Starting phenix.real_space_refine on Sat Dec 28 14:42:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejc_28177/12_2024/8ejc_28177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejc_28177/12_2024/8ejc_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_28177/12_2024/8ejc_28177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejc_28177/12_2024/8ejc_28177.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejc_28177/12_2024/8ejc_28177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejc_28177/12_2024/8ejc_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.59, per 1000 atoms: 0.65 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: 2.50 Conformation dependent library (CDL) restraints added in 990.6 milliseconds 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: 1.24 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: 2.72 Time building geometry restraints manager: 2.76 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: 0.410 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.590 Find NCS groups from input model: 0.120 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.840 ------------------------------------------------------------------------------- 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 : 1.036 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: 1.3766 time to fit residues: 235.2406 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 : 1.057 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 1.056 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: B 16 ASN cc_start: 0.8726 (m-40) cc_final: 0.8185 (m110) REVERT: B 17 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7746 (tm-30) REVERT: B 20 ASP cc_start: 0.8060 (m-30) cc_final: 0.7760 (m-30) REVERT: B 175 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7888 (mp10) REVERT: E 93 MET cc_start: 0.7948 (tpt) cc_final: 0.7699 (tpt) REVERT: E 201 ASP cc_start: 0.7956 (p0) cc_final: 0.7690 (t70) REVERT: R 53 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8507 (tp) REVERT: R 137 HIS cc_start: 0.8235 (t-90) cc_final: 0.7805 (t-90) REVERT: R 161 ASN cc_start: 0.8205 (t0) cc_final: 0.7914 (t0) REVERT: R 170 CYS cc_start: 0.7864 (m) cc_final: 0.7608 (m) REVERT: R 221 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6241 (ttm170) REVERT: R 240 TYR cc_start: 0.8606 (t80) cc_final: 0.8263 (t80) outliers start: 18 outliers final: 7 residues processed: 144 average time/residue: 1.2266 time to fit residues: 188.4140 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 : 1.104 ------------------------------------------------------------------------------- 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 56 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8855 Z= 0.338 Angle : 0.615 7.735 12042 Z= 0.320 Chirality : 0.044 0.139 1356 Planarity : 0.004 0.050 1543 Dihedral : 5.494 76.576 1249 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.43 % Allowed : 13.40 % Favored : 82.17 % 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 (0.25), residues: 1118 helix: 2.05 (0.26), residues: 383 sheet: 0.58 (0.33), residues: 278 loop : -0.18 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 131 HIS 0.007 0.001 HIS B 183 PHE 0.012 0.002 PHE B 199 TYR 0.016 0.002 TYR E 190 ARG 0.006 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 166 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: B 20 ASP cc_start: 0.8062 (m-30) cc_final: 0.7858 (m-30) REVERT: E 19 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8768 (tttm) REVERT: E 51 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8652 (tp) REVERT: E 93 MET cc_start: 0.7866 (tpt) cc_final: 0.7576 (tpt) REVERT: E 201 ASP cc_start: 0.7989 (p0) cc_final: 0.7533 (t0) REVERT: R 23 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8513 (t0) REVERT: R 52 ASP cc_start: 0.8224 (t70) cc_final: 0.7913 (t70) REVERT: R 53 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8617 (tp) REVERT: R 137 HIS cc_start: 0.8220 (t-90) cc_final: 0.7829 (t-90) REVERT: R 161 ASN cc_start: 0.8083 (t0) cc_final: 0.7739 (t0) REVERT: R 170 CYS cc_start: 0.7943 (m) cc_final: 0.7674 (m) REVERT: R 221 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6263 (ttm170) REVERT: R 240 TYR cc_start: 0.8672 (t80) cc_final: 0.8311 (t80) outliers start: 40 outliers final: 17 residues processed: 143 average time/residue: 1.2781 time to fit residues: 195.3371 Evaluate side-chains 139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 