Starting phenix.real_space_refine on Sat Jul 4 17:51:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psn_17857/07_2026/8psn_17857_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psn_17857/07_2026/8psn_17857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8psn_17857/07_2026/8psn_17857_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psn_17857/07_2026/8psn_17857_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8psn_17857/07_2026/8psn_17857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psn_17857/07_2026/8psn_17857.map" } resolution = 2.73 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= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 31 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 7004 2.51 5 N 1995 2.21 5 O 2202 1.98 5 H 10965 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22266 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6651 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 7973 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Chain: "C" Number of atoms: 6714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 6714 Classifications: {'peptide': 429} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "S" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 486 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CTP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2584 SG CYS A 161 54.626 54.626 106.057 1.00 39.15 S ATOM 4472 SG CYS A 282 53.091 56.918 108.861 1.00 41.12 S ATOM 18270 SG CYS C 233 21.302 50.756 19.577 1.00 58.83 S ATOM 18294 SG CYS C 235 21.162 49.313 23.166 1.00 50.34 S ATOM 16936 SG CYS C 146 9.377 44.286 40.307 1.00 70.66 S ATOM 17124 SG CYS C 159 9.121 40.913 38.498 1.00 67.27 S ATOM 17180 SG CYS C 163 12.142 43.135 38.007 1.00 61.34 S ATOM 17190 SG CYS C 164 11.578 41.277 41.302 1.00 62.59 S Time building chain proxies: 2.84, per 1000 atoms: 0.13 Number of scatterers: 22266 At special positions: 0 Unit cell: (95.76, 105.84, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 64 16.00 P 31 15.00 Mg 2 11.99 O 2202 8.00 N 1995 7.00 C 7004 6.00 H 10965 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.65 Conformation dependent library (CDL) restraints added in 541.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 233 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 235 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " Number of angles added : 9 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 41.4% alpha, 14.1% beta 4 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.713A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.822A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.325A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.624A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 4.249A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.709A pdb=" N ILE A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.751A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.541A pdb=" N GLN B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.647A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.759A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.721A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.642A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 434 removed outlier: 4.042A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.622A pdb=" N LYS C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.548A pdb=" N HIS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.676A pdb=" N SER C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 281 through 289 removed outlier: 3.578A pdb=" N VAL C 289 " --> pdb=" O GLN C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 317 removed outlier: 4.011A pdb=" N ARG C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 421 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.758A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.232A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.232A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 159 removed outlier: 3.767A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS B 142 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 83 removed outlier: 4.970A pdb=" N ALA C 118 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N LEU C 76 " --> pdb=" O PRO C 116 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER C 78 " --> pdb=" O ASN C 114 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASN C 114 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N LEU C 80 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N VAL C 112 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 221 through 224 removed outlier: 6.846A pdb=" N GLY C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 360 through 363 Processing sheet with id=AB5, first strand: chain 'C' and resid 383 through 388 removed outlier: 6.718A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10933 1.03 - 1.23: 47 1.23 - 1.42: 4879 1.42 - 1.62: 6605 1.62 - 1.81: 88 Bond restraints: 22552 