Starting phenix.real_space_refine on Wed Mar 12 11:09:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wha_21669/03_2025/6wha_21669.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wha_21669/03_2025/6wha_21669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wha_21669/03_2025/6wha_21669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wha_21669/03_2025/6wha_21669.map" model { file = "/net/cci-nas-00/data/ceres_data/6wha_21669/03_2025/6wha_21669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wha_21669/03_2025/6wha_21669.cif" } resolution = 3.36 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= 0.005 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 44 5.16 5 C 5016 2.51 5 N 1355 2.21 5 O 1473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7888 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1679 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain breaks: 5 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1650 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2471 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'U0G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.85, per 1000 atoms: 0.61 Number of scatterers: 7888 At special positions: 0 Unit cell: (97.1394, 113.329, 121.85, 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 44 16.00 O 1473 8.00 N 1355 7.00 C 5016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 36.2% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 84 through 99 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.919A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 146 through 179 removed outlier: 4.377A pdb=" N VAL A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 removed outlier: 3.691A pdb=" N PHE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 208 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.366A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.297A pdb=" N VAL A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 245 through 261 Processing helix chain 'A' and resid 316 through 347 removed outlier: 3.802A pdb=" N LYS A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.595A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 Proline residue: A 377 - end of helix removed outlier: 3.726A pdb=" N TYR A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.684A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.787A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.884A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.356A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.547A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 184 through 203 removed outlier: 3.813A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.963A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 23 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.983A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.019A 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 removed outlier: 3.947A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.867A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.048A 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 sheet with id=AA1, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.713A pdb=" N ASP B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 72 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 83 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 84 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.481A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.842A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.146A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.984A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.736A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.862A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.633A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG C 304 " --> pdb=" O ASP C 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 10 through 12 removed outlier: 3.627A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.627A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.880A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.911A pdb=" N GLN E 219 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 148 403 hydrogen bonds defined for protein. 