B 110 ASN C 44 HIS R 23 ASN R 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8855 Z= 0.156 Angle : 0.543 7.306 12042 Z= 0.278 Chirality : 0.041 0.137 1356 Planarity : 0.004 0.051 1543 Dihedral : 5.033 66.259 1249 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.10 % Allowed : 17.61 % Favored : 79.29 % 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: 1.30 (0.26), residues: 1118 helix: 2.21 (0.26), residues: 384 sheet: 0.73 (0.33), residues: 268 loop : -0.15 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 131 HIS 0.003 0.001 HIS B 142 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR A 204 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 158 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7707 (ttp-110) REVERT: B 20 ASP cc_start: 0.8037 (m-30) cc_final: 0.7792 (m-30) REVERT: B 217 MET cc_start: 0.7185 (pp-130) cc_final: 0.6976 (pp-130) REVERT: E 51 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8568 (tp) REVERT: E 109 ASP cc_start: 0.8068 (p0) cc_final: 0.7765 (p0) REVERT: E 118 THR cc_start: 0.7018 (OUTLIER) cc_final: 0.6740 (m) REVERT: R 53 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8566 (tp) REVERT: R 137 HIS cc_start: 0.8129 (t-90) cc_final: 0.7815 (t-90) REVERT: R 161 ASN cc_start: 0.8087 (t0) cc_final: 0.7737 (t0) REVERT: R 170 CYS cc_start: 0.7802 (m) cc_final: 0.7498 (m) REVERT: R 240 TYR cc_start: 0.8617 (t80) cc_final: 0.8268 (t80) outliers start: 28 outliers final: 5 residues processed: 141 average time/residue: 1.2002 time to fit residues: 180.6213 Evaluate side-chains 127 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 118 THR 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 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 R 23 ASN R 47 ASN R 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8855 Z= 0.246 Angle : 0.575 8.086 12042 Z= 0.296 Chirality : 0.042 0.133 1356 Planarity : 0.004 0.050 1543 Dihedral : 5.137 59.310 1249 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.77 % Allowed : 18.27 % Favored : 77.96 % 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: 1.27 (0.26), residues: 1118 helix: 2.19 (0.26), residues: 384 sheet: 0.63 (0.33), residues: 278 loop : -0.12 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 131 HIS 0.006 0.001 HIS B 183 PHE 0.011 0.001 PHE B 180 TYR 0.013 0.001 TYR B 59 ARG 0.008 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 159 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7786 (ttp-110) REVERT: B 20 ASP cc_start: 0.8047 (m-30) cc_final: 0.7792 (m-30) REVERT: B 254 ASP cc_start: 0.8194 (t0) cc_final: 0.7936 (t0) REVERT: E 19 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8755 (tttm) REVERT: E 51 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8592 (tp) REVERT: E 109 ASP cc_start: 0.8107 (p0) cc_final: 0.7773 (p0) REVERT: R 36 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7133 (mm) REVERT: R 53 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8598 (tp) REVERT: R 161 ASN cc_start: 0.8055 (t0) cc_final: 0.7722 (t0) REVERT: R 170 CYS cc_start: 0.7770 (m) cc_final: 0.7447 (m) REVERT: R 240 TYR cc_start: 0.8619 (t80) cc_final: 0.8272 (t80) outliers start: 34 outliers final: 15 residues processed: 143 average time/residue: 1.2224 time to fit residues: 186.6491 Evaluate side-chains 134 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 19 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 38 ARG 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 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 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 61 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 B 75 GLN E 77 ASN R 23 ASN R 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8855 Z= 0.163 Angle : 0.553 8.074 12042 Z= 0.282 Chirality : 0.041 0.138 1356 Planarity : 0.004 0.051 1543 Dihedral : 4.907 65.180 1249 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.77 % Allowed : 19.27 % 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: 1.35 (0.26), residues: 1118 helix: 2.32 (0.27), residues: 378 sheet: 0.76 (0.33), residues: 278 loop : -0.17 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 131 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.011 0.001 TYR A 204 ARG 0.006 0.000 ARG R 118 *********************** 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 163 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7696 (ttp-110) REVERT: B 20 ASP cc_start: 0.8051 (m-30) cc_final: 0.7727 (m-30) REVERT: B 254 ASP cc_start: 0.8165 (t0) cc_final: 0.7868 (t0) REVERT: E 19 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8746 (tttm) REVERT: E 51 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8574 (tp) REVERT: E 109 ASP cc_start: 0.8141 (p0) cc_final: 0.7769 (p0) REVERT: R 23 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8416 (t0) REVERT: R 52 ASP cc_start: 0.8227 (t70) cc_final: 0.7954 (t70) REVERT: R 53 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8583 (tp) REVERT: R 137 HIS cc_start: 0.8085 (t70) cc_final: 0.7660 (t-90) REVERT: R 161 ASN cc_start: 0.8074 (t0) cc_final: 0.7732 (t0) REVERT: R 170 CYS cc_start: 0.7535 (m) cc_final: 0.7302 (m) REVERT: R 240 TYR cc_start: 0.8590 (t80) cc_final: 0.8241 (t80) outliers start: 34 outliers final: 11 residues processed: 146 average time/residue: 1.2379 time to fit residues: 193.1383 Evaluate side-chains 134 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 B residue 318 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 19 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 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 78 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 R 23 ASN R 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8855 Z= 0.242 Angle : 0.593 8.234 12042 Z= 0.302 Chirality : 0.042 0.134 1356 Planarity : 0.004 0.050 1543 Dihedral : 5.069 68.728 1249 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.88 % Allowed : 20.38 % Favored : 76.74 % 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: 1.26 (0.26), residues: 1118 helix: 2.22 (0.26), residues: 380 sheet: 0.65 (0.32), residues: 287 loop : -0.19 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 131 HIS 0.006 0.001 HIS B 183 PHE 0.010 0.001 PHE B 180 TYR 0.012 0.001 TYR E 190 ARG 0.009 0.000 ARG E 160 *********************** 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 149 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7720 (ttp-110) REVERT: B 20 ASP cc_start: 0.8051 (m-30) cc_final: 0.7783 (m-30) REVERT: B 254 ASP cc_start: 0.8185 (t0) cc_final: 0.7883 (t0) REVERT: E 19 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8756 (tttm) REVERT: E 51 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8600 (tp) REVERT: E 109 ASP cc_start: 0.8095 (p0) cc_final: 0.7769 (p0) REVERT: R 53 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8593 (tp) REVERT: R 137 HIS cc_start: 0.8181 (t70) cc_final: 0.7788 (t-90) REVERT: R 161 ASN cc_start: 0.8043 (t0) cc_final: 0.7684 (t0) REVERT: R 240 TYR cc_start: 0.8639 (t80) cc_final: 0.8349 (t80) outliers start: 26 outliers final: 15 residues processed: 134 average time/residue: 1.3260 time to fit residues: 189.1033 Evaluate side-chains 135 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 19 ARG Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 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 25 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 B 75 GLN E 77 ASN R 23 ASN R 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 0.036 8855 Z= 0.159 Angle : 0.570 9.319 12042 Z= 0.285 Chirality : 0.040 0.139 1356 Planarity : 0.004 0.050 1543 Dihedral : 4.829 70.494 1249 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.55 % Allowed : 21.04 % Favored : 76.41 % 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: 2.28 (0.26), residues: 380 sheet: 0.70 (0.32), residues: 286 loop : -0.13 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 131 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.011 0.001 TYR A 204 ARG 0.014 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 152 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8244 (mtmm) cc_final: 0.8037 (mtmm) REVERT: B 19 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7656 (ttp-110) REVERT: B 20 ASP cc_start: 0.8044 (m-30) cc_final: 0.7731 (m-30) REVERT: E 51 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8532 (tp) REVERT: E 109 ASP cc_start: 0.8110 (p0) cc_final: 0.7788 (p0) REVERT: E 220 GLU cc_start: 0.7693 (mp0) cc_final: 0.7152 (mp0) REVERT: R 137 HIS cc_start: 0.8150 (t70) cc_final: 0.7754 (t-90) REVERT: R 161 ASN cc_start: 0.8099 (t0) cc_final: 0.7761 (t0) REVERT: R 170 CYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6668 (m) REVERT: R 190 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8891 (mp) REVERT: R 240 TYR cc_start: 0.8620 (t80) cc_final: 0.8345 (t80) outliers