Sorted by residual: bond pdb=" O3B CTP E 1 " pdb=" PG CTP E 1 " ideal model delta sigma weight residual 1.751 1.613 0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" O3A CTP E 1 " pdb=" PB CTP E 1 " ideal model delta sigma weight residual 1.675 1.601 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" N ILE B 443 " pdb=" CA ILE B 443 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.29e+00 bond pdb=" O5' CTP E 1 " pdb=" PA CTP E 1 " ideal model delta sigma weight residual 1.660 1.603 0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" N THR B 442 " pdb=" CA THR B 442 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.31e-02 5.83e+03 7.48e+00 ... (remaining 22547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 40451 2.25 - 4.50: 261 4.50 - 6.75: 9 6.75 - 9.00: 1 9.00 - 11.25: 2 Bond angle restraints: 40724 Sorted by residual: angle pdb=" C THR A 267 " pdb=" CA THR A 267 " pdb=" CB THR A 267 " ideal model delta sigma weight residual 110.42 120.60 -10.18 1.99e+00 2.53e-01 2.62e+01 angle pdb=" N PRO A 61 " pdb=" CD PRO A 61 " pdb=" CG PRO A 61 " ideal model delta sigma weight residual 103.20 97.23 5.97 1.50e+00 4.44e-01 1.59e+01 angle pdb=" CA PRO A 61 " pdb=" N PRO A 61 " pdb=" CD PRO A 61 " ideal model delta sigma weight residual 112.00 106.83 5.17 1.40e+00 5.10e-01 1.36e+01 angle pdb=" CB PRO A 61 " pdb=" CG PRO A 61 " pdb=" CD PRO A 61 " ideal model delta sigma weight residual 106.10 94.85 11.25 3.20e+00 9.77e-02 1.24e+01 angle pdb=" C THR B 442 " pdb=" N ILE B 443 " pdb=" CA ILE B 443 " ideal model delta sigma weight residual 120.60 125.06 -4.46 1.29e+00 6.01e-01 1.19e+01 ... (remaining 40719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 10124 33.70 - 67.41: 503 67.41 - 101.11: 32 101.11 - 134.81: 3 134.81 - 168.51: 3 Dihedral angle restraints: 10665 sinusoidal: 6066 harmonic: 4599 Sorted by residual: dihedral pdb=" C4' G S 1 " pdb=" C3' G S 1 " pdb=" O3' G S 1 " pdb=" P U S 2 " ideal model delta sinusoidal sigma weight residual -110.00 58.51 -168.51 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' G S 3 " pdb=" C3' G S 3 " pdb=" O3' G S 3 " pdb=" P A S 4 " ideal model delta sinusoidal sigma weight residual 220.00 79.02 140.98 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" CA LEU B 265 " pdb=" C LEU B 265 " pdb=" N MET B 266 " pdb=" CA MET B 266 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 10662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1455 0.041 - 0.083: 224 0.083 - 0.124: 94 0.124 - 0.165: 5 0.165 - 0.207: 2 Chirality restraints: 1780 Sorted by residual: chirality pdb=" C2' CTP E 1 " pdb=" C1' CTP E 1 " pdb=" C3' CTP E 1 " pdb=" O2' CTP E 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.73 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE B 443 " pdb=" N ILE B 443 " pdb=" C ILE B 443 " pdb=" CB ILE B 443 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" C1' CTP E 1 " pdb=" C2' CTP E 1 " pdb=" N1 CTP E 1 " pdb=" O4' CTP E 1 " both_signs ideal model delta sigma weight residual False 2.35 2.49 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 1777 not shown) Planarity restraints: 3243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 445 " 0.099 2.00e-02 2.50e+03 1.06e-01 1.68e+02 pdb=" CD GLN B 445 " -0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN B 445 " -0.095 2.00e-02 2.50e+03 pdb=" NE2 GLN B 445 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 445 " -0.154 2.00e-02 2.50e+03 pdb="HE22 GLN B 445 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 268 " -0.012 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" N SER A 269 " 0.038 2.00e-02 2.50e+03 pdb=" CA SER A 269 " -0.010 2.00e-02 2.50e+03 pdb=" H SER A 269 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 265 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ARG A 265 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG A 265 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO A 266 " 0.012 2.00e-02 2.50e+03 ... (remaining 3240 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 777 2.15 - 2.76: 41164 2.76 - 3.37: 62999 3.37 - 3.99: 83686 3.99 - 4.60: 129804 Nonbonded interactions: 318430 Sorted by model distance: nonbonded pdb=" OD2 ASP B 467 " pdb=" HE ARG B 490 " model vdw 1.535 2.450 nonbonded pdb=" H GLY C 85 " pdb=" OD1 ASP C 110 " model vdw 1.556 2.450 nonbonded pdb=" O LEU B 179 " pdb=" HG SER B 183 " model vdw 1.618 2.450 nonbonded pdb=" OD2 ASP B 222 " pdb="HH22 ARG B 247 " model vdw 1.632 2.450 nonbonded pdb="HO2' A S 8 " pdb=" O4' A S 9 " model vdw 1.634 2.450 ... (remaining 318425 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 24.280 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 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 : 0.003 0.138 11599 Z= 0.159 Angle : 0.536 11.253 15809 Z= 0.294 Chirality : 0.037 0.207 1780 Planarity : 0.004 0.051 1932 Dihedral : 18.663 168.513 4535 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 20.53 % Favored : 76.90 % Cbeta Deviations : 0.08 % 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: 1.12 (0.23), residues: 1355 helix: 1.91 (0.24), residues: 514 sheet: -0.05 (0.45), residues: 120 loop : 0.10 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.009 0.001 TYR A 403 PHE 0.010 0.001 PHE C 175 TRP 0.004 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (11587) covalent geometry : angle 0.53509 / 0.29 (15800) hydrogen bonds : bond 0.12755 / 8.27 ( 479) hydrogen bonds : angle 5.34667 / 3.74 ( 1326) metal coordination : bond 0.00242 / 0.16 ( 12) metal coordination : angle 1.48726 / 0.