1134 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: 2.30 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1289 1.26 - 1.41: 2048 1.41 - 1.55: 4643 1.55 - 1.70: 1 1.70 - 1.84: 61 Bond restraints: 8042 Sorted by residual: bond pdb=" C05 U0G A 501 " pdb=" C06 U0G A 501 " ideal model delta sigma weight residual 1.422 1.536 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C22 U0G A 501 " pdb=" O23 U0G A 501 " ideal model delta sigma weight residual 1.354 1.464 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" N ILE C 93 " pdb=" CA ILE C 93 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.68e+01 bond pdb=" N VAL E 135 " pdb=" CA VAL E 135 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.68e+01 bond pdb=" N VAL D 54 " pdb=" CA VAL D 54 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.70e-03 1.32e+04 1.46e+01 ... (remaining 8037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 9769 1.99 - 3.97: 1098 3.97 - 5.96: 75 5.96 - 7.94: 9 7.94 - 9.93: 2 Bond angle restraints: 10953 Sorted by residual: angle pdb=" CA GLY E 10 " pdb=" C GLY E 10 " pdb=" O GLY E 10 " ideal model delta sigma weight residual 122.37 117.88 4.49 7.30e-01 1.88e+00 3.78e+01 angle pdb=" N PRO A 209 " pdb=" CA PRO A 209 " pdb=" C PRO A 209 " ideal model delta sigma weight residual 113.53 120.38 -6.85 1.39e+00 5.18e-01 2.43e+01 angle pdb=" CA GLY E 230 " pdb=" C GLY E 230 " pdb=" O GLY E 230 " ideal model delta sigma weight residual 121.88 118.38 3.50 7.80e-01 1.64e+00 2.02e+01 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" C CYS A 337 " ideal model delta sigma weight residual 109.81 119.50 -9.69 2.21e+00 2.05e-01 1.92e+01 angle pdb=" CA VAL B 86 " pdb=" C VAL B 86 " pdb=" O VAL B 86 " ideal model delta sigma weight residual 121.68 118.42 3.26 7.90e-01 1.60e+00 1.70e+01 ... (remaining 10948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 4381 21.04 - 42.09: 272 42.09 - 63.13: 38 63.13 - 84.18: 5 84.18 - 105.22: 3 Dihedral angle restraints: 4699 sinusoidal: 1595 harmonic: 3104 Sorted by residual: dihedral pdb=" C THR E 198 " pdb=" N THR E 198 " pdb=" CA THR E 198 " pdb=" CB THR E 198 " ideal model delta harmonic sigma weight residual -122.00 -132.23 10.23 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" C ARG E 179 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " pdb=" CB ARG E 179 " ideal model delta harmonic sigma weight residual -122.60 -132.45 9.85 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" C TYR E 102 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" CB TYR E 102 " ideal model delta harmonic sigma weight residual -122.60 -131.81 9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 748 0.063 - 0.126: 357 0.126 - 0.189: 144 0.189 - 0.251: 32 0.251 - 0.314: 4 Chirality restraints: 1285 Sorted by residual: chirality pdb=" CA THR E 198 " pdb=" N THR E 198 " pdb=" C THR E 198 " pdb=" CB THR E 198 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ARG E 179 " pdb=" N ARG E 179 " pdb=" C ARG E 179 " pdb=" CB ARG E 179 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LEU C 79 " pdb=" N LEU C 79 " pdb=" C LEU C 79 " pdb=" CB LEU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1282 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 240 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C PHE A 240 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE A 240 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 241 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 163 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C ILE A 163 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE A 163 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 164 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 179 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ARG E 179 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG E 179 " -0.015 2.00e-02 2.50e+03 pdb=" N MET E 180 " -0.013 2.00e-02 2.50e+03 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1873 2.81 - 3.33: 6931 3.33 - 3.85: 11304 3.85 - 4.38: 13025 4.38 - 4.90: 23519 Nonbonded interactions: 56652 Sorted by model distance: nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.284 3.040 nonbonded pdb=" O SER B 204 " pdb=" OG SER B 204 " model vdw 2.291 3.040 nonbonded pdb=" O ASP C 195 " pdb=" OG1 THR C 196 " model vdw 2.381 3.040 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.384 3.040 nonbonded pdb=" OG SER C 161 " pdb=" N GLY C 162 " model vdw 2.391 3.120 ... (remaining 56647 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: 0.530 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.150 Find NCS groups