Starting phenix.real_space_refine on Tue Mar 3 18:37:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rmi_24572/03_2026/7rmi_24572.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rmi_24572/03_2026/7rmi_24572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rmi_24572/03_2026/7rmi_24572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rmi_24572/03_2026/7rmi_24572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rmi_24572/03_2026/7rmi_24572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rmi_24572/03_2026/7rmi_24572.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.006 sd= 0.375 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1045 atoms to isotropic. 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 52 5.16 5 C 4667 2.51 5 N 1220 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7205 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1517 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "R" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2221 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 13, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "S" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 51 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2319 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'ASP:plan': 13, 'ASN:plan1': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 245 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 851 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 1.68, per 1000 atoms: 0.23 Number of scatterers: 7205 At special positions: 0 Unit cell: (67.635, 98.53, 128.59, 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 52 16.00 O 1266 8.00 N 1220 7.00 C 4667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 296.1 milliseconds 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 11 sheets defined 39.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 25 through 39 removed outlier: 3.773A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.729A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 No H-bonds generated for 'chain 'A' and resid 252 through 264' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.819A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.741A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.655A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 60 removed outlier: 3.698A pdb=" N HIS R 60 " --> pdb=" O ILE R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 67 No H-bonds generated for 'chain 'R' and resid 65 through 67' Processing helix chain 'R' and resid 68 through 94 Processing helix chain 'R' and resid 100 through 135 removed outlier: 4.284A pdb=" N TYR R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 143 through 168 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 190 through 205 removed outlier: 3.908A pdb=" N LYS R 194 " --> pdb=" O LYS R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 224 removed outlier: 3.683A pdb=" N LEU R 209 " --> pdb=" O TYR R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 270 removed outlier: 3.654A pdb=" N LYS R 243 " --> pdb=" O GLN R 239 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 271 through 273 No H-bonds generated for 'chain 'R' and resid 271 through 273' Processing helix chain 'R' and resid 274 through 278 removed outlier: 4.001A pdb=" N LEU R 277 " --> pdb=" O ASN R 274 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR R 278 " --> pdb=" O PRO R 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 274 through 278' Processing helix chain 'R' and resid 281 through 296 Processing helix chain 'R' and resid 299 through 309 removed outlier: 3.619A pdb=" N ILE R 303 " --> pdb=" O MET R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 320 removed outlier: 3.650A pdb=" N ARG R 313 " --> pdb=" O ASN R 309 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE R 320 " --> pdb=" O PHE R 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.965A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.705A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.811A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.506A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 169 through 174 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.300A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.055A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.936A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.972A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.977A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.011A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.510A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.602A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 