Starting phenix.real_space_refine on Tue Sep 24 10:14:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/09_2024/6wha_21669.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/09_2024/6wha_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/09_2024/6wha_21669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/09_2024/6wha_21669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/09_2024/6wha_21669.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/09_2024/6wha_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-5461/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: 4.77, per 1000 atoms: 0.60 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: 1.91 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: 1.03 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: 2.39 Time building geometry restraints manager: 2.16 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: 0.460 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.670 Find NCS groups from input model: 0.110 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.841 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: 0.2101 time to fit residues: 40.9064 Evaluate side-chains 115 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.845 Fit side-chains REVERT: A 343 ASN cc_start: 0.6713 (t0) cc_final: 0.6443 (t0) REVERT: B 17 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7509 (mttt) REVERT: B 73 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8129 (tmtt) REVERT: B 126 LYS cc_start: 0.8698 (tttt) cc_final: 0.8376 (ttpt) REVERT: B 164 PHE cc_start: 0.7383 (m-80) cc_final: 0.7038 (m-80) REVERT: B 166 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6307 (tm-30) REVERT: B 195 LYS cc_start: 0.8706 (tmmt) cc_final: 0.8443 (tppt) REVERT: C 268 ASN cc_start: 0.6771 (m-40) cc_final: 0.6189 (t0) REVERT: D 42 GLU cc_start: 0.7523 (tt0) cc_final: 0.7229 (tt0) outliers start: 21 outliers final: 14 residues processed: 132 average time/residue: 0.1967 time to fit residues: 35.1623 Evaluate side-chains 118 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 53 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8042 Z= 0.156 Angle : 0.512 7.219 10953 Z= 0.275 Chirality : 0.042 0.199 1285 Planarity : 0.003 0.034 1392 Dihedral : 5.846 101.990 1152 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.12 % Allowed : 18.34 % Favored : 78.54 % 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: 1.07 (0.26), residues: 1042 helix: 2.77 (0.27), residues: 358 sheet: 0.66 (0.33), residues: 270 loop : -1.18 (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 0.016 0.001 PHE E 80 TYR 0.014 0.001 TYR E 178 ARG 0.002 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 fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.798 Fit side-chains REVERT: A 343 ASN cc_start: 0.6631 (t0) cc_final: 0.6355 (t0) REVERT: B 48 THR cc_start: 0.8276 (m) cc_final: 0.7985 (p) REVERT: B 73 LYS cc_start: 0.8385 (ttpt) cc_final: 0.8092 (tmtt) REVERT: B 77 ASP cc_start: 0.7230 (t0) cc_final: 0.6986 (t0) REVERT: B 126 LYS cc_start: 0.8730 (tttt) cc_final: 0.8403 (ttpt) REVERT: B 164 PHE cc_start: 0.7318 (m-80) cc_final: 0.6980 (m-80) REVERT: B 166 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6310 (tm-30) REVERT: B 195 LYS cc_start: 0.8711 (tmmt) cc_final: 0.8307 (tppt) REVERT: C 268 ASN cc_start: 0.6752 (m-40) cc_final: 0.6155 (t0) REVERT: D 42 GLU cc_start: 0.7603 (tt0) cc_final: 0.7311 (tt0) outliers start: 24 outliers final: 17 residues processed: 132 average time/residue: 0.1923 time to fit residues: 35.2017 Evaluate side-chains 121 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL 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 D residue 25 ILE Chi-restraints excluded: chain E residue 143 VAL 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 95 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8042 Z= 0.288 Angle : 0.618 8.789 10953 Z= 0.331 Chirality : 0.046 0.256 1285 Planarity : 0.004 0.041 1392 Dihedral : 6.305 103.630 1152 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.90 % Allowed : 17.04 % Favored : 79.06 % 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: 0.83 (0.26), residues: 1042 helix: 2.49 (0.27), residues: 362 sheet: 0.45 (0.31), residues: 280 loop : -1.25 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 151 HIS 0.006 0.002 HIS E 220 PHE 