Starting phenix.real_space_refine on Sun Aug 24 19:48:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psn_17857/08_2025/8psn_17857_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psn_17857/08_2025/8psn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8psn_17857/08_2025/8psn_17857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psn_17857/08_2025/8psn_17857.map" model { file = "/net/cci-nas-00/data/ceres_data/8psn_17857/08_2025/8psn_17857_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psn_17857/08_2025/8psn_17857_trim.cif" } 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-2.0-5787/lib/python3.9/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: 2.93, 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: 1.30 Conformation dependent library (CDL) restraints added in 475.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.59 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: 4.91 Time building geometry restraints manager: 1.85 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=" 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=" 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 bond pdb=" N THR B 442 " pdb=" H THR B 442 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.26e+00 bond pdb=" N SER C 356 " pdb=" H SER C 356 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.26e+00 bond pdb=" N SER A 269 " pdb=" H SER A 269 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.24e+00 ... (remaining 22547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 40597 2.82 - 5.65: 115 5.65 - 8.47: 5 8.47 - 11.30: 6 11.30 - 14.12: 1 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=" PA CTP E 1 " pdb=" O3A CTP E 1 " pdb=" PB CTP E 1 " ideal model delta sigma weight residual 120.50 134.62 -14.12 3.00e+00 1.11e-01 2.22e+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=" C2' CTP E 1 " pdb=" C3' CTP E 1 " pdb=" C4' CTP E 1 " ideal model delta sigma weight residual 111.00 99.73 11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" PB CTP E 1 " pdb=" O3B CTP E 1 " pdb=" PG CTP E 1 " ideal model delta sigma weight residual 120.50 131.71 -11.21 3.00e+00 1.11e-01 1.40e+01 ... (remaining 40719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 10108 33.70 - 67.41: 500 67.41 - 101.11: 24 101.11 - 134.81: 5 134.81 - 168.51: 4 Dihedral angle restraints: 10641 sinusoidal: 6042 harmonic: 4599 Sorted by residual: dihedral pdb=" O3B CTP E 1 " pdb=" O3A CTP E 1 " pdb=" PB CTP E 1 " pdb=" PA CTP E 1 " ideal model delta sinusoidal sigma weight residual 320.71 161.43 159.28 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O1G CTP E 1 " pdb=" O3B CTP E 1 " pdb=" PG CTP E 1 " pdb=" PB CTP E 1 " ideal model delta sinusoidal sigma weight residual 82.72 -44.76 127.48 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" O3A CTP E 1 " pdb=" O3B CTP E 1 " pdb=" PB CTP E 1 " pdb=" PG CTP E 1 " ideal model delta sinusoidal sigma weight residual -155.50 -51.90 -103.60 1 2.00e+01 2.50e-03 2.96e+01 ... (remaining 10638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1575 0.051 - 0.102: 160 0.102 - 0.153: 43 0.153 - 0.204: 1 0.204 - 0.254: 1 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 -2.47 -2.73 0.25 2.00e-01 2.50e+01 1.62e+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=" C3' G S 1 " pdb=" C4' G S 1 " pdb=" O3' G S 1 " pdb=" C2' G S 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.61 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 1777 not shown) Planarity restraints: 3244 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 3241 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: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 24.990 Find NCS groups from input model: 0.070 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:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 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 0.049 11599 Z= 0.140 Angle : 0.575 14.120 15809 Z= 0.296 Chirality : 0.037 0.254 1780 Planarity : 0.004 0.051 1933 Dihedral : 18.647 168.513 4511 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 aren 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 covalent geometry : bond 0.00268 (11587) covalent geometry : angle 0.57369 (15800) hydrogen bonds : bond 0.12755 ( 479) hydrogen bonds : angle 5.34667 ( 1326) metal coordination : bond 0.00242 ( 12) metal coordination : angle 1.48726 ( 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 : 0.389 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: 1.3580 time to fit residues: 224.2496 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 : 0.568 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.117669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.096030 restraints weight = 37561.960| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.25 r_work: 0.2889 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0759 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= 0.156 Angle : 0.533 7.109 15809 Z= 0.277 Chirality : 0.039 0.153 1780 Planarity : 0.005 0.050 1933 Dihedral : 13.379 163.863 1960 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 2.74 % Allowed : 19.85 % 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 aren not related in a simple way. whole: 0.92 (0.22), residues: 1355 helix: 1.74 (0.23), residues: 522 sheet: -0.19 (0.44), residues: 120 loop : -0.02 