59 through 60 removed outlier: 3.664A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1035 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: 1.11 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2259 1.35 - 1.46: 1946 1.46 - 1.58: 3096 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 7376 Sorted by residual: bond pdb=" CB ASN B 155 " pdb=" CG ASN B 155 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.47e+00 bond pdb=" CG1 ILE R 290 " pdb=" CD1 ILE R 290 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.73e+00 bond pdb=" C LEU R 262 " pdb=" N PRO R 263 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.25e-02 6.40e+03 2.29e+00 bond pdb=" CB GLN N 39 " pdb=" CG GLN N 39 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.22e+00 bond pdb=" C PHE R 163 " pdb=" N PRO R 164 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.28e-02 6.10e+03 1.97e+00 ... (remaining 7371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 9844 2.50 - 5.01: 189 5.01 - 7.51: 28 7.51 - 10.01: 4 10.01 - 12.52: 2 Bond angle restraints: 10067 Sorted by residual: angle pdb=" CB MET G 21 " pdb=" CG MET G 21 " pdb=" SD MET G 21 " ideal model delta sigma weight residual 112.70 124.23 -11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C ASN A 292 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " ideal model delta sigma weight residual 122.82 128.27 -5.45 1.42e+00 4.96e-01 1.47e+01 angle pdb=" CA LEU B 308 " pdb=" CB LEU B 308 " pdb=" CG LEU B 308 " ideal model delta sigma weight residual 116.30 128.82 -12.52 3.50e+00 8.16e-02 1.28e+01 angle pdb=" CA ASN B 155 " pdb=" CB ASN B 155 " pdb=" CG ASN B 155 " ideal model delta sigma weight residual 112.60 116.09 -3.49 1.00e+00 1.00e+00 1.21e+01 angle pdb=" CB GLN N 39 " pdb=" CG GLN N 39 " pdb=" CD GLN N 39 " ideal model delta sigma weight residual 112.60 118.41 -5.81 1.70e+00 3.46e-01 1.17e+01 ... (remaining 10062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 3906 17.03 - 34.06: 293 34.06 - 51.10: 49 51.10 - 68.13: 4 68.13 - 85.16: 5 Dihedral angle restraints: 4257 sinusoidal: 1445 harmonic: 2812 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA MET R 299 " pdb=" C MET R 299 " pdb=" N TYR R 300 " pdb=" CA TYR R 300 " ideal model delta harmonic sigma weight residual -180.00 -158.03 -21.97 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 4254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 814 0.048 - 0.095: 268 0.095 - 0.143: 74 0.143 - 0.191: 19 0.191 - 0.239: 2 Chirality restraints: 1177 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU B 255 " pdb=" CB LEU B 255 " pdb=" CD1 LEU B 255 " pdb=" CD2 LEU B 255 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CB ILE N 70 " pdb=" CA ILE N 70 " pdb=" CG1 ILE N 70 " pdb=" CG2 ILE N 70 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 1174 not shown) Planarity restraints: 1255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " -0.043 2.00e-02 2.50e+03 3.80e-02 3.60e+01 pdb=" CG TRP B 332 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.050 5.00e-02 4.00e+02 7.50e-02 8.99e+00 pdb=" N PRO B 236 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 82 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C ALA R 82 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA R 82 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 83 " 0.015 2.00e-02 2.50e+03 ... (remaining 1252 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2074 2.82 - 3.34: 6135 3.34 - 3.86: 11901 3.86 - 4.38: 12954 4.38 - 4.90: 23826 Nonbonded interactions: 56890 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.296 3.040 nonbonded pdb=" O ASP N 90 " pdb=" OH TYR N 94 " model vdw 2.296 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.301 3.040 nonbonded pdb=" O VAL R 116 " pdb=" OG SER R 119 " model vdw 2.324 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.328 3.040 ... (remaining 56885 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 7380 Z= 0.236 Angle : 0.843 12.516 10073 Z= 0.456 Chirality : 0.053 0.239 1177 Planarity : 0.007 0.075 1255 Dihedral : 12.681 85.159 2426 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.26), residues: 934 helix: -0.65 (0.24), residues: 338 sheet: 0.24 (0.36), residues: 201 loop : -1.09 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 137 TYR 0.025 0.002 TYR N 60 PHE 0.021 0.002 PHE B 241 TRP 0.102 0.003 TRP B 332 HIS 0.007 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7376) covalent geometry : angle 0.84215 (10067) SS BOND : bond 0.00255 ( 3) SS BOND : angle 1.76402 ( 6) hydrogen