Starting phenix.real_space_refine on Thu Jun 19 13:22:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psn_17857/06_2025/8psn_17857_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psn_17857/06_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_17857/06_2025/8psn_17857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psn_17857/06_2025/8psn_17857.map" model { file = "/net/cci-nas-00/data/ceres_data/8psn_17857/06_2025/8psn_17857_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psn_17857/06_2025/8psn_17857_trim.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.91, per 1000 atoms: 0.53 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: 6.38 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 11.92 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: 8.77 Time building geometry restraints manager: 7.75 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: 1.670 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: 0.350 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 71.550 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:15.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), 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 TRP 0.004 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 175 TYR 0.009 0.001 TYR A 403 ARG 0.002 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.12755 ( 479) hydrogen bonds : angle 5.34667 ( 1326) metal coordination : bond 0.00242 ( 12) metal coordination : angle 1.48726 ( 9) covalent geometry : bond 0.00268 (11587) covalent geometry : angle 0.57369 (15800) *********************** 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 : 1.795 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: 3.1064 time to fit residues: 512.7562 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 : 1.921 ------------------------------------------------------------------------------- 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 114 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.117369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.095737 restraints weight = 37416.683| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.25 r_work: 0.2885 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11599 Z= 0.168 Angle : 0.536 7.353 15809 Z= 0.279 Chirality : 0.039 0.149 1780 Planarity : 0.005 0.050 1933 Dihedral : 13.467 164.073 1960 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 2.82 % Allowed : 20.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1355 helix: 1.72 (0.23), residues: 522 sheet: -0.19 (0.45), residues: 120 loop : -0.03 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 2 HIS 0.005 0.001 HIS A 367 PHE 0.013 0.001 PHE B 377 TYR 0.016 0.001 TYR A 403 ARG 0.005 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 479) hydrogen bonds : angle 4.62723 ( 1326) metal coordination : bond 0.00491 ( 12) metal coordination : angle 1.77616 ( 9) covalent geometry : bond 0.00388 (11587) covalent geometry : angle 0.53445 (15800) *********************** 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 152 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7975 (mm) cc_final: 0.7720 (mp) REVERT: A 85 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: C 124 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7630 (t0) outliers start: 33 outliers final: 19 residues processed: 147 average time/residue: 3.0968 time to fit residues: 487.7476 Evaluate side-chains 137 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 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 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 4 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 155 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 = 0.3308 r_free = 0.3308 target = 0.118754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.097308 restraints weight = 37195.735| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.23 r_work: 0.2887 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0857 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= 0.130 Angle : 0.503 7.026 15809 Z= 0.261 Chirality : 0.038 0.148 1780 Planarity : 0.004 0.049 1933 Dihedral : 12.730 163.935 1941 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.70 % Favored : 98.23 % Rotamer: Outliers : 2.48 % Allowed : 20.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1355 helix: 1.81 (0.23), residues: 522 sheet: -0.15 (0.45), residues: 120 loop : -0.06 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 209 HIS 0.005 0.001 HIS A 367 PHE 0.011 0.001 PHE C 175 TYR 0.014 0.001 TYR A 403 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 479) hydrogen bonds : angle 4.44940 ( 1326) metal coordination : bond 0.00397 ( 12) metal coordination : angle 1.78742 ( 9) covalent geometry : bond 0.00299 (11587) covalent geometry : angle 0.50091 (15800) *********************** 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 149 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7932 (mm) cc_final: 0.7707 (mp) REVERT: A 85 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6865 (tt0) outliers start: 29 outliers final: 15 residues processed: 147 average time/residue: 3.1381 time to fit residues: 495.7849 Evaluate side-chains 127 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 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 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 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.093667 restraints weight = 37843.711| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.27 r_work: 0.2843 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11599 Z= 0.226 Angle : 0.578 8.179 15809 Z= 0.304 Chirality : 0.041 0.150 1780 Planarity : 0.005 0.053 1933 Dihedral : 13.117 162.077 1934 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.51 % Favored : 97.42 % Rotamer: Outliers : 3.08 % Allowed : 19.