restraints weight = 15758.203| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.63 r_work: 0.2958 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8855 Z= 0.307 Angle : 0.606 10.367 12042 Z= 0.310 Chirality : 0.043 0.134 1356 Planarity : 0.004 0.050 1543 Dihedral : 5.378 69.039 1249 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.99 % Allowed : 17.28 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.14 (0.26), residues: 1118 helix: 2.08 (0.27), residues: 383 sheet: 0.54 (0.33), residues: 278 loop : -0.19 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 131 HIS 0.006 0.001 HIS B 183 PHE 0.012 0.002 PHE B 180 TYR 0.013 0.002 TYR E 190 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: B 20 ASP cc_start: 0.8258 (m-30) cc_final: 0.8044 (m-30) REVERT: B 215 GLU cc_start: 0.8438 (pt0) cc_final: 0.8225 (pp20) REVERT: B 217 MET cc_start: 0.8051 (pp-130) cc_final: 0.7835 (pp-130) REVERT: E 19 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8780 (tttm) REVERT: E 51 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8808 (tp) REVERT: E 160 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8256 (ttm110) REVERT: R 23 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8673 (t0) REVERT: R 52 ASP cc_start: 0.8847 (t70) cc_final: 0.8499 (t70) REVERT: R 53 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8786 (tp) REVERT: R 137 HIS cc_start: 0.8311 (t-90) cc_final: 0.7911 (t-90) REVERT: R 161 ASN cc_start: 0.8255 (t0) cc_final: 0.7887 (t0) REVERT: R 170 CYS cc_start: 0.8068 (m) cc_final: 0.7763 (m) REVERT: R 221 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6830 (ttm170) outliers start: 36 outliers final: 19 residues processed: 137 average time/residue: 1.2178 time to fit residues: 178.0271 Evaluate side-chains 136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 221 ARG Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 32 optimal weight: 0.0970 chunk 53 optimal weight: 0.0040 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 77 optimal weight: 0.0030 chunk 84 optimal weight: 3.9990 overall best weight: 0.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 229 GLN E 77 ASN R 23 ASN R 47 ASN R 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.085394 restraints weight = 15736.197| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.65 r_work: 0.3033 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8855 Z= 0.146 Angle : 0.540 9.633 12042 Z= 0.275 Chirality : 0.040 0.137 1356 Planarity : 0.004 0.051 1543 Dihedral : 4.886 58.510 1249 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.10 % Allowed : 18.72 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.35 (0.26), residues: 1118 helix: 2.26 (0.26), residues: 384 sheet: 0.78 (0.34), residues: 267 loop : -0.14 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 131 HIS 0.002 0.001 HIS B 183 PHE 0.011 0.001 PHE B 199 TYR 0.009 0.001 TYR A 204 ARG 0.006 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7706 (ttp-110) REVERT: B 20 ASP cc_start: 0.8286 (m-30) cc_final: 0.8006 (m-30) REVERT: B 215 GLU cc_start: 0.8518 (pt0) cc_final: 0.8114 (pp20) REVERT: B 217 MET cc_start: 0.7974 (pp-130) cc_final: 0.7620 (pp-130) REVERT: E 51 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8751 (tp) REVERT: R 53 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8774 (tp) REVERT: R 137 HIS cc_start: 0.8087 (t-90) cc_final: 0.7723 (t-90) REVERT: R 161 ASN cc_start: 0.8247 (t0) cc_final: 0.7875 (t0) REVERT: R 170 CYS cc_start: 0.7713 (m) cc_final: 0.7469 (m) REVERT: R 240 TYR cc_start: 0.8705 (t80) cc_final: 0.8291 (t80) outliers start: 28 outliers final: 5 residues processed: 139 average time/residue: 1.2464 time to fit residues: 184.9210 Evaluate side-chains 126 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 75 GLN R 23 ASN R 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.113641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.085433 restraints weight = 15547.814| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.65 r_work: 0.3038 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8855 Z= 0.157 Angle : 0.552 8.857 12042 Z= 0.279 Chirality : 0.041 0.136 1356 Planarity : 0.004 0.052 1543 Dihedral : 4.780 65.752 1249 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.88 % Allowed : 20.16 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.48 (0.26), residues: 1118 helix: 2.37 (0.27), residues: 380 sheet: 0.83 (0.33), residues: 283 loop : -0.07 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 131 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.013 0.001 TYR A 204 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8103 (ttp-110) cc_final: 0.7777 (ttp-110) REVERT: B 20 ASP cc_start: 0.8194 (m-30) cc_final: 0.7873 (m-30) REVERT: B 254 ASP cc_start: 0.8690 (t0) cc_final: 0.8469 (t0) REVERT: E 51 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8753 (tp) REVERT: E 109 ASP cc_start: 0.8714 (p0) cc_final: 0.8399 (p0) REVERT: E 160 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8212 (ttm110) REVERT: R 53 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8751 (tp) REVERT: R 137 HIS cc_start: 0.8079 (t-90) cc_final: 0.7737 (t-90) REVERT: R 161 ASN cc_start: 0.8236 (t0) cc_final: 0.7880 (t0) REVERT: R 240 TYR cc_start: 0.8705 (t80) cc_final: 0.8346 (t80) outliers start: 26 outliers final: 7 residues processed: 145 average time/residue: 1.2459 time to fit residues: 192.8990 Evaluate side-chains 132 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN R 23 ASN R 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.085978 restraints weight = 15728.892| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.65 r_work: 0.3046 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8855 Z= 0.158 Angle : 0.558 8.549 12042 Z= 0.282 Chirality : 0.040 0.137 1356 Planarity : 0.004 0.052 1543 Dihedral : 4.752 69.756 1249 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.66 % Allowed : 20.82 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.47 (0.26), residues: 1118 helix: 2.36 (0.26), residues: 380 sheet: 0.82 (0.33), residues: 279 loop : -0.06 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 131 HIS 0.003 0.001 HIS B 183 PHE 0.009 0.001 PHE B 199 TYR 0.012 0.001 TYR A 204 ARG 0.013 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7735 (ttp-110) REVERT: B 20 ASP cc_start: 0.8186 (m-30) cc_final: 0.7842 (m-30) REVERT: E 51 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8735 (tp) REVERT: E 109 ASP cc_start: 0.8695 (p0) cc_final: 0.8386 (p0) REVERT: E 160 ARG cc_start: 0.8517 (mtp85) cc_final: 0.8186 (ttm110) REVERT: R 23 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8619 (t0) REVERT: R 52 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8385 (t70) REVERT: R 137 HIS cc_start: 0.7995 (t-90) cc_final: 0.7708 (t-90) REVERT: R 161 ASN cc_start: 0.8263 (t0) cc_final: 0.7907 (t0) REVERT: R 170 CYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6901 (m) REVERT: R 240 TYR cc_start: 0.8692 (t80) cc_final: 0.8317 (t80) outliers start: 24 outliers final: 10 residues processed: 140 average time/residue: 1.1995 time to fit residues: 179.3059 Evaluate side-chains 135 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 220 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 75 GLN E 77 ASN R 23 ASN R 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.085150 restraints weight = 15839.077| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.67 r_work: 0.3031 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8855 Z= 0.180 Angle : 0.572 9.300 12042 Z= 0.288 Chirality : 0.041 0.136 1356 Planarity : 0.004 0.050 1543 Dihedral : 4.791 71.549 1249 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.66 % Allowed : 21.15 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.46 (0.26), residues: 1118 helix: 2.32 (0.26), residues: 380 sheet: 0.89 (0.33), residues: 277 loop : -0.09 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 131 HIS 0.004 0.001 HIS B 183 PHE 0.009 0.001 PHE B 199 TYR 0.012 0.001 TYR R 202 ARG 0.012 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7687 (ttp-110) REVERT: B 20 ASP cc_start: 0.8216 (m-30) cc_final: 0.7871 (m-30) REVERT: B 254 ASP cc_start: 0.8718 (t0) cc_final: 0.8405 (t0) REVERT: E 51 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8762 (tp) REVERT: E 109 ASP cc_start: 0.8752 (p0) cc_final: 0.8430 (p0) REVERT: E 160 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8165 (ttm110) REVERT: E 220 GLU cc_start: 0.7519 (mp0) cc_final: 0.7099 (mp0) REVERT: R 23 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8583 (t0) REVERT: R 36 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7114 (mm) REVERT: R 52 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8292 (t70) REVERT: R 137 HIS cc_start: 0.8029 (t-90) cc_final: 0.7711 (t-90) REVERT: R 161 ASN cc_start: 0.8401 (t0) cc_final: 0.7985 (t0) REVERT: R 170 CYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6948 (m) outliers start: 24 outliers final: 15 residues processed: 135 average time/residue: 1.1959 time to fit residues: 172.5438 Evaluate side-chains 139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 232 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 110 ASN R 23 ASN R 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083526 restraints weight = 15746.998| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.65 