Starting phenix.real_space_refine on Tue Sep 24 15:08:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/09_2024/8dzq_27805.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/09_2024/8dzq_27805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/09_2024/8dzq_27805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/09_2024/8dzq_27805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/09_2024/8dzq_27805.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/09_2024/8dzq_27805.cif" } resolution = 2.82 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5337 2.51 5 N 1397 2.21 5 O 1550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8342 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2484 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 292 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1770 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1648 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2117 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 265} Chain breaks: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'U99': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.61 Number of scatterers: 8342 At special positions: 0 Unit cell: (90.64, 121.44, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1550 8.00 N 1397 7.00 C 5337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 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: 2.15 Conformation dependent library (CDL) restraints added in 1.0 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 36.0% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'C' and resid 5 through 25 Processing helix chain 'C' and resid 128 through 132 removed outlier: 4.171A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.610A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.158A 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 'B' and resid 6 through 31 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.538A pdb=" N CYS B 215 " --> pdb=" O TRP B 212 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 217 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 removed outlier: 4.534A pdb=" N ASP B 232 " --> pdb=" O SER B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 296 through 310 removed outlier: 4.342A pdb=" N ALA B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.165A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 87 Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 92 through 110 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 127 through 162 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 171 through 197 removed outlier: 3.869A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 235 Processing helix chain 'A' and resid 235 through 255 removed outlier: 4.289A pdb=" N SER A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 299 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 306 through 331 removed outlier: 3.720A pdb=" N TYR A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.786A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.763A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.194A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.863A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.533A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.686A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.650A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.311A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.600A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.662A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 198 through 200 441 hydrogen bonds defined for protein. 1233 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: 2.28 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1566 1.33 - 1.45: 2172 1.45 - 1.57: 4689 1.57 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 8510 Sorted by residual: bond pdb=" N LEU E 166 " pdb=" CA LEU E 166 " ideal model delta sigma weight residual 1.455 1.477 -0.022 1.25e-02 6.40e+03 3.01e+00 bond pdb=" CG1 ILE B 342 " pdb=" CD1 ILE B 342 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.60e+00 bond pdb=" CA ILE C 37 " pdb=" C ILE C 37 " ideal model delta sigma weight residual 1.518 1.533 -0.014 1.13e-02 7.83e+03 1.58e+00 bond pdb=" CG LEU B 38 " pdb=" CD2 LEU B 38 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CG1 ILE A 178 " pdb=" CD1 ILE A 178 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 ... (remaining 8505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11163 1.80 - 3.60: 333 3.60 - 5.40: 47 5.40 - 7.21: 14 7.21 - 9.01: 8 Bond angle restraints: 11565 Sorted by residual: angle pdb=" N VAL B 202 " pdb=" CA VAL B 202 " pdb=" C VAL B 202 " ideal model delta sigma weight residual 111.88 106.75 5.13 1.06e+00 8.90e-01 2.34e+01 angle pdb=" C ASN B 295 " pdb=" N THR B 296 " pdb=" CA THR B 296 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 angle pdb=" N ARG C 68 " pdb=" CA ARG C 68 " pdb=" C ARG C 68 " ideal model delta sigma weight residual 114.56 109.40 5.16 1.27e+00 6.20e-01 1.65e+01 angle pdb=" C ASN A 122 " pdb=" N SER A 123 " pdb=" CA SER A 123 " ideal model delta sigma weight residual 121.54 114.59 6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" N ILE C 37 " pdb=" CA ILE C 