bonds : bond 0.13572 ( 360) hydrogen bonds : angle 6.10937 ( 1035) Misc. bond : bond 0.10071 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.261 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.0783 time to fit residues: 16.9464 Evaluate side-chains 113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 267 GLN R 136 HIS B 220 GLN B 230 ASN B 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.133806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115333 restraints weight = 15797.403| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.27 r_work: 0.3529 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7380 Z= 0.225 Angle : 0.624 7.798 10073 Z= 0.339 Chirality : 0.045 0.150 1177 Planarity : 0.005 0.058 1255 Dihedral : 4.525 24.727 1029 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.86 % Allowed : 9.29 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.27), residues: 934 helix: 0.79 (0.27), residues: 343 sheet: 0.33 (0.36), residues: 206 loop : -0.86 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 314 TYR 0.014 0.002 TYR N 95 PHE 0.024 0.002 PHE B 292 TRP 0.060 0.002 TRP B 332 HIS 0.005 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 7376) covalent geometry : angle 0.62187 (10067) SS BOND : bond 0.00480 ( 3) SS BOND : angle 2.37692 ( 6) hydrogen bonds : bond 0.04977 ( 360) hydrogen bonds : angle 4.91074 ( 1035) Misc. bond : bond 0.00123 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.266 Fit side-chains REVERT: A 368 ASP cc_start: 0.8524 (t0) cc_final: 0.8049 (t0) REVERT: A 378 ASP cc_start: 0.8567 (m-30) cc_final: 0.8231 (m-30) REVERT: A 381 ASP cc_start: 0.9329 (t70) cc_final: 0.9121 (t0) REVERT: S 6 GLN cc_start: 0.8299 (pm20) cc_final: 0.8057 (pt0) REVERT: B 308 LEU cc_start: 0.7424 (mm) cc_final: 0.6755 (tt) REVERT: B 325 MET cc_start: 0.6995 (ptt) cc_final: 0.6643 (ptt) REVERT: B 332 TRP cc_start: 0.7330 (m-90) cc_final: 0.7125 (m-90) REVERT: N 53 GLN cc_start: 0.8378 (mp10) cc_final: 0.8139 (mp10) outliers start: 6 outliers final: 5 residues processed: 121 average time/residue: 0.0691 time to fit residues: 11.9859 Evaluate side-chains 114 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 12 optimal weight: 0.1980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.134798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.116502 restraints weight = 15639.975| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.18 r_work: 0.3551 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7380 Z= 0.136 Angle : 0.533 6.254 10073 Z= 0.284 Chirality : 0.042 0.137 1177 Planarity : 0.004 0.050 1255 Dihedral : 4.196 22.157 1029 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.71 % Allowed : 11.57 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.28), residues: 934 helix: 1.35 (0.28), residues: 350 sheet: 0.34 (0.35), residues: 208 loop : -0.66 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 374 TYR 0.019 0.001 TYR N 94 PHE 0.014 0.001 PHE N 27 TRP 0.045 0.001 TRP B 332 HIS 0.006 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7376) covalent geometry : angle 0.53156 (10067) SS BOND : bond 0.00589 ( 3) SS BOND : angle 1.87624 ( 6) hydrogen bonds : bond 0.04190 ( 360) hydrogen bonds : angle 4.61876 ( 1035) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8549 (t0) cc_final: 0.7947 (t0) REVERT: A 378 ASP cc_start: 0.8602 (m-30) cc_final: 0.8223 (m-30) REVERT: A 381 ASP cc_start: 0.9303 (t70) cc_final: 0.9075 (t0) REVERT: R 54 MET cc_start: 0.7394 (mmt) cc_final: 0.7099 (mmt) REVERT: B 292 PHE cc_start: 0.7778 (m-10) cc_final: 0.7560 (m-10) REVERT: B 308 LEU cc_start: 0.7472 (mm) cc_final: 0.6855 (tt) REVERT: B 332 TRP cc_start: 0.7521 (m-90) cc_final: 0.7244 (m-90) REVERT: N 53 GLN cc_start: 0.8465 (mp10) cc_final: 0.8229 (mp10) REVERT: N 80 TYR cc_start: 0.6514 (m-80) cc_final: 0.6168 (m-80) outliers start: 12 outliers final: 7 residues processed: 128 average time/residue: 0.0720 time to fit residues: 13.1140 Evaluate side-chains 120 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.134108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115269 restraints weight = 15736.577| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.34 r_work: 0.3527 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7380 Z= 0.144 Angle : 0.534 7.824 10073 Z= 0.282 Chirality : 0.042 0.136 1177 Planarity : 0.004 0.046 1255 Dihedral : 4.079 20.969 1029 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.29 % Allowed : 12.57 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.28), residues: 934 helix: 1.60 (0.28), residues: 349 sheet: 0.44 (0.35), residues: 206 loop : -0.58 