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 62 TYR 0.016 0.001 TYR A 403 PHE 0.012 0.001 PHE B 377 TRP 0.004 0.001 TRP A 346 HIS 0.006 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00363 (11587) covalent geometry : angle 0.53099 (15800) hydrogen bonds : bond 0.04684 ( 479) hydrogen bonds : angle 4.59042 ( 1326) metal coordination : bond 0.00470 ( 12) metal coordination : angle 1.77919 ( 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 : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7953 (mm) cc_final: 0.7691 (mp) REVERT: A 85 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6860 (tt0) REVERT: C 124 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7664 (t0) outliers start: 32 outliers final: 19 residues processed: 145 average time/residue: 1.3696 time to fit residues: 212.4023 Evaluate side-chains 138 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 444 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 148 SER Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 227 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: 0.6980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.0050 chunk 13 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 87 GLN C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.119722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098147 restraints weight = 37476.806| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.24 r_work: 0.2916 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11599 Z= 0.101 Angle : 0.482 6.829 15809 Z= 0.250 Chirality : 0.037 0.146 1780 Planarity : 0.004 0.050 1933 Dihedral : 12.577 164.385 1940 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.70 % Favored : 98.23 % Rotamer: Outliers : 2.05 % Allowed : 20.70 % 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 aren not related in a simple way. whole: 1.09 (0.23), residues: 1355 helix: 1.96 (0.23), residues: 522 sheet: -0.05 (0.45), residues: 120 loop : -0.00 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 267 TYR 0.012 0.001 TYR A 403 PHE 0.010 0.001 PHE C 175 TRP 0.004 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00228 (11587) covalent geometry : angle 0.48024 (15800) hydrogen bonds : bond 0.03949 ( 479) hydrogen bonds : angle 4.37569 ( 1326) metal coordination : bond 0.00312 ( 12) metal coordination : angle 1.65341 ( 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 148 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7957 (mm) cc_final: 0.7734 (mp) REVERT: C 124 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7646 (t0) outliers start: 24 outliers final: 9 residues processed: 145 average time/residue: 1.3842 time to fit residues: 214.7300 Evaluate side-chains 126 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 463 GLU 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 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 106 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 116 optimal weight: 0.0870 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.096733 restraints weight = 37511.967| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.25 r_work: 0.2887 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11599 Z= 0.135 Angle : 0.499 7.084 15809 Z= 0.260 Chirality : 0.038 0.147 1780 Planarity : 0.004 0.049 1933 Dihedral : 12.569 163.556 1929 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.93 % Rotamer: Outliers : 2.48 % Allowed : 20.44 % 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 aren not related in a simple way. whole: 1.00 (0.22), residues: 1355 helix: 1.87 (0.23), residues: 522 sheet: -0.15 (0.45), residues: 120 loop : -0.04 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 C 209 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00314 (11587) covalent geometry : angle 0.49762 (15800) hydrogen bonds : bond 0.04258 ( 479) hydrogen bonds : angle 4.38251 ( 1326) metal coordination : bond 0.00434 ( 12) metal coordination : angle 1.60014 ( 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 145 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7918 (mm) cc_final: 0.7711 (mp) REVERT: A 85 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6844 (tt0) outliers start: 29 outliers final: 14 residues processed: 142 average time/residue: 1.4074 time to fit residues: 213.4356 Evaluate side-chains 128 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 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 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 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: 0.0770 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.094811 restraints weight = 37361.441| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.25 r_work: 0.2860 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1053 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= 0.173 Angle : 0.536 7.525 15809 Z= 0.280 Chirality : 0.039 0.147 1780 Planarity : 0.005 0.051 1933 Dihedral : 12.806 162.573 1929 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 2.65 % Allowed : 20.02 % Favored : 77.33 % 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 aren not related in a simple way. whole: 0.80 (0.22), residues: 1355 helix: 1.66 (0.23), residues: 522 sheet: -0.07 (0.46), residues: 116 loop : -0.16 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 267 TYR 0.016 0.001 TYR A 403 PHE 0.012 0.001 PHE B 287 TRP 0.005 0.001 TRP C 263 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00404 (11587) covalent geometry : angle 0.53396 (15800) hydrogen bonds : bond 0.04788 ( 479) hydrogen bonds : angle 4.48110 ( 1326) metal coordination : bond 0.00545 ( 12) metal coordination : angle 1.82412 ( 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 145 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6864 (tt0) outliers start: 31 outliers final: 16 residues processed: 140 average time/residue: 1.3527 time to fit residues: 202.3335 Evaluate side-chains 124 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 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 140 ASP Chi-restraints excluded: chain C residue 148 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: 2.