0.016 0.002 PHE B 197 TYR 0.017 0.002 TYR E 178 ARG 0.003 0.001 ARG E 67 *********************** 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 140 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.937 Fit side-chains REVERT: A 343 ASN cc_start: 0.6804 (t0) cc_final: 0.6542 (t0) REVERT: B 73 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8114 (tmtt) REVERT: B 126 LYS cc_start: 0.8778 (tttt) cc_final: 0.8482 (ttpt) REVERT: B 151 GLU cc_start: 0.7847 (tp30) cc_final: 0.7547 (tt0) REVERT: B 164 PHE cc_start: 0.7325 (m-80) cc_final: 0.6973 (m-80) REVERT: B 166 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6217 (tm-30) REVERT: C 153 ASP cc_start: 0.7113 (m-30) cc_final: 0.6906 (m-30) REVERT: C 268 ASN cc_start: 0.6767 (m-40) cc_final: 0.6240 (t0) REVERT: D 19 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8341 (mp) REVERT: D 42 GLU cc_start: 0.7637 (tt0) cc_final: 0.7412 (tt0) outliers start: 30 outliers final: 22 residues processed: 131 average time/residue: 0.1922 time to fit residues: 35.0412 Evaluate side-chains 125 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8042 Z= 0.230 Angle : 0.557 8.142 10953 Z= 0.300 Chirality : 0.044 0.264 1285 Planarity : 0.004 0.042 1392 Dihedral : 6.151 98.783 1152 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.42 % Allowed : 18.21 % Favored : 77.37 % 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: 0.82 (0.26), residues: 1042 helix: 2.59 (0.27), residues: 361 sheet: 0.31 (0.31), residues: 280 loop : -1.26 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 151 HIS 0.004 0.001 HIS E 220 PHE 0.015 0.002 PHE C 199 TYR 0.014 0.001 TYR E 178 ARG 0.003 0.000 ARG E 67 *********************** 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 137 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 0.927 Fit side-chains REVERT: A 343 ASN cc_start: 0.6779 (t0) cc_final: 0.6547 (t0) REVERT: B 8 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.5780 (mp0) REVERT: B 48 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8041 (p) REVERT: B 73 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8018 (tmtt) REVERT: B 126 LYS cc_start: 0.8787 (tttt) cc_final: 0.8494 (ttpt) REVERT: B 164 PHE cc_start: 0.7301 (m-80) cc_final: 0.6941 (m-80) REVERT: B 166 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6214 (tm-30) REVERT: B 195 LYS cc_start: 0.8751 (tmmt) cc_final: 0.8379 (tppt) REVERT: B 242 GLU cc_start: 0.7044 (tt0) cc_final: 0.6556 (tp30) REVERT: C 52 ARG cc_start: 0.8315 (ptp-170) cc_final: 0.7972 (ptp90) REVERT: C 153 ASP cc_start: 0.7075 (m-30) cc_final: 0.6815 (m-30) REVERT: C 268 ASN cc_start: 0.6747 (m-40) cc_final: 0.6286 (t0) REVERT: D 42 GLU cc_start: 0.7622 (tt0) cc_final: 0.7397 (tt0) outliers start: 34 outliers final: 24 residues processed: 127 average time/residue: 0.1758 time to fit residues: 31.4399 Evaluate side-chains 127 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 317 CYS 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 92 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8042 Z= 0.251 Angle : 0.572 7.980 10953 Z= 0.308 Chirality : 0.045 0.280 1285 Planarity : 0.004 0.041 1392 Dihedral : 5.921 95.863 1152 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.29 % Allowed : 18.86 % Favored : 76.85 % 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: 0.72 (0.26), residues: 1042 helix: 2.53 (0.27), residues: 361 sheet: 0.19 (0.31), residues: 287 loop : -1.29 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 151 HIS 0.005 0.001 HIS E 220 PHE 0.015 0.002 PHE C 199 TYR 0.016 0.001 TYR E 178 ARG 0.003 0.000 ARG E 67 *********************** 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 138 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 0.861 Fit side-chains REVERT: A 343 ASN cc_start: 0.6826 (t0) cc_final: 0.6600 (t0) REVERT: B 8 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.5796 (mp0) REVERT: B 48 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7989 (p) REVERT: B 73 LYS cc_start: 0.8416 (ttpt) cc_final: 0.7985 (tmtt) REVERT: B 126 LYS cc_start: 0.8798 (tttt) cc_final: 0.8493 (ttpt) REVERT: B 164 PHE cc_start: 0.7234 (m-80) cc_final: 0.6893 (m-80) REVERT: B 166 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6262 (tm-30) REVERT: C 52 ARG cc_start: 0.8310 (ptp-170) cc_final: 0.7957 (ptp90) REVERT: C 153 ASP