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.8048 (mm) cc_final: 0.7752 (mp) outliers start: 30 outliers final: 27 residues processed: 154 average time/residue: 1.2016 time to fit residues: 199.3174 Evaluate side-chains 139 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.097422 restraints weight = 37550.537| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.23 r_work: 0.2894 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11599 Z= 0.162 Angle : 0.522 4.487 15809 Z= 0.277 Chirality : 0.039 0.159 1780 Planarity : 0.005 0.050 1932 Dihedral : 13.695 164.889 1984 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 2.74 % Allowed : 20.19 % Favored : 77.07 % 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: 0.93 (0.22), residues: 1355 helix: 1.78 (0.23), residues: 521 sheet: -0.09 (0.45), residues: 120 loop : -0.07 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.013 0.001 TYR A 403 PHE 0.014 0.001 PHE B 377 TRP 0.004 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (11587) covalent geometry : angle 0.52064 / 0.28 (15800) hydrogen bonds : bond 0.04850 / 3.09 ( 479) hydrogen bonds : angle 4.66475 / 3.34 ( 1326) metal coordination : bond 0.00506 / 0.32 ( 12) metal coordination : angle 1.78380 / 1.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7939 (mm) cc_final: 0.7687 (mp) REVERT: C 124 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7600 (t0) outliers start: 32 outliers final: 22 residues processed: 147 average time/residue: 1.2240 time to fit residues: 194.2132 Evaluate side-chains 140 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 124 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 GLN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.097420 restraints weight = 37458.232| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.24 r_work: 0.2896 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11599 Z= 0.126 Angle : 0.488 4.556 15809 Z= 0.258 Chirality : 0.038 0.144 1780 Planarity : 0.004 0.050 1932 Dihedral : 13.245 165.070 1974 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Rotamer: Outliers : 2.82 % Allowed : 20.27 % Favored : 76.90 % 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: 0.95 (0.22), residues: 1355 helix: 1.83 (0.23), residues: 521 sheet: -0.11 (0.45), residues: 120 loop : -0.09 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 267 TYR 0.014 0.001 TYR A 403 PHE 0.011 0.001 PHE B 377 TRP 0.004 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (11587) covalent geometry : angle 0.48626 / 0.26 (15800) hydrogen bonds : bond 0.04561 / 2.89 ( 479) hydrogen bonds : angle 4.52997 / 3.25 ( 1326) metal coordination : bond 0.00439 / 0.26 ( 12) metal coordination : angle 1.73622 / 0.93 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.478 Fit side-chains REVERT: A 72 ILE cc_start: 0.7948 (mm) cc_final: 0.7695 (mp) REVERT: A 85 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6851 (tt0) REVERT: C 124 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7492 (t0) outliers start: 33 outliers final: 17 residues processed: 148 average time/residue: 1.2498 time to fit residues: 199.2506 Evaluate side-chains 132 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 106 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096505 restraints weight = 37598.876| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.24 r_work: 0.2886 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11599 Z= 0.145 Angle : 0.499 4.799 15809 Z= 0.265 Chirality : 0.038 0.150 1780 Planarity : 0.005 0.056 1932 Dihedral : 12.912 164.216 1962 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 2.40 % Allowed : 20.36 % Favored : 77.25 % 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: 0.90 (0.22), residues: 1355 helix: 1.80 (0.23), residues: 522 sheet: -0.13 (0.46), residues: 120 loop : -0.12 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 245 TYR 0.015 0.001 TYR A 403 PHE 0.012 0.001 PHE B 377 TRP 0.004 0.001 TRP B 2 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11587) covalent geometry : angle 0.49760 / 0.26 (15800) hydrogen bonds : bond 0.04475 / 2.83 ( 479) hydrogen bonds : angle 4.48505 / 3.22 ( 1326) metal coordination : bond 0.00442 / 0.27 ( 12) metal coordination : angle 1.73324 / 0.91 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.472 Fit side-chains REVERT: A 72 ILE cc_start: 0.7951 (mm) cc_final: 0.7716 (mp) REVERT: A 85 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6856 (tt0) REVERT: C 124 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7476 (t0) outliers start: 28 outliers final: 18 residues processed: 140 average time/residue: 1.2922 time to fit residues: 194.9092 Evaluate side-chains 133 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 110 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.094813 restraints weight = 37494.433| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.27 r_work: 0.2858 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11599 Z= 0.198 Angle : 0.530 4.843 15809 Z= 0.282 Chirality : 0.040 0.152 1780 Planarity : 0.005 0.054 1932 Dihedral : 13.053 163.261 1959 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.51 % Favored : 97.42 % Rotamer: Outliers : 2.91 % Allowed : 19.85 % Favored : 77.25 % 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: 0.74 (0.22), residues: 1355 helix: 1.66 (0.23), residues: 521 sheet: -0.06 (0.46), residues: 116 loop : -0.24 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 245 TYR 0.016 0.001 TYR A 403 PHE 0.015 0.002 PHE B 287 TRP 0.005 0.001 TRP C 209 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (11587) covalent geometry : angle 0.52826 / 0.28 (15800) hydrogen bonds : bond 0.04966 / 3.15 ( 479) hydrogen bonds : angle 4.54071 / 3.26 ( 1326) metal coordination : bond 0.00636 / 0.36 ( 12) metal coordination : angle 1.95705 / 1.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7952 (mm) cc_final: 0.7747 (mp) REVERT: A 85 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6871 (tt0) outliers start: 34 outliers final: 22 residues processed: 141 average time/residue: 1.3176 time to fit residues: 200.4220 Evaluate side-chains 134 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.095598 restraints weight = 37748.121| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.23 r_work: 0.2863 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11599 Z= 0.157 Angle : 0.509 4.608 15809 Z= 0.271 Chirality : 0.039 0.148 1780 Planarity : 0.005 0.051 1932 Dihedral : 12.979 163.298 1959 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 2.57 % Allowed : 20.02 % Favored : 77.42 % 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: 0.75 (0.22), residues: 1355 helix: 1.68 (0.23), residues: 522 sheet: -0.09 (0.46), residues: 116 loop : -0.24 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 267 TYR 0.014 0.001 TYR A 403 PHE 0.013 0.001 PHE B 287 TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (11587) covalent geometry : angle 0.50771 / 0.27 (15800) hydrogen bonds : bond 0.04657 / 2.94 ( 479) hydrogen bonds : angle 4.50398 / 3.23 ( 1326) metal coordination : bond 0.00463 / 0.27 ( 12) metal coordination : angle 1.76153 / 0.91 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.547 Fit side-chains REVERT: A 85 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6872 (tt0) REVERT: A 160 GLU cc_start: 0.8189 (mp0) cc_final: 0.7834 (mp0) outliers start: 30 outliers final: 22 residues processed: 143 average time/residue: 1.3635 time to fit residues: 209.8998 Evaluate side-chains 136 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.095030 restraints weight = 37412.234| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.24 r_work: 0.2855 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11599 Z= 0.190 Angle : 0.532 4.698 15809 Z= 0.284 Chirality : 0.040 0.148 1780 Planarity : 0.005 0.051 1932 Dihedral : 13.091 162.660 1959 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.51 % Favored : 97.42 % Rotamer: Outliers : 2.91 % Allowed : 19.93 % Favored : 77.16 % 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: 0.64 (0.22), residues: 1355 helix: 1.59 (0.22), residues: 520 sheet: -0.17 (0.46), residues: 116 loop : -0.30 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 267 TYR 0.016 0.001 TYR A 403 PHE 0.014 0.002 PHE B 287 TRP 0.005 0.001 TRP C 209 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (11587) covalent geometry : angle 0.53009 / 0.28 (15800) hydrogen bonds : bond 0.04923 / 3.12 ( 479) hydrogen bonds : angle 4.51972 / 3.24 ( 1326) metal coordination : bond 0.00581 / 0.33 ( 12) metal coordination : angle 1.86869 / 0.94 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.668 Fit side-chains REVERT: A 85 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: A 160 GLU cc_start: 0.8200 (mp0) cc_final: 0.7857 (mp0) outliers start: 34 outliers final: 22 residues processed: 142 average time/residue: 1.2717 time to fit residues: 194.3979 Evaluate side-chains 135 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.094853 restraints weight = 37260.216| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.25 r_work: 0.2857 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11599 Z= 0.176 Angle : 0.525 4.782 15809 Z= 0.280 Chirality : 0.039 0.148 1780 Planarity : 0.005 0.051 1932 Dihedral : 13.076 162.567 1957 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 20.27 % Favored : 77.16 % 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 (0.22), residues: 1355 helix: 1.57 (0.22), residues: 521 sheet: -0.14 (0.46), residues: 116 loop : -0.30 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 267 TYR 0.015 0.001 TYR A 403 PHE 0.013 0.001 PHE B 287 TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (11587) covalent geometry : angle 0.52366 / 0.28 (15800) hydrogen bonds : bond 0.04831 / 3.05 ( 479) hydrogen bonds : angle 4.50478 / 3.23 ( 1326) metal coordination : bond 0.00515 / 0.29 ( 12) metal coordination : angle 1.78559 / 0.90 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.477 Fit side-chains REVERT: A 85 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: A 119 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7673 (mtp180) REVERT: A 160 GLU cc_start: 0.8201 (mp0) cc_final: 0.7882 (mp0) outliers start: 30 outliers final: 22 residues processed: 140 average time/residue: 1.3360 time to fit residues: 200.5471 Evaluate side-chains 136 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.095602 restraints weight = 37307.031| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.24 r_work: 0.2869 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11599 Z= 0.124 Angle : 0.496 4.731 15809 Z= 0.264 Chirality : 0.038 0.147 1780 Planarity : 0.005 0.063 1932 Dihedral : 12.872 163.094 1957 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 2.40 % Allowed : 20.53 % Favored : 77.07 % 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: 0.76 (0.22), residues: 1355 helix: 1.70 (0.23), residues: 522 sheet: -0.11 (0.46), residues: 116 loop : -0.24 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 267 TYR 0.013 0.001 TYR A 403 PHE 0.011 0.001 PHE C 175 TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (11587) covalent geometry : angle 0.49505 / 0.26 (15800) hydrogen bonds : bond 0.04368 / 2.75 ( 479) hydrogen bonds : angle 4.42514 / 3.18 ( 1326) metal coordination : bond 0.00388 / 0.22 ( 12) metal coordination : angle 1.57250 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.625 Fit side-chains REVERT: A 85 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6855 (tt0) outliers start: 28 outliers final: 21 residues processed: 139 average time/residue: 1.3778 time to fit residues: 205.5697 Evaluate side-chains 132 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 104 optimal weight: 1.9990 chunk 126 optimal weight: 0.0870 chunk 110 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 116 optimal weight: 0.0470 chunk 11 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.097640 restraints weight = 37346.403| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.25 r_work: 0.2901 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11599 Z= 0.094 Angle : 0.477 4.499 15809 Z= 0.253 Chirality : 0.037 0.144 1780 Planarity : 0.004 0.048 1932 Dihedral : 12.560 163.731 1957 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.77 % Favored : 98.15 % Rotamer: Outliers : 1.71 % Allowed : 21.39 % Favored : 76.90 % 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: 0.94 (0.23), residues: 1355 helix: 1.88 (0.23), residues: 523 sheet: -0.11 (0.46), residues: 116 loop : -0.14 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 267 TYR 0.016 0.001 TYR C 271 PHE 0.010 0.001 PHE C 175 TRP 0.007 0.001 TRP C 209 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (11587) covalent geometry : angle 0.47569 / 0.25 (15800) hydrogen bonds : bond 0.03865 / 2.41 ( 479) hydrogen bonds : angle 4.31826 / 3.10 ( 1326) metal coordination : bond 0.00365 / 0.21 ( 12) metal coordination : angle 1.56744 / 0.78 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.639 Fit side-chains REVERT: A 85 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6842 (tt0) outliers start: 20 outliers final: 17 residues processed: 133 average time/residue: 1.4311 time to fit residues: 203.9702 Evaluate side-chains 129 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.096003 restraints weight = 37235.719| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.22 r_work: 0.2867 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11599 Z= 0.151 Angle : 0.505 4.746 15809 Z= 0.268 Chirality : 0.038 0.144 1780 Planarity : 0.005 0.050 1932 Dihedral : 12.687 163.188 1957 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 1.88 % Allowed : 21.21 % Favored : 76.90 % 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: 0.82 (0.22), residues: 1355 helix: 1.76 (0.23), residues: 522 sheet: -0.12 (0.46), residues: 116 loop : -0.20 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 267 TYR 0.014 0.001 TYR A 403 PHE 0.012 0.001 PHE B 287 TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (11587) covalent geometry : angle 0.50386 / 0.27 (15800) hydrogen bonds : bond 0.04375 / 2.74 ( 479) hydrogen bonds : angle 4.35777 / 3.13 ( 1326) metal coordination : bond 0.00464 / 0.26 ( 12) metal coordination : angle 1.67005 / 0.86 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6672.33 seconds wall clock time: 113 minutes 28.58 seconds (6808.58 seconds total)