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.014 0.001 TYR N 94 PHE 0.011 0.001 PHE R 264 TRP 0.034 0.001 TRP B 332 HIS 0.006 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7376) covalent geometry : angle 0.53265 (10067) SS BOND : bond 0.00350 ( 3) SS BOND : angle 1.86235 ( 6) hydrogen bonds : bond 0.04094 ( 360) hydrogen bonds : angle 4.52225 ( 1035) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8551 (t0) cc_final: 0.7887 (t0) REVERT: A 381 ASP cc_start: 0.9317 (t70) cc_final: 0.9060 (t0) REVERT: B 304 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6456 (ptp90) REVERT: B 308 LEU cc_start: 0.7600 (mm) cc_final: 0.7020 (tt) REVERT: B 332 TRP cc_start: 0.7666 (m-10) cc_final: 0.7417 (m-90) REVERT: N 53 GLN cc_start: 0.8437 (mp10) cc_final: 0.8190 (mp10) outliers start: 16 outliers final: 8 residues processed: 125 average time/residue: 0.0739 time to fit residues: 13.1330 Evaluate side-chains 120 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.131302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112743 restraints weight = 15889.006| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.30 r_work: 0.3499 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 7380 Z= 0.179 Angle : 0.572 7.973 10073 Z= 0.301 Chirality : 0.043 0.139 1177 Planarity : 0.004 0.045 1255 Dihedral : 4.158 21.561 1029 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.71 % Allowed : 14.29 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.28), residues: 934 helix: 1.57 (0.27), residues: 350 sheet: 0.37 (0.35), residues: 207 loop : -0.61 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.014 0.002 TYR A 391 PHE 0.011 0.001 PHE B 151 TRP 0.027 0.001 TRP B 332 HIS 0.006 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7376) covalent geometry : angle 0.57008 (10067) SS BOND : bond 0.00335 ( 3) SS BOND : angle 2.05768 ( 6) hydrogen bonds : bond 0.04368 ( 360) hydrogen bonds : angle 4.62322 ( 1035) Misc. bond : bond 0.00091 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8636 (t0) cc_final: 0.7972 (t0) REVERT: A 381 ASP cc_start: 0.9339 (t70) cc_final: 0.9080 (t0) REVERT: B 304 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6354 (ptp90) REVERT: B 308 LEU cc_start: 0.7832 (mm) cc_final: 0.7279 (tt) REVERT: B 332 TRP cc_start: 0.7867 (m-10) cc_final: 0.7508 (m-90) REVERT: B 340 ASN cc_start: 0.7425 (t0) cc_final: 0.6897 (p0) REVERT: N 53 GLN cc_start: 0.8508 (mp10) cc_final: 0.8258 (mp10) REVERT: N 117 TYR cc_start: 0.7897 (m-80) cc_final: 0.7566 (m-80) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.0710 time to fit residues: 12.6323 Evaluate side-chains 130 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 68 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.132724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.113970 restraints weight = 16010.048| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.33 r_work: 0.3518 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7380 Z= 0.132 Angle : 0.534 7.254 10073 Z= 0.279 Chirality : 0.042 0.135 1177 Planarity : 0.003 0.044 1255 Dihedral : 4.011 20.413 1029 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.29 % Allowed : 16.00 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.28), residues: 934 helix: 1.88 (0.28), residues: 349 sheet: 0.35 (0.35), residues: 207 loop : -0.55 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.012 0.001 TYR N 95 PHE 0.011 0.001 PHE R 264 TRP 0.020 0.001 TRP B 332 HIS 0.004 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7376) covalent geometry : angle 0.53210 (10067) SS BOND : bond 0.00464 ( 3) SS BOND : angle 1.80587 ( 6) hydrogen bonds : bond 0.04063 ( 360) hydrogen bonds : angle 4.49273 ( 1035) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8638 (t0) cc_final: 0.7960 (t0) REVERT: A 381 ASP cc_start: 0.9323 (t70) cc_final: 0.9074 (t0) REVERT: B 59 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.7009 (m-80) REVERT: B 227 SER cc_start: 0.8764 (t) cc_final: 0.8033 (p) REVERT: B 304 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6318 (ptp90) REVERT: B 308 LEU cc_start: 0.7892 (mm) cc_final: 0.7346 (tt) REVERT: B 332 TRP cc_start: 0.7932 (m-10) cc_final: 0.7365 (m-90) REVERT: N 53 GLN cc_start: 0.8527 (mp10) cc_final: 0.8299 (mp10) REVERT: N 80 TYR cc_start: 0.6405 (m-80) cc_final: 0.6060 (m-80) REVERT: N 117 TYR cc_start: 0.7786 (m-80) cc_final: 0.7499 (m-80) outliers start: 16 outliers final: 12 residues processed: 129 average time/residue: 0.0730 time to fit residues: 13.4136 Evaluate side-chains 129 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 299 