cc_start: 0.7111 (m-30) cc_final: 0.6840 (m-30) REVERT: C 268 ASN cc_start: 0.6855 (m-40) cc_final: 0.6396 (t0) outliers start: 33 outliers final: 26 residues processed: 129 average time/residue: 0.1620 time to fit residues: 29.7517 Evaluate side-chains 132 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 317 CYS Chi-restraints excluded: chain C residue 336 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 11 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8042 Z= 0.231 Angle : 0.558 7.789 10953 Z= 0.300 Chirality : 0.044 0.292 1285 Planarity : 0.004 0.042 1392 Dihedral : 5.802 95.703 1152 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.55 % Allowed : 18.99 % 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: 0.72 (0.26), residues: 1042 helix: 2.59 (0.27), residues: 361 sheet: 0.21 (0.31), residues: 281 loop : -1.36 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 151 HIS 0.005 0.001 HIS E 220 PHE 0.015 0.002 PHE C 199 TYR 0.027 0.001 TYR B 115 ARG 0.002 0.000 ARG E 67 *********************** 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 140 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 105 time to evaluate : 0.904 Fit side-chains REVERT: A 343 ASN cc_start: 0.6821 (t0) cc_final: 0.6524 (t0) REVERT: B 8 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.5795 (mp0) REVERT: B 48 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.8014 (p) REVERT: B 73 LYS cc_start: 0.8403 (ttpt) cc_final: 0.7980 (tmtt) REVERT: B 126 LYS cc_start: 0.8783 (tttt) cc_final: 0.8498 (ttpt) REVERT: B 164 PHE cc_start: 0.7221 (m-80) cc_final: 0.6879 (m-80) REVERT: B 166 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6501 (tm-30) REVERT: B 242 GLU cc_start: 0.7075 (tt0) cc_final: 0.6646 (tp30) REVERT: C 52 ARG cc_start: 0.8249 (ptp-170) cc_final: 0.7894 (ptp90) REVERT: C 153 ASP cc_start: 0.7048 (m-30) cc_final: 0.6771 (m-30) REVERT: C 268 ASN cc_start: 0.6946 (m-40) cc_final: 0.6493 (t0) outliers start: 35 outliers final: 28 residues processed: 131 average time/residue: 0.1659 time to fit residues: 31.0928 Evaluate side-chains 131 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 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 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 30 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2867 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= 0.175 Angle : 0.520 7.646 10953 Z= 0.279 Chirality : 0.043 0.296 1285 Planarity : 0.003 0.040 1392 Dihedral : 5.547 93.951 1152 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.42 % Allowed : 19.51 % 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: 2.76 (0.27), residues: 361 sheet: 0.28 (0.30), residues: 291 loop : -1.25 (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 0.019 0.001 PHE E 80 TYR 0.021 0.001 TYR B 115 ARG 0.001 0.000 ARG E 168 *********************** 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 140 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 0.824 Fit side-chains REVERT: A 343 ASN cc_start: 0.6705 (t0) cc_final: 0.6428 (t0) REVERT: B 48 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8015 (p) REVERT: B 73 LYS cc_start: 0.8410 (ttpt) cc_final: 0.7979 (tmtt) REVERT: B 126 LYS cc_start: 0.8782 (tttt) cc_final: 0.8506 (ttpt) REVERT: B 164 PHE cc_start: 0.7244 (m-80) cc_final: 0.6860 (m-80) REVERT: B 166 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6470 (tm-30) REVERT: C 52 ARG cc_start: 0.8210 (ptp-170) cc_final: 0.7862 (ptp90) REVERT: C 153 ASP cc_start: 0.7101 (m-30) cc_final: 0.6805 (m-30) REVERT: C 268 ASN cc_start: 0.6933 (m-40) cc_final: 0.6496 (t0) outliers start: 34 outliers final: 28 residues processed: 132 average time/residue: 0.1774 time to fit residues: 32.9617 Evaluate side-chains 133 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 250 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0970 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8042 Z= 0.122 Angle : 0.475 7.111 10953 Z= 0.252 Chirality : 0.042 0.284 1285 Planarity : 0.003 0.036 1392 Dihedral : 5.169 90.337 1152 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.47 % Allowed : 21.59 % Favored : 75.94 % 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: 1.17 (0.26), residues: 1042 helix: 3.04 (0.27), residues: 361 sheet: 0.41 (0.31), residues: 287 loop : -1.17 