from input model: 0.100 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.012 0.114 8042 Z= 0.809 Angle : 1.196 9.929 10953 Z= 0.828 Chirality : 0.084 0.314 1285 Planarity : 0.005 0.049 1392 Dihedral : 13.683 105.222 2683 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.99 % Allowed : 15.99 % Favored : 81.01 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.33 % 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: -0.19 (0.26), residues: 1042 helix: 1.17 (0.28), residues: 352 sheet: 0.33 (0.35), residues: 263 loop : -1.54 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 169 HIS 0.009 0.002 HIS C 54 PHE 0.031 0.002 PHE B 197 TYR 0.023 0.002 TYR C 289 ARG 0.007 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.875 Fit side-chains REVERT: A 343 ASN cc_start: 0.6964 (t0) cc_final: 0.6685 (t0) REVERT: B 73 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8073 (tmtt) REVERT: B 126 LYS cc_start: 0.8836 (tttt) cc_final: 0.8467 (ttpt) REVERT: B 164 PHE cc_start: 0.7415 (m-80) cc_final: 0.7177 (m-80) REVERT: B 166 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6257 (tm-30) REVERT: B 195 LYS cc_start: 0.8872 (tmmt) cc_final: 0.8599 (tppt) REVERT: C 76 ASP cc_start: 0.7410 (p0) cc_final: 0.7003 (p0) REVERT: C 153 ASP cc_start: 0.7201 (m-30) cc_final: 0.6999 (m-30) REVERT: C 268 ASN cc_start: 0.6963 (m-40) cc_final: 0.6618 (t0) REVERT: D 42 GLU cc_start: 0.7674 (tt0) cc_final: 0.7413 (tt0) REVERT: E 116 THR cc_start: 0.8275 (t) cc_final: 0.8058 (m) outliers start: 23 outliers final: 14 residues processed: 146 average time/residue: 0.2168 time to fit residues: 42.2747 Evaluate side-chains 115 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.0020 chunk 96 optimal weight: 6.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114889 restraints weight = 11042.378| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.56 r_work: 0.3183 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8042 Z= 0.159 Angle : 0.539 8.095 10953 Z= 0.293 Chirality : 0.043 0.139 1285 Planarity : 0.003 0.040 1392 Dihedral : 6.579 102.206 1166 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.73 % Allowed : 16.78 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.66 (0.26), residues: 1042 helix: 2.27 (0.27), residues: 357 sheet: 0.40 (0.33), residues: 272 loop : -1.21 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE C 199 TYR 0.014 0.001 TYR B 243 ARG 0.006 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.826 Fit side-chains REVERT: A 343 ASN cc_start: 0.6852 (t0) cc_final: 0.6549 (t0) REVERT: B 17 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7651 (mttt) REVERT: B 73 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8191 (tmtt) REVERT: B 77 ASP cc_start: 0.7581 (t0) cc_final: 0.7362 (t0) REVERT: B 126 LYS cc_start: 0.8949 (tttt) cc_final: 0.8557 (ttpt) REVERT: B 164 PHE cc_start: 0.7415 (m-80) cc_final: 0.7030 (m-80) REVERT: B 166 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6654 (tm-30) REVERT: B 195 LYS cc_start: 0.8875 (tmmt) cc_final: 0.8482 (tppt) REVERT: C 138 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8415 (mt-10) REVERT: C 268 ASN cc_start: 0.7015 (m-40) cc_final: 0.6253 (t0) REVERT: D 42 GLU cc_start: 0.7918 (tt0) cc_final: 0.7610 (tt0) outliers start: 21 outliers final: 14 residues processed: 132 average time/residue: 0.2057 time to fit residues: 36.6928 Evaluate side-chains 118 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112368 restraints weight = 11224.954| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.56 r_work: 0.3138 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8042 Z= 0.176 Angle : 0.530 7.319 10953 Z= 0.284 Chirality : 0.043 0.223 1285 Planarity : 0.003 0.034 1392 Dihedral : 5.921 102.838 1152 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.51 % Allowed : 17.82 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1042 helix: 2.71 (0.27), residues: 358 sheet: 0.65 (0.33), residues: 270 loop : -1.21 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 151 HIS 0.004 0.001 HIS C 54 PHE 0.018 0.001 PHE E 80 TYR 0.015 0.001 TYR E 178 ARG 0.003 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.842 Fit side-chains REVERT: A 343 ASN cc_start: 0.6743 (t0) cc_final: 0.6436 (t0) REVERT: B 48 THR cc_start: 0.8383 (m) cc_final: 0.8040 (p) REVERT: B 73 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8145 (tmtt) REVERT: B 77 ASP cc_start: 0.7584 (t0) cc_final: 0.7323 (t0) REVERT: B 126 LYS cc_start: 0.8992 (tttt) cc_final: 0.8590 (ttpt) REVERT: B 164 PHE cc_start: 0.7379 (m-80) cc_final: 0.7000 (m-80) REVERT: B 166 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6642 (tm-30) REVERT: B 195 LYS cc_start: 0.8884 (tmmt) cc_final: 0.8381 (tppt) REVERT: C 138 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8404 (mt-10) REVERT: C 268 ASN cc_start: 0.6978 (m-40) cc_final: 0.6199 (t0) REVERT: D 42 GLU cc_start: 0.7986 (tt0) cc_final: 0.7681 (tt0) outliers start: 27 outliers final: 17 residues processed: 131 average time/residue: 0.1906 time to fit residues: 34.5458 Evaluate side-chains 122 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111435 restraints weight = 11078.634| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.66 r_work: 0.3105 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8042 Z= 0.176 Angle : 0.526 7.460 10953 Z= 0.281 Chirality : 0.043 0.259 1285 Planarity : 0.003 0.036 1392 Dihedral : 5.892 100.786 1152 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.25 % Allowed : 18.08 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.06 (0.26), residues: 1042 helix: 2.81 (0.27), residues: 359 sheet: 0.51 (0.32), residues: 273 loop : -1.13 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS E 220 PHE 0.015 0.001 PHE E 80 TYR 0.014 0.001 TYR E 178 ARG 0.006 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.814 Fit side-chains REVERT: A 343 ASN cc_start: 0.6769 (t0) cc_final: 0.6467 (t0) REVERT: B 73 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8163 (tmtt) REVERT: B 77 ASP cc_start: 0.7591 (t0) cc_final: 0.7329 (t0) REVERT: B 126 LYS cc_start: 0.9027 (tttt) cc_final: 0.8642 (ttpt) REVERT: B 164 PHE cc_start: 0.7404 (m-80) cc_final: 0.7039 (m-80) REVERT: B 166 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6698 (tm-30) REVERT: B 195 LYS cc_start: 0.8843 (tmmt) cc_final: 0.8370 (tppt) REVERT: C 268 ASN cc_start: 0.6941 (m-40) cc_final: 0.6182 (t0) REVERT: D 42 GLU cc_start: 0.8059 (tt0) cc_final: 0.7791 (tt0) outliers start: 25 outliers final: 22 residues processed: 123 average time/residue: 0.2076 time to fit residues: 36.0737 Evaluate side-chains 119 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 5.9990 chunk 95 optimal weight: 0.1980 chunk 42 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111272 restraints weight = 10942.069| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.64 r_work: 0.3112 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8042 Z= 0.162 Angle : 0.504 7.307 10953 Z= 0.270 Chirality : 0.043 0.263 1285 Planarity : 0.003 0.036 1392 Dihedral : 5.797 93.879 1152 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.51 % Allowed : 18.08 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.15 (0.26), residues: 1042 helix: 2.94 (0.27), residues: 360 sheet: 0.36 (0.31), residues: 280 loop : -1.02 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 151 HIS 0.003 0.001 HIS E 220 PHE 0.012 0.001 PHE C 199 TYR 0.014 0.001 TYR E 178 ARG 0.005 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.881 Fit side-chains REVERT: A 343 ASN cc_start: 0.6795 (t0) cc_final: 0.6489 (t0) REVERT: B 48 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8062 (p) REVERT: B 73 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8141 (tmtt) REVERT: B 77 ASP cc_start: 0.7651 (t0) cc_final: 0.7405 (t0) REVERT: B 126 LYS cc_start: 0.9028 (tttt) cc_final: 0.8664 (ttpt) REVERT: B 164 PHE cc_start: 0.7360 (m-80) cc_final: 0.6966 (m-80) REVERT: B 166 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6680 (tm-30) REVERT: B 195 LYS cc_start: 0.8825 (tmmt) cc_final: 0.8355 (tppt) REVERT: B 242 GLU cc_start: 0.7437 (tt0) cc_final: 0.6924 (tp30) REVERT: C 52 ARG cc_start: 0.8753 (ptp-170) cc_final: 0.8447 (ptp90) REVERT: C 268 ASN cc_start: 0.6955 (m-40) cc_final: 0.6289 (t0) REVERT: D 42 GLU cc_start: 0.8066 (tt0) cc_final: 0.7826 (tt0) outliers start: 27 outliers final: 23 residues processed: 120 average time/residue: 0.1760 time to fit residues: 29.8639 Evaluate side-chains 120 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098008 restraints weight = 11149.457| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.25 r_work: 0.2869 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8042 Z= 0.330 Angle : 0.615 9.090 10953 Z= 0.331 Chirality : 0.047 0.275 1285 Planarity : 0.004 0.044 1392 Dihedral : 6.107 94.986 1152 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.29 % Allowed : 18.99 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.76 (0.26), residues: 1042 helix: 2.54 (0.27), residues: 361 sheet: 0.22 (0.31), residues: 287 loop : -1.24 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 151 HIS 0.006 0.001 HIS E 220 PHE 0.016 0.002 PHE C 199 TYR 0.016 0.002 TYR E 178 ARG 0.005 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.969 Fit side-chains REVERT: A 206 ILE cc_start: 0.6450 (tp) cc_final: 0.6238 (tp) REVERT: A 343 ASN cc_start: 0.6788 (t0) cc_final: 0.6515 (t0) REVERT: B 8 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.5884 (mp0) REVERT: B 48 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8000 (p) REVERT: B 73 LYS cc_start: 0.8660 (ttpt) cc_final: 0.7951 (tmtt) REVERT: B 77 ASP cc_start: 0.7693 (t0) cc_final: 0.7438 (t0) REVERT: B 126 LYS cc_start: 0.8900 (tttt) cc_final: 0.8452 (ttpt) REVERT: B 164 PHE cc_start: 0.7104 (m-80) cc_final: 0.6699 (m-80) REVERT: B 166 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: C 52 ARG cc_start: 0.8919 (ptp-170) cc_final: 0.8509 (ptp90) REVERT: C 268 ASN cc_start: 0.7018 (m-40) cc_final: 0.6292 (t0) REVERT: D 19 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8227 (mp) REVERT: D 42 GLU cc_start: 0.7956 (tt0) cc_final: 0.7726 (tt0) outliers start: 33 outliers final: 24 residues processed: 129 average time/residue: 0.1802 time to fit residues: 32.9410 Evaluate side-chains 132 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109527 restraints weight = 11139.038| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.65 r_work: 0.3092 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8042 Z= 0.173 Angle : 0.517 7.653 10953 Z= 0.276 Chirality : 0.043 0.295 1285 Planarity : 0.003 0.040 1392 Dihedral : 5.626 92.269 1152 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.16 % Allowed : 19.25 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.94 (0.26), residues: 1042 helix: 2.81 (0.27), residues: 361 sheet: 0.24 (0.31), residues: 291 loop : -1.22 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS E 220 PHE 0.013 0.001 PHE C 199 TYR 0.024 0.001 TYR B 115 ARG 0.004 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.759 Fit side-chains REVERT: A 343 ASN cc_start: 0.6881 (t0) cc_final: 0.6608 (t0) REVERT: B 48 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 73 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8085 (tmtt) REVERT: B 126 LYS cc_start: 0.9052 (tttt) cc_final: 0.8701 (ttpt) REVERT: B 164 PHE cc_start: 0.7341 (m-80) cc_final: 0.6955 (m-80) REVERT: B 166 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6965 (tm-30) REVERT: C 52 ARG cc_start: 0.8708 (ptp-170) cc_final: 0.8359 (ptp90) REVERT: C 268 ASN cc_start: 0.7110 (m-40) cc_final: 0.6461 (t0) REVERT: D 42 GLU cc_start: 0.8050 (tt0) cc_final: 0.7787 (tt0) outliers start: 32 outliers final: 26 residues processed: 128 average time/residue: 0.1844 time to fit residues: 32.9430 Evaluate side-chains 131 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104795 restraints weight = 11053.081| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.01 r_work: 0.2919 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8042 Z= 0.303 Angle : 0.607 8.749 10953 Z= 0.326 Chirality : 0.046 0.297 1285 Planarity : 0.004 0.044 1392 Dihedral : 5.925 95.455 1152 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.29 % Allowed : 19.25 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1042 helix: 2.50 (0.27), residues: 363 sheet: 0.20 (0.31), residues: 287 loop : -1.36 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 151 HIS 0.006 0.001 HIS E 220 PHE 0.015 0.002 PHE C 199 TYR 0.022 0.002 TYR B 115 ARG 0.004 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.883 Fit side-chains REVERT: A 343 ASN cc_start: 0.6691 (t0) cc_final: 0.6429 (t0) REVERT: B 8 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6066 (mp0) REVERT: B 48 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7971 (p) REVERT: B 73 LYS cc_start: 0.8684 (ttpt) cc_final: 0.7885 (tmtt) REVERT: B 126 LYS cc_start: 0.8832 (tttt) cc_final: 0.8384 (ttpt) REVERT: B 164 PHE cc_start: 0.6992 (m-80) cc_final: 0.6595 (m-80) REVERT: B 166 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: C 52 ARG cc_start: 0.8922 (ptp-170) cc_final: 0.8484 (ptp90) REVERT: C 254 ASP cc_start: 0.8870 (t0) cc_final: 0.8665 (t0) REVERT: C 268 ASN cc_start: 0.7107 (m-40) cc_final: 0.6317 (t0) REVERT: D 19 