37 " pdb=" C ILE C 37 " ideal model delta sigma weight residual 112.98 108.49 4.49 1.25e+00 6.40e-01 1.29e+01 ... (remaining 11560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 4573 17.01 - 34.02: 405 34.02 - 51.03: 60 51.03 - 68.04: 9 68.04 - 85.04: 7 Dihedral angle restraints: 5054 sinusoidal: 1868 harmonic: 3186 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 210 " pdb=" CB CYS A 210 " ideal model delta sinusoidal sigma weight residual -86.00 -165.52 79.52 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CA LEU B 199 " pdb=" C LEU B 199 " pdb=" N PHE B 200 " pdb=" CA PHE B 200 " ideal model delta harmonic sigma weight residual 180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N LEU C 79 " pdb=" CA LEU C 79 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1156 0.068 - 0.136: 197 0.136 - 0.203: 6 0.203 - 0.271: 1 0.271 - 0.339: 2 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CG LEU B 269 " pdb=" CB LEU B 269 " pdb=" CD1 LEU B 269 " pdb=" CD2 LEU B 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C22 U99 A 401 " pdb=" C20 U99 A 401 " pdb=" C23 U99 A 401 " pdb=" C8 U99 A 401 " both_signs ideal model delta sigma weight residual False -2.23 -1.93 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL B 202 " pdb=" CA VAL B 202 " pdb=" CG1 VAL B 202 " pdb=" CG2 VAL B 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1359 not shown) Planarity restraints: 1445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 137 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C ARG C 137 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG C 137 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU C 138 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 165 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C PHE E 165 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE E 165 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU E 166 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 246 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C ALA B 246 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA B 246 " 0.013 2.00e-02 2.50e+03 pdb=" N SER B 247 " 0.011 2.00e-02 2.50e+03 ... (remaining 1442 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1635 2.78 - 3.31: 7688 3.31 - 3.84: 13707 3.84 - 4.37: 15878 4.37 - 4.90: 28121 Nonbonded interactions: 67029 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.244 3.040 nonbonded pdb=" O GLY E 8 " pdb=" OG1 THR E 115 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP C 186 " pdb=" OG SER B 207 " model vdw 2.295 3.040 nonbonded pdb=" O ALA C 231 " pdb=" OG1 THR C 243 " model vdw 2.309 3.040 ... (remaining 67024 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: 0.960 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.410 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:10.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8510 Z= 0.262 Angle : 0.750 9.007 11565 Z= 0.396 Chirality : 0.049 0.339 1362 Planarity : 0.004 0.043 1445 Dihedral : 13.130 85.045 2988 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1072 helix: 1.13 (0.27), residues: 355 sheet: -0.04 (0.30), residues: 276 loop : -1.68 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 164 HIS 0.017 0.002 HIS E 155 PHE 0.019 0.002 PHE C 278 TYR 0.023 0.002 TYR A 140 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: E 95 TYR cc_start: 0.6503 (m-10) cc_final: 0.6295 (m-10) REVERT: A 228 ILE cc_start: 0.7726 (mm) cc_final: 0.7472 (mm) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.7959 time to fit residues: 144.4328 Evaluate side-chains 150 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 230 ASN C 293 ASN E 219 GLN B 233 GLN A 122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8510 Z= 0.242 Angle : 0.602 7.577 11565 Z= 0.319 Chirality : 0.044 0.162 1362 Planarity : 0.004 0.034 1445 Dihedral : 4.642 40.163 1239 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.83 % Allowed : 11.23 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1072 helix: 1.78 (0.28), residues: 349 sheet: -0.05 (0.30), residues: 274 loop : -1.63 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 169 HIS 0.004 0.001 HIS B 189 PHE 0.022 0.002 PHE B 200 TYR 0.017 0.002 TYR A 140 ARG 0.007 0.001 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: C 217 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6349 (pmt) REVERT: E 180 MET cc_start: 0.4546 (ttp) cc_final: 0.4288 (ttp) REVERT: A 228 ILE cc_start: 0.7803 (mm) cc_final: 0.7563 (OUTLIER) outliers start: 16 outliers final: 3 residues processed: 161 average time/residue: 0.8983 time to fit residues: 156.9995 Evaluate side-chains 147 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain B residue 296 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.0040 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 293 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8510 Z= 0.231 Angle : 0.595 8.164 11565 Z= 0.311 Chirality : 0.043 0.138 1362 Planarity : 0.004 0.032 1445 Dihedral : 4.502 35.448 1239 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.18 % Allowed : 14.43 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 1072 helix: 1.86 (0.28), residues: 351 sheet: 0.07 (0.31), residues: 282 loop : -1.63 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 169 HIS 0.005 0.001 HIS B 189 PHE 0.019 0.002 PHE B 200 TYR 0.018 0.002 TYR A 140 ARG 0.005 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: C 217 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6329 (pmt) REVERT: E 180 MET cc_start: 0.4642 (ttp) cc_final: 0.4353 (ttp) REVERT: E 208 GLU cc_start: 0.6944 (mp0) cc_final: 0.6578 (mp0) REVERT: B 309 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: A 228 ILE cc_start: 0.7849 (mm) cc_final: 0.7628 (OUTLIER) outliers start: 19 outliers final: 7 residues processed: 155 average time/residue: 0.8844 time to fit residues: 148.6494 Evaluate side-chains 150 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.0000 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8510 Z= 0.209 Angle : 0.576 8.342 11565 Z= 0.301 Chirality : 0.043 0.142 1362 Planarity : 0.004 0.032 1445 Dihedral : 4.399 36.367 1239 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.63 % Allowed : 16.84 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 1072 helix: 1.88 (0.28), residues: 358 sheet: 0.13 (0.31), residues: 281 loop : -1.62 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 169 HIS 0.005 0.001 HIS B 189 PHE 0.015 0.001 PHE C 253 TYR 0.018 0.002 TYR A 140 ARG 0.006 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 0.916 Fit side-chains REVERT: C 217 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6325 (pmt) REVERT: E 180 MET cc_start: 0.4614 (ttp) cc_final: 0.4332 (ttp) REVERT: E 208 GLU cc_start: 0.6959 (mp0) cc_final: 0.6588 (mp0) REVERT: B 309 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6482 (mp0) REVERT: A 107 LEU cc_start: 0.8032 (mt) cc_final: 0.7811 (mp) REVERT: A 169 PHE cc_start: 0.6240 (m-10) cc_final: 0.6012 (m-10) outliers start: 23 outliers final: 7 residues processed: 167 average time/residue: 0.8597 time to fit residues: 156.0908 Evaluate side-chains 165 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0040 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 0.0270 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 0.0570 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN E 219 GLN B 189 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8510 Z= 0.169 Angle : 0.559 8.619 11565 Z= 0.292 Chirality : 0.042 0.145 1362 Planarity : 0.003 0.030 1445 Dihedral : 4.235 34.811 1239 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.41 % Allowed : 19.01 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.27), residues: 1072 helix: 2.06 (0.28), residues: 357 sheet: 0.16 (0.31), residues: 280 loop : -1.57 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.003 0.001 HIS B 189 PHE 0.012 0.001 PHE C 199 TYR 0.020 0.001 TYR A 140 ARG 0.007 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: E 208 GLU cc_start: 0.6933 (mp0) cc_final: 0.6568 (mp0) REVERT: B 309 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: A 81 MET cc_start: 0.6279 (mmt) cc_final: 0.6072 (mmt) REVERT: A 107 LEU cc_start: 0.7972 (mt) cc_final: 0.7724 (mp) REVERT: A 112 MET cc_start: 0.3252 (mmt) cc_final: 0.2437 (mmp) REVERT: A 228 ILE cc_start: 0.7795 (mm) cc_final: 0.7583 (mm) outliers start: 21 outliers final: 10 residues processed: 169 average time/residue: 0.8044 time to fit residues: 148.7224 Evaluate side-chains 160 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain A residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 220 GLN C 268 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8510 Z= 0.240 Angle : 0.594 8.789 11565 Z= 0.310 Chirality : 0.043 0.152 1362 Planarity : 0.004 0.032 1445 Dihedral : 4.349 35.537 1239 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.01 % Allowed : 17.98 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 1072 helix: 1.99 (0.28), residues: 358 sheet: 0.14 (0.31), residues: 281 loop : -1.59 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.004 0.001 HIS E 155 PHE 0.019 0.002 PHE C 253 TYR 0.019 0.002 TYR A 140 ARG 0.007 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 0.856 Fit side-chains REVERT: C 217 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6343 (pmt) REVERT: E 180 MET cc_start: 0.4535 (ttp) cc_final: 0.4235 (ttp) REVERT: E 208 GLU cc_start: 0.6987 (mp0) cc_final: 0.6591 (mp0) REVERT: B 309 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: A 107 LEU cc_start: 0.7989 (mt) cc_final: 0.7708 (mp) outliers start: 35 outliers final: 14 residues processed: 168 average time/residue: 0.8501 time to fit residues: 155.2449 Evaluate side-chains 163 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 0.0040 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 220 GLN C 268 ASN C 293 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8510 Z= 0.258 Angle : 0.610 9.009 11565 Z= 0.318 Chirality : 0.044 0.159 1362 Planarity : 0.004 0.048 1445 Dihedral : 4.420 32.643 1239 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.44 % Allowed : 19.59 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1072 helix: 1.92 (0.28), residues: 357 sheet: 0.07 (0.31), residues: 281 loop : -1.61 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.019 0.002 PHE C 253 TYR 0.019 0.002 TYR A 140 ARG 0.007 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 0.902 