r_work: 0.3007 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8855 Z= 0.231 Angle : 0.616 14.199 12042 Z= 0.314 Chirality : 0.042 0.222 1356 Planarity : 0.004 0.082 1543 Dihedral : 4.976 73.970 1249 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.88 % Allowed : 21.15 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.33 (0.26), residues: 1118 helix: 2.22 (0.26), residues: 380 sheet: 0.85 (0.33), residues: 280 loop : -0.20 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 131 HIS 0.006 0.001 HIS B 183 PHE 0.010 0.001 PHE B 151 TYR 0.010 0.001 TYR E 190 ARG 0.011 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7691 (ttp-110) REVERT: B 20 ASP cc_start: 0.8216 (m-30) cc_final: 0.7868 (m-30) REVERT: B 254 ASP cc_start: 0.8816 (t0) cc_final: 0.8512 (t0) REVERT: E 51 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8750 (tp) REVERT: E 93 MET cc_start: 0.8610 (tpt) cc_final: 0.8394 (tpt) REVERT: E 160 ARG cc_start: 0.8490 (mtp85) cc_final: 0.8184 (ttm110) REVERT: R 52 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8374 (t70) REVERT: R 53 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8792 (tp) REVERT: R 161 ASN cc_start: 0.8304 (t0) cc_final: 0.7911 (t0) REVERT: R 170 CYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7110 (m) REVERT: R 190 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8942 (mp) REVERT: R 240 TYR cc_start: 0.8642 (t80) cc_final: 0.8395 (t80) outliers start: 26 outliers final: 11 residues processed: 137 average time/residue: 1.1946 time to fit residues: 174.6894 Evaluate side-chains 134 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN E 77 ASN R 23 ASN R 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085730 restraints weight = 15718.140| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.66 r_work: 0.3043 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8855 Z= 0.163 Angle : 0.591 10.437 12042 Z= 0.297 Chirality : 0.041 0.138 1356 Planarity : 0.004 0.050 1543 Dihedral : 4.840 75.289 1249 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.88 % Allowed : 22.26 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.26), residues: 1118 helix: 2.34 (0.26), residues: 374 sheet: 0.82 (0.33), residues: 284 loop : -0.07 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 131 HIS 0.004 0.001 HIS B 183 PHE 0.009 0.001 PHE B 199 TYR 0.013 0.001 TYR A 204 ARG 0.011 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7730 (ttp-110) REVERT: B 20 ASP cc_start: 0.8227 (m-30) cc_final: 0.7894 (m-30) REVERT: B 32 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8591 (tp-100) REVERT: B 215 GLU cc_start: 0.8549 (pt0) cc_final: 0.8333 (pp20) REVERT: E 51 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8750 (tp) REVERT: E 93 MET cc_start: 0.8582 (tpt) cc_final: 0.8376 (tpt) REVERT: E 109 ASP cc_start: 0.8605 (p0) cc_final: 0.8341 (p0) REVERT: E 160 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8174 (ttm110) REVERT: R 23 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8572 (t0) REVERT: R 52 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8226 (t70) REVERT: R 137 HIS cc_start: 0.7988 (t70) cc_final: 0.7526 (t-90) REVERT: R 161 ASN cc_start: 0.8262 (t0) cc_final: 0.7814 (t0) REVERT: R 170 CYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6932 (m) REVERT: R 240 TYR cc_start: 0.8646 (t80) cc_final: 0.8416 (t80) outliers start: 17 outliers final: 10 residues processed: 138 average time/residue: 1.1899 time to fit residues: 175.8768 Evaluate side-chains 138 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 0.4980 chunk 62 optimal weight: 0.0060 chunk 77 optimal weight: 0.0000 chunk 60 optimal weight: 0.0470 chunk 78 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN R 23 ASN R 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.116170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088674 restraints weight = 15569.479| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.62 r_work: 0.3093 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8855 Z= 0.148 Angle : 0.587 10.748 12042 Z= 0.292 Chirality : 0.040 0.139 1356 Planarity : 0.004 0.051 1543 Dihedral : 4.691 78.451 1249 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.66 % Allowed : 22.70 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.51 (0.26), residues: 1118 helix: 2.34 (0.26), residues: 374 sheet: 0.91 (0.33), residues: 284 loop : -0.02 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 131 HIS 0.003 0.000 HIS B 183 PHE 0.009 0.001 PHE A 66 TYR 0.012 0.001 TYR E 95 ARG 0.010 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6818.23 seconds wall clock time: 120 minutes 53.60 seconds (7253.60 seconds total)