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8145 (mp) REVERT: D 42 GLU cc_start: 0.7927 (tt0) cc_final: 0.7714 (tt0) outliers start: 33 outliers final: 26 residues processed: 129 average time/residue: 0.2052 time to fit residues: 37.4839 Evaluate side-chains 133 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 82 optimal weight: 0.0370 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110619 restraints weight = 11201.510| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.60 r_work: 0.3111 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8042 Z= 0.175 Angle : 0.516 7.719 10953 Z= 0.277 Chirality : 0.043 0.307 1285 Planarity : 0.003 0.040 1392 Dihedral : 5.553 93.320 1152 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.77 % Allowed : 20.16 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.92 (0.26), residues: 1042 helix: 2.81 (0.27), residues: 362 sheet: 0.31 (0.31), residues: 289 loop : -1.35 (0.27), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS E 220 PHE 0.014 0.001 PHE C 199 TYR 0.018 0.001 TYR B 115 ARG 0.003 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.962 Fit side-chains REVERT: A 228 LEU cc_start: 0.5790 (mt) cc_final: 0.5511 (pp) REVERT: A 343 ASN cc_start: 0.6913 (t0) cc_final: 0.6540 (t0) REVERT: B 48 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8155 (p) REVERT: B 73 LYS cc_start: 0.8619 (ttpt) cc_final: 0.8060 (tmtt) REVERT: B 126 LYS cc_start: 0.9025 (tttt) cc_final: 0.8668 (ttpt) REVERT: B 164 PHE cc_start: 0.7316 (m-80) cc_final: 0.6945 (m-80) REVERT: B 166 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: C 52 ARG cc_start: 0.8657 (ptp-170) cc_final: 0.8289 (ptp90) REVERT: C 268 ASN cc_start: 0.7223 (m-40) cc_final: 0.6581 (t0) REVERT: D 42 GLU cc_start: 0.8007 (tt0) cc_final: 0.7764 (tt0) outliers start: 29 outliers final: 25 residues processed: 129 average time/residue: 0.2495 time to fit residues: 45.6597 Evaluate side-chains 129 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 20 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109821 restraints weight = 11078.910| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.67 r_work: 0.3096 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8042 Z= 0.171 Angle : 0.514 7.447 10953 Z= 0.275 Chirality : 0.043 0.299 1285 Planarity : 0.003 0.040 1392 Dihedral : 5.458 92.445 1152 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.64 % Allowed : 20.81 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1042 helix: 2.89 (0.27), residues: 362 sheet: 0.35 (0.31), residues: 291 loop : -1.27 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 151 HIS 0.003 0.001 HIS E 220 PHE 0.013 0.001 PHE C 199 TYR 0.018 0.001 TYR B 115 ARG 0.004 0.000 ARG B 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.920 Fit side-chains REVERT: A 343 ASN cc_start: 0.6837 (t0) cc_final: 0.6456 (t0) REVERT: B 48 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8159 (p) REVERT: B 73 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8060 (tmtt) REVERT: B 126 LYS cc_start: 0.9050 (tttt) cc_final: 0.8698 (ttpt) REVERT: B 164 PHE cc_start: 0.7351 (m-80) cc_final: 0.6949 (m-80) REVERT: B 166 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6943 (tm-30) REVERT: C 52 ARG cc_start: 0.8702 (ptp-170) cc_final: 0.8330 (ptp90) REVERT: C 268 ASN cc_start: 0.7249 (m-40) cc_final: 0.6611 (t0) REVERT: D 42 GLU cc_start: 0.8052 (tt0) cc_final: 0.7808 (tt0) outliers start: 28 outliers final: 25 residues processed: 126 average time/residue: 0.1743 time to fit residues: 31.1233 Evaluate side-chains 128 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099544 restraints weight = 11233.164| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.18 r_work: 0.2877 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8042 Z= 0.336 Angle : 0.628 9.135 10953 Z= 0.336 Chirality : 0.047 0.308 1285 Planarity : 0.004 0.045 1392 Dihedral : 5.872 95.245 1151 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.77 % Allowed : 20.68 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.63 (0.25), residues: 1042 helix: 2.46 (0.27), residues: 363 sheet: 0.26 (0.31), residues: 280 loop : -1.45 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.007 0.001 HIS E 220 PHE 0.016 0.002 PHE C 199 TYR 0.020 0.002 TYR B 115 ARG 0.004 0.001 ARG B 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4457.59 seconds wall clock time: 80 minutes 2.12 seconds (4802.12 seconds total)