Fit side-chains REVERT: C 217 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6319 (pmt) REVERT: E 206 ARG cc_start: 0.6665 (mmp80) cc_final: 0.6310 (mmp80) REVERT: E 208 GLU cc_start: 0.6991 (mp0) cc_final: 0.6599 (mp0) REVERT: B 309 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: A 107 LEU cc_start: 0.8007 (mt) cc_final: 0.7716 (mp) outliers start: 30 outliers final: 15 residues processed: 162 average time/residue: 0.8759 time to fit residues: 154.1899 Evaluate side-chains 150 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 220 GLN C 268 ASN C 293 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8510 Z= 0.236 Angle : 0.602 9.148 11565 Z= 0.315 Chirality : 0.043 0.162 1362 Planarity : 0.004 0.042 1445 Dihedral : 4.404 31.915 1239 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.32 % Allowed : 20.50 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1072 helix: 1.81 (0.27), residues: 364 sheet: 0.05 (0.31), residues: 280 loop : -1.61 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.003 0.001 HIS E 220 PHE 0.017 0.002 PHE C 253 TYR 0.019 0.002 TYR A 140 ARG 0.007 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: C 217 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6312 (pmt) REVERT: C 273 ILE cc_start: 0.7406 (mp) cc_final: 0.7195 (mp) REVERT: E 208 GLU cc_start: 0.6977 (mp0) cc_final: 0.6593 (mp0) REVERT: B 309 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: A 107 LEU cc_start: 0.7936 (mt) cc_final: 0.7641 (mp) outliers start: 29 outliers final: 17 residues processed: 156 average time/residue: 0.9277 time to fit residues: 156.6387 Evaluate side-chains 158 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8510 Z= 0.245 Angle : 0.612 9.248 11565 Z= 0.318 Chirality : 0.043 0.168 1362 Planarity : 0.004 0.041 1445 Dihedral : 4.424 31.680 1239 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.63 % Allowed : 21.65 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1072 helix: 1.81 (0.27), residues: 363 sheet: 0.11 (0.31), residues: 277 loop : -1.65 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.003 0.001 HIS E 220 PHE 0.018 0.002 PHE C 253 TYR 0.019 0.002 TYR A 140 ARG 0.007 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 0.941 Fit side-chains REVERT: C 217 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6303 (pmt) REVERT: C 273 ILE cc_start: 0.7366 (mp) cc_final: 0.7152 (mp) REVERT: E 206 ARG cc_start: 0.6653 (mmp80) cc_final: 0.6288 (mmp80) REVERT: E 208 GLU cc_start: 0.6975 (mp0) cc_final: 0.6592 (mp0) REVERT: B 309 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: A 107 LEU cc_start: 0.7937 (mt) cc_final: 0.7664 (mp) outliers start: 23 outliers final: 18 residues processed: 164 average time/residue: 0.8929 time to fit residues: 158.5377 Evaluate side-chains 158 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 220 GLN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8510 Z= 0.219 Angle : 0.603 9.406 11565 Z= 0.313 Chirality : 0.043 0.170 1362 Planarity : 0.004 0.036 1445 Dihedral : 4.377 31.517 1239 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.52 % Allowed : 21.76 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1072 helix: 1.82 (0.27), residues: 364 sheet: 0.04 (0.31), residues: 280 loop : -1.64 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE C 253 TYR 0.020 0.002 TYR A 140 ARG 0.007 0.000 ARG C 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 0.788 Fit side-chains REVERT: C 217 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6305 (pmt) REVERT: C 273 ILE cc_start: 0.7355 (mp) cc_final: 0.7137 (mp) REVERT: E 206 ARG cc_start: 0.6648 (mmp80) cc_final: 0.6294 (mmp80) REVERT: E 208 GLU cc_start: 0.6967 (mp0) cc_final: 0.6586 (mp0) REVERT: B 309 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: A 107 LEU cc_start: 0.7917 (mt) cc_final: 0.7646 (mp) REVERT: A 112 MET cc_start: 0.3450 (OUTLIER) cc_final: 0.2721 (mmp) outliers start: 22 outliers final: 17 residues processed: 157 average time/residue: 0.8765 time to fit residues: 149.1530 Evaluate side-chains 156 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0970 chunk 26 optimal weight: 0.4980 chunk 79 optimal weight: 0.0270 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.0040 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 overall best weight: 0.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.160601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.143322 restraints weight = 11546.170| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.90 r_work: 0.3832 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 8510 Z= 0.153 Angle : 0.561 9.342 11565 Z= 0.291 Chirality : 0.041 0.154 1362 Planarity : 0.003 0.032 1445 Dihedral : 4.109 33.576 1239 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.72 % Allowed : 22.57 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1072 helix: 2.21 (0.28), residues: 356 sheet: 0.08 (0.31), residues: 279 loop : -1.56 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 124 HIS 0.003 0.001 HIS E 155 PHE 0.012 0.001 PHE C 151 TYR 0.023 0.001 TYR A 140 ARG 0.007 0.000 ARG C 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3259.83 seconds wall clock time: 57 minutes 53.33 seconds (3473.33 seconds total)