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.002 0.000 HIS B 209 PHE 0.018 0.001 PHE E 80 TYR 0.018 0.001 TYR B 115 ARG 0.005 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 125 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.887 Fit side-chains REVERT: A 343 ASN cc_start: 0.6547 (t0) cc_final: 0.6326 (t0) REVERT: B 48 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8009 (p) REVERT: B 73 LYS cc_start: 0.8372 (ttpt) cc_final: 0.7943 (tmtt) REVERT: B 126 LYS cc_start: 0.8747 (tttt) cc_final: 0.8474 (ttpt) REVERT: B 164 PHE cc_start: 0.7191 (m-80) cc_final: 0.6842 (m-80) REVERT: B 166 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6470 (tm-30) REVERT: C 52 ARG cc_start: 0.8118 (ptp-170) cc_final: 0.7784 (ptp90) REVERT: C 153 ASP cc_start: 0.6926 (m-30) cc_final: 0.6613 (m-30) REVERT: C 268 ASN cc_start: 0.6846 (m-40) cc_final: 0.6418 (t0) outliers start: 19 outliers final: 15 residues processed: 121 average time/residue: 0.1730 time to fit residues: 29.5660 Evaluate side-chains 115 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 381 THR 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 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 E residue 2 VAL Chi-restraints excluded: chain E residue 146 SER 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 61 optimal weight: 6.9990 chunk 47 optimal weight: 0.2980 chunk 69 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 97 optimal weight: 0.0370 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3118 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= 0.141 Angle : 0.492 6.968 10953 Z= 0.262 Chirality : 0.042 0.287 1285 Planarity : 0.003 0.038 1392 Dihedral : 5.177 90.111 1151 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.34 % Allowed : 22.11 % 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: 1.24 (0.26), residues: 1042 helix: 3.05 (0.26), residues: 362 sheet: 0.42 (0.31), residues: 293 loop : -1.08 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.003 0.001 HIS E 220 PHE 0.012 0.001 PHE C 241 TYR 0.018 0.001 TYR B 115 ARG 0.007 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 119 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.784 Fit side-chains REVERT: A 343 ASN cc_start: 0.6548 (t0) cc_final: 0.6304 (t0) REVERT: B 48 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8118 (p) REVERT: B 73 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8034 (tmtt) REVERT: B 123 ASN cc_start: 0.7413 (m110) cc_final: 0.7192 (m110) REVERT: B 126 LYS cc_start: 0.8756 (tttt) cc_final: 0.8453 (ttpt) REVERT: B 164 PHE cc_start: 0.7123 (m-80) cc_final: 0.6821 (m-80) REVERT: B 166 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6469 (tm-30) REVERT: C 52 ARG cc_start: 0.8188 (ptp-170) cc_final: 0.7824 (ptp90) REVERT: C 153 ASP cc_start: 0.7031 (m-30) cc_final: 0.6744 (m-30) REVERT: C 268 ASN cc_start: 0.6880 (m-40) cc_final: 0.6418 (t0) outliers start: 18 outliers final: 14 residues processed: 114 average time/residue: 0.1723 time to fit residues: 27.4646 Evaluate side-chains 115 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 381 THR 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 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 E residue 2 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 25 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 12 optimal weight: 0.0040 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.129611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.100420 restraints weight = 11119.588| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.24 r_work: 0.2917 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3012 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= 0.206 Angle : 0.540 7.519 10953 Z= 0.288 Chirality : 0.044 0.299 1285 Planarity : 0.003 0.040 1392 Dihedral : 5.410 91.732 1151 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.21 % Allowed : 22.24 % 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: 1.12 (0.26), residues: 1042 helix: 2.91 (0.26), residues: 363 sheet: 0.37 (0.30), residues: 296 loop : -1.15 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 151 HIS 0.004 0.001 HIS E 220 PHE 0.020 0.001 PHE E 80 TYR 0.019 0.001 TYR B 115 ARG 0.008 0.000 ARG B 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1781.12 seconds wall clock time: 32 minutes 26.15 seconds (1946.15 seconds total)