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 87 GLN C 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095202 restraints weight = 37557.065| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.25 r_work: 0.2864 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1131 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= 0.161 Angle : 0.524 7.186 15809 Z= 0.274 Chirality : 0.039 0.147 1780 Planarity : 0.005 0.050 1933 Dihedral : 12.755 162.561 1929 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.93 % Rotamer: Outliers : 2.65 % Allowed : 20.02 % Favored : 77.33 % 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 aren not related in a simple way. whole: 0.77 (0.22), residues: 1355 helix: 1.66 (0.23), residues: 522 sheet: -0.10 (0.46), residues: 116 loop : -0.19 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 267 TYR 0.014 0.001 TYR A 403 PHE 0.012 0.001 PHE B 377 TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00375 (11587) covalent geometry : angle 0.52220 (15800) hydrogen bonds : bond 0.04592 ( 479) hydrogen bonds : angle 4.43102 ( 1326) metal coordination : bond 0.00457 ( 12) metal coordination : angle 1.66209 ( 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 142 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6886 (tt0) outliers start: 31 outliers final: 19 residues processed: 139 average time/residue: 1.3009 time to fit residues: 193.9890 Evaluate side-chains 129 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 413 THR Chi-restraints excluded: chain B residue 82 GLU 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 397 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 468 LEU 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 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: 1.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.095047 restraints weight = 37388.452| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.25 r_work: 0.2862 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11599 Z= 0.164 Angle : 0.528 7.243 15809 Z= 0.277 Chirality : 0.039 0.147 1780 Planarity : 0.005 0.050 1933 Dihedral : 12.775 162.395 1929 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 2.74 % Allowed : 20.44 % Favored : 76.82 % 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 aren not related in a simple way. whole: 0.74 (0.22), residues: 1355 helix: 1.63 (0.23), residues: 522 sheet: -0.14 (0.45), residues: 116 loop : -0.21 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 267 TYR 0.015 0.001 TYR A 403 PHE 0.013 0.001 PHE B 377 TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00381 (11587) covalent geometry : angle 0.52714 (15800) hydrogen bonds : bond 0.04629 ( 479) hydrogen bonds : angle 4.43872 ( 1326) metal coordination : bond 0.00476 ( 12) metal coordination : angle 1.64611 ( 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 140 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: A 119 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7654 (mtp180) outliers start: 32 outliers final: 21 residues processed: 138 average time/residue: 1.3860 time to fit residues: 203.9313 Evaluate side-chains 129 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 119 ARG Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 82 GLU 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 468 LEU 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 216 LYS 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: 0.9980 chunk 14 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 74 ASN 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 = 0.117166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.095617 restraints weight = 37254.590| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.24 r_work: 0.2867 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11599 Z= 0.155 Angle : 0.521 7.185 15809 Z= 0.272 Chirality : 0.039 0.147 1780 Planarity : 0.005 0.050 1933 Dihedral : 12.750 162.450 1929 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.93 % Rotamer: Outliers : 2.57 % Allowed : 20.44 % Favored : 76.99 % 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 aren not related in a simple way. whole: 0.76 (0.22), residues: 1355 helix: 1.65 (0.23), residues: 522 sheet: -0.14 (0.45), residues: 116 loop : -0.19 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 267 TYR 0.014 0.001 TYR A 403 PHE 0.012 0.001 PHE B 377 TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00359 (11587) covalent geometry : angle 0.51937 (15800) hydrogen bonds : bond 0.04509 ( 479) hydrogen bonds : angle 4.40277 ( 1326) metal coordination : bond 0.00458 ( 12) metal coordination : angle 1.60259 ( 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 135 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6902 (tt0) outliers start: 30 outliers final: 21 residues processed: 132 average time/residue: 1.3600 time to fit residues: 192.1536 Evaluate side-chains 127 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 82 GLU 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 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 468 LEU 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 216 LYS 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: 3.9990 chunk 10 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 122 optimal weight: 0.0270 chunk 129 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.097052 restraints weight = 37288.039| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.24 r_work: 0.2882 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1181 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= 0.120 Angle : 0.495 6.793 15809 Z= 0.258 Chirality : 0.038 0.144 1780 Planarity : 0.004 0.048 1933 Dihedral : 12.594 162.706 1929 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.77 % Favored : 98.15 % Rotamer: Outliers : 2.40 % Allowed : 20.79 % Favored : 76.82 % 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 aren not related in a simple way. whole: 0.91 (0.22), residues: 1355 helix: 1.78 (0.23), residues: 523 sheet: -0.09 (0.46), residues: 116 loop : -0.11 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 267 TYR 0.012 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 covalent geometry : bond 0.00275 (11587) covalent geometry : angle 0.49367 (15800) hydrogen bonds : bond 0.04092 ( 479) hydrogen bonds : angle 4.29979 ( 1326) metal coordination : bond 0.00348 ( 12) metal coordination : angle 1.46409 ( 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 : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6855 (tt0) outliers start: 28 outliers final: 22 residues processed: 139 average time/residue: 1.3633 time to fit residues: 202.1346 Evaluate side-chains 130 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 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 A residue 391 GLU Chi-restraints excluded: chain B residue 82 GLU 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 468 LEU 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 216 LYS 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: 2.9990 chunk 110 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.096795 restraints weight = 37431.835| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.26 r_work: 0.2878 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11599 Z= 0.118 Angle : 0.495 6.697 15809 Z= 0.258 Chirality : 0.038 0.142 1780 Planarity : 0.004 0.048 1933 Dihedral : 12.568 162.690 1929 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.62 % Favored : 98.30 % Rotamer: Outliers : 1.97 % Allowed : 21.04 % Favored : 76.99 % 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 aren not related in a simple way. whole: 0.96 (0.23), residues: 1355 helix: 1.83 (0.23), residues: 523 sheet: -0.07 (0.46), residues: 116 loop : -0.09 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 267 TYR 0.012 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 covalent geometry : bond 0.00272 (11587) covalent geometry : angle 0.49347 (15800) hydrogen bonds : bond 0.04036 ( 479) hydrogen bonds : angle 4.27899 ( 1326) metal coordination : bond 0.00370 ( 12) metal coordination : angle 1.45742 ( 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 134 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6842 (tt0) REVERT: A 160 GLU cc_start: 0.8264 (mp0) cc_final: 0.7943 (mp0) outliers start: 23 outliers final: 22 residues processed: 131 average time/residue: 1.4823 time to fit residues: 207.1924 Evaluate side-chains 130 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 391 GLU Chi-restraints excluded: chain B residue 82 GLU 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 468 LEU 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 216 LYS 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: 1.9990 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: 0.9990 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.096998 restraints weight = 37293.801| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.24 r_work: 0.2884 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11599 Z= 0.118 Angle : 0.493 6.732 15809 Z= 0.257 Chirality : 0.038 0.144 1780 Planarity : 0.004 0.048 1933 Dihedral : 12.556 162.573 1929 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.70 % Favored : 98.23 % Rotamer: Outliers : 2.05 % Allowed : 20.87 % 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 aren not related in a simple way. whole: 1.00 (0.22), residues: 1355 helix: 1.87 (0.23), residues: 523 sheet: 0.01 (0.46), residues: 114 loop : -0.08 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 267 TYR 0.012 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 covalent geometry : bond 0.00271 (11587) covalent geometry : angle 0.49167 (15800) hydrogen bonds : bond 0.04012 ( 479) hydrogen bonds : angle 4.26223 ( 1326) metal coordination : bond 0.00364 ( 12) metal coordination : angle 1.44760 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6334.38 seconds wall clock time: 107 minutes 38.10 seconds (6458.10 seconds total)