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 67 optimal weight: 7.9990 chunk 6 optimal weight: 0.2980 chunk 49 optimal weight: 0.0060 chunk 87 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.133304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114471 restraints weight = 15941.103| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.33 r_work: 0.3528 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7380 Z= 0.131 Angle : 0.539 7.296 10073 Z= 0.279 Chirality : 0.042 0.172 1177 Planarity : 0.003 0.042 1255 Dihedral : 3.958 20.551 1029 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.14 % Allowed : 16.71 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.28), residues: 934 helix: 1.97 (0.28), residues: 349 sheet: 0.38 (0.35), residues: 206 loop : -0.54 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.013 0.001 TYR N 95 PHE 0.014 0.001 PHE A 340 TRP 0.018 0.001 TRP B 332 HIS 0.004 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7376) covalent geometry : angle 0.53710 (10067) SS BOND : bond 0.00427 ( 3) SS BOND : angle 1.82516 ( 6) hydrogen bonds : bond 0.04014 ( 360) hydrogen bonds : angle 4.47023 ( 1035) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.4658 (OUTLIER) cc_final: 0.4260 (mmm160) REVERT: A 368 ASP cc_start: 0.8664 (t0) cc_final: 0.8009 (t0) REVERT: A 381 ASP cc_start: 0.9335 (t70) cc_final: 0.9095 (t0) REVERT: B 59 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: B 227 SER cc_start: 0.8742 (t) cc_final: 0.8000 (p) REVERT: B 308 LEU cc_start: 0.7907 (mm) cc_final: 0.7633 (mm) REVERT: B 332 TRP cc_start: 0.7980 (m-10) cc_final: 0.7452 (m-90) REVERT: N 53 GLN cc_start: 0.8560 (mp10) cc_final: 0.8326 (mp10) REVERT: N 80 TYR cc_start: 0.6406 (m-80) cc_final: 0.6047 (m-80) REVERT: N 117 TYR cc_start: 0.7747 (m-80) cc_final: 0.7494 (m-80) outliers start: 15 outliers final: 12 residues processed: 130 average time/residue: 0.0703 time to fit residues: 12.7459 Evaluate side-chains 133 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 299 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 70 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.133708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114884 restraints weight = 16092.172| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.37 r_work: 0.3530 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7380 Z= 0.126 Angle : 0.537 6.995 10073 Z= 0.278 Chirality : 0.042 0.155 1177 Planarity : 0.003 0.042 1255 Dihedral : 3.919 20.072 1029 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.71 % Allowed : 17.14 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.28), residues: 934 helix: 2.07 (0.28), residues: 349 sheet: 0.46 (0.35), residues: 206 loop : -0.52 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.012 0.001 TYR N 95 PHE 0.011 0.001 PHE A 340 TRP 0.017 0.001 TRP B 332 HIS 0.002 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7376) covalent geometry : angle 0.53594 (10067) SS BOND : bond 0.00411 ( 3) SS BOND : angle 1.71156 ( 6) hydrogen bonds : bond 0.03935 ( 360) hydrogen bonds : angle 4.44161 ( 1035) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.4614 (OUTLIER) cc_final: 0.4243 (mmm160) REVERT: A 368 ASP cc_start: 0.8667 (t0) cc_final: 0.8007 (t0) REVERT: A 381 ASP cc_start: 0.9333 (t70) cc_final: 0.9097 (t0) REVERT: B 59 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: B 227 SER cc_start: 0.8728 (t) cc_final: 0.7983 (p) REVERT: B 304 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6389 (ptp90) REVERT: B 308 LEU cc_start: 0.7922 (mm) cc_final: 0.7383 (tt) REVERT: B 332 TRP cc_start: 0.7990 (m-10) cc_final: 0.7487 (m-90) REVERT: N 80 TYR cc_start: 0.6411 (m-80) cc_final: 0.6048 (m-80) REVERT: N 117 TYR cc_start: 0.7715 (m-80) cc_final: 0.7470 (m-80) outliers start: 19 outliers final: 13 residues processed: 132 average time/residue: 0.0805 time to fit residues: 14.3829 Evaluate side-chains 134 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 299 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 79 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.133792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115214 restraints weight = 15771.262| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.29 r_work: 0.3544 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7380 Z= 0.117 Angle : 0.530 6.827 10073 Z= 0.274 Chirality : 0.042 0.144 1177 Planarity : 0.003 0.041 1255 Dihedral : 3.874 19.513 1029 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.43 % Allowed : 17.43 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.28), residues: 934 helix: 2.17 (0.28), residues: 349 sheet: 0.48 (0.36), residues: 203 loop : -0.52 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.012 0.001 TYR A 391 PHE 0.010 0.001 PHE R 264 TRP 0.017 0.001 TRP B 332 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7376) covalent geometry : angle 0.52830 (10067) SS BOND : bond 0.00403 ( 3) SS BOND : angle 1.56337 ( 6) hydrogen bonds : bond 0.03800 ( 360) hydrogen bonds : angle 4.38168 ( 1035) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8670 (t0) cc_final: 0.8029 (t0) REVERT: A 381 ASP cc_start: 0.9323 (t70) cc_final: 0.9095 (t0) REVERT: B 59 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: B 227 SER cc_start: 0.8703 (t) cc_final: 0.8010 (p) REVERT: B 304 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6400 (ptp90) REVERT: B 308 LEU cc_start: 0.7927 (mm) cc_final: 0.7394 (tt) REVERT: B 332 TRP cc_start: 0.7989 (m-10) cc_final: 0.7467 (m-90) REVERT: N 39 GLN cc_start: 0.8320 (tp40) cc_final: 0.8067 (tp40) REVERT: N 80 TYR cc_start: 0.6463 (m-80) cc_final: 0.6104 (m-80) REVERT: N 117 TYR cc_start: 0.7697 (m-80) cc_final: 0.7459 (m-80) outliers start: 17 outliers final: 13 residues processed: 132 average time/residue: 0.0796 time to fit residues: 14.4949 Evaluate side-chains 133 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 299 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 0.0020 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.135575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.117039 restraints weight = 15803.720| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.30 r_work: 0.3560 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 7380 Z= 0.106 Angle : 0.521 7.827 10073 Z= 0.268 Chirality : 0.042 0.148 1177 Planarity : 0.003 0.041 1255 Dihedral : 3.793 19.113 1029 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.14 % Allowed : 17.57 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.28), residues: 934 helix: 2.26 (0.28), residues: 350 sheet: 0.52 (0.36), residues: 201 loop : -0.50 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 72 TYR 0.011 0.001 TYR A 391 PHE 0.009 0.001 PHE A 340 TRP 0.016 0.001 TRP B 332 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7376) covalent geometry : angle 0.51969 (10067) SS BOND : bond 0.00389 ( 3) SS BOND : angle 1.41478 ( 6) hydrogen bonds : bond 0.03643 ( 360) hydrogen bonds : angle 4.31962 ( 1035) Misc. bond : bond 0.00021 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.4682 (OUTLIER) cc_final: 0.4276 (mmm160) REVERT: A 368 ASP cc_start: 0.8670 (t0) cc_final: 0.8054 (t0) REVERT: A 381 ASP cc_start: 0.9330 (t70) cc_final: 0.9113 (t0) REVERT: R 54 MET cc_start: 0.7644 (mmt) cc_final: 0.7378 (mmt) REVERT: B 227 SER cc_start: 0.8669 (t) cc_final: 0.7953 (p) REVERT: B 304 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6471 (ptp90) REVERT: B 308 LEU cc_start: 0.7896 (mm) cc_final: 0.7376 (tt) REVERT: B 332 TRP cc_start: 0.7975 (m-10) cc_final: 0.7637 (m-90) REVERT: N 39 GLN cc_start: 0.8279 (tp40) cc_final: 0.8026 (tp40) REVERT: N 80 TYR cc_start: 0.6430 (m-80) cc_final: 0.6070 (m-80) REVERT: N 117 TYR cc_start: 0.7637 (m-80) cc_final: 0.7396 (m-80) outliers start: 15 outliers final: 12 residues processed: 130 average time/residue: 0.0756 time to fit residues: 13.7725 Evaluate side-chains 130 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 202 VAL Chi-restraints excluded: chain R residue 250 MET Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 299 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.132871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.114256 restraints weight = 15899.850| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.34 r_work: 0.3523 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7380 Z= 0.145 Angle : 0.552 8.469 10073 Z= 0.286 Chirality : 0.043 0.140 1177 Planarity : 0.003 0.041 1255 Dihedral : 3.894 19.257 1029 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.71 % Allowed : 17.86 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.28), residues: 934 helix: 2.13 (0.28), residues: 350 sheet: 0.58 (0.36), residues: 200 loop : -0.54 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.014 0.001 TYR A 391 PHE 0.013 0.001 PHE R 264 TRP 0.017 0.001 TRP B 332 HIS 0.003 0.001 HIS R 197 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7376) covalent geometry : angle 0.55026 (10067) SS BOND : bond 0.00410 ( 3) SS BOND : angle 1.70095 ( 6) hydrogen bonds : bond 0.03965 ( 360) hydrogen bonds : angle 4.39828 ( 1035) Misc. bond : bond 0.00067 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.81 seconds wall clock time: 27 minutes 23.32 seconds (1643.32 seconds total)