start: 23 outliers final: 12 residues processed: 141 average time/residue: 1.2005 time to fit residues: 180.9101 Evaluate side-chains 136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 65 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8855 Z= 0.160 Angle : 0.844 42.110 12042 Z= 0.394 Chirality : 0.041 0.137 1356 Planarity : 0.004 0.078 1543 Dihedral : 4.797 73.342 1249 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: 1.45 (0.26), residues: 1118 helix: 2.44 (0.26), residues: 374 sheet: 0.74 (0.33), residues: 286 loop : -0.08 (0.29), residues: 458 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 0.011 0.001 TYR E 95 ARG 0.013 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 155 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7627 (ttp-110) REVERT: B 20 ASP cc_start: 0.8078 (m-30) cc_final: 0.7754 (m-30) REVERT: B 318 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8295 (tt) REVERT: E 51 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8558 (tp) REVERT: E 109 ASP cc_start: 0.8092 (p0) cc_final: 0.7744 (p0) REVERT: E 193 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8101 (m) REVERT: R 137 HIS cc_start: 0.7895 (t70) cc_final: 0.7600 (t-90) REVERT: R 161 ASN cc_start: 0.8110 (t0) cc_final: 0.7697 (t0) REVERT: R 170 CYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6833 (m) REVERT: R 240 TYR cc_start: 0.8598 (t80) cc_final: 0.8308 (t80) outliers start: 24 outliers final: 9 residues processed: 146 average time/residue: 1.2080 time to fit residues: 188.7197 Evaluate side-chains 136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 318 LEU 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 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 50 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 6 GLN R 23 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8855 Z= 0.181 Angle : 0.607 10.729 12042 Z= 0.305 Chirality : 0.041 0.137 1356 Planarity : 0.004 0.050 1543 Dihedral : 4.879 75.606 1249 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.55 % Allowed : 22.37 % Favored : 76.08 % 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: 1.45 (0.26), residues: 1118 helix: 2.37 (0.26), residues: 374 sheet: 0.83 (0.33), residues: 283 loop : -0.07 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 131 HIS 0.004 0.001 HIS B 183 PHE 0.009 0.001 PHE B 199 TYR 0.027 0.001 TYR E 95 ARG 0.013 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 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7622 (ttp-110) REVERT: B 20 ASP cc_start: 0.8041 (m-30) cc_final: 0.7709 (m-30) REVERT: E 51 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8573 (tp) REVERT: E 160 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7781 (mtp85) REVERT: R 137 HIS cc_start: 0.7967 (t70) cc_final: 0.7573 (t-90) REVERT: R 161 ASN cc_start: 0.8073 (t0) cc_final: 0.7703 (t0) REVERT: R 170 CYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6852 (m) REVERT: R 240 TYR cc_start: 0.8582 (t80) cc_final: 0.8292 (t80) outliers start: 14 outliers final: 10 residues processed: 139 average time/residue: 1.1858 time to fit residues: 176.4915 Evaluate side-chains 139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 318 LEU 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 193 SER 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 81 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.0670 chunk 77 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN R 6 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 = 0.3631 r_free = 0.3631 target = 0.115288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087461 restraints weight = 15681.198| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.64 r_work: 0.3069 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8855 Z= 0.163 Angle : 0.615 11.691 12042 Z= 0.306 Chirality : 0.041 0.139 1356 Planarity : 0.004 0.049 1543 Dihedral : 4.841 79.202 1249 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.77 % Allowed : 22.48 % Favored : 75.75 % 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: 1.49 (0.26), residues: 1118 helix: 2.37 (0.26), residues: 374 sheet: 0.78 (0.33), residues: 288 loop : 0.03 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 131 HIS 0.003 0.001 HIS B 183 PHE 0.009 0.001 PHE B 151 TYR 0.021 0.001 TYR E 95 ARG 0.012 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3505.14 seconds wall clock time: 63 minutes 56.29 seconds (3836.29 seconds total)