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1355 helix: 1.49 (0.22), residues: 520 sheet: -0.08 (0.45), residues: 116 loop : -0.26 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 263 HIS 0.006 0.001 HIS B 174 PHE 0.014 0.002 PHE B 287 TYR 0.017 0.002 TYR A 403 ARG 0.005 0.000 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.05325 ( 479) hydrogen bonds : angle 4.62057 ( 1326) metal coordination : bond 0.00706 ( 12) metal coordination : angle 2.05342 ( 9) covalent geometry : bond 0.00531 (11587) covalent geometry : angle 0.57641 (15800) *********************** 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 148 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 2.052 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7981 (mm) cc_final: 0.7771 (mp) REVERT: A 85 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: A 119 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7671 (mtp180) outliers start: 36 outliers final: 19 residues processed: 144 average time/residue: 3.7301 time to fit residues: 581.7022 Evaluate side-chains 130 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.950 ------------------------------------------------------------------------------- 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 B residue 82 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 182 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 22 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.116287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094628 restraints weight = 37474.598| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.25 r_work: 0.2857 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11599 Z= 0.167 Angle : 0.532 7.235 15809 Z= 0.279 Chirality : 0.039 0.150 1780 Planarity : 0.005 0.051 1933 Dihedral : 12.888 162.526 1931 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.93 % Rotamer: Outliers : 2.99 % Allowed : 19.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1355 helix: 1.56 (0.23), residues: 521 sheet: -0.10 (0.46), residues: 116 loop : -0.25 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.013 0.001 PHE B 377 TYR 0.014 0.001 TYR A 403 ARG 0.005 0.000 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 479) hydrogen bonds : angle 4.50742 ( 1326) metal coordination : bond 0.00503 ( 12) metal coordination : angle 1.73817 ( 9) covalent geometry : bond 0.00389 (11587) covalent geometry : angle 0.53032 (15800) *********************** 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 147 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 3.531 Fit side-chains revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7939 (mm) cc_final: 0.7709 (mp) REVERT: A 85 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6903 (tt0) REVERT: A 160 GLU cc_start: 0.8192 (mp0) cc_final: 0.7865 (mp0) outliers start: 35 outliers final: 20 residues processed: 142 average time/residue: 4.0089 time to fit residues: 617.0744 Evaluate side-chains 133 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 2.077 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain B residue 182 VAL 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 227 SER Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 278 SER 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 102 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.118421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.096832 restraints weight = 37264.527| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.24 r_work: 0.2886 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1114 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= 0.114 Angle : 0.492 6.673 15809 Z= 0.257 Chirality : 0.038 0.146 1780 Planarity : 0.004 0.050 1933 Dihedral : 12.607 163.230 1931 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.70 % Favored : 98.23 % Rotamer: Outliers : 2.14 % Allowed : 20.36 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1355 helix: 1.77 (0.23), residues: 522 sheet: -0.10 (0.46), residues: 116 loop : -0.16 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.008 0.000 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 479) hydrogen bonds : angle 4.33638 ( 1326) metal coordination : bond 0.00325 ( 12) metal coordination : angle 1.52545 ( 9) covalent geometry : bond 0.00263 (11587) covalent geometry : angle 0.49080 (15800) *********************** 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 145 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.941 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8227 (mp0) cc_final: 0.7953 (mp0) REVERT: C 124 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7732 (t0) outliers start: 25 outliers final: 17 residues processed: 142 average time/residue: 3.1769 time to fit residues: 485.2728 Evaluate side-chains 124 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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 413 THR Chi-restraints excluded: chain B residue 118 VAL 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 124 ASN Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 278 SER 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 69 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.116635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.094973 restraints weight = 37419.386| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.25 r_work: 0.2862 rms_B_bonded: 1.59 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: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11599 Z= 0.167 Angle : 0.531 7.498 15809 Z= 0.278 Chirality : 0.039 0.146 1780 Planarity : 0.005 0.050 1933 Dihedral : 12.823 162.467 1931 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 2.91 % Allowed : 20.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1355 helix: 1.64 (0.23), residues: 521 sheet: -0.15 (0.46), residues: 116 loop : -0.21 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.013 0.001 PHE B 377 TYR 0.015 0.001 TYR A 403 ARG 0.003 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 479) hydrogen bonds : angle 4.41586 ( 1326) metal coordination : bond 0.00507 ( 12) metal coordination : angle 1.67457 ( 9) covalent geometry : bond 0.00391 (11587) covalent geometry : angle 0.52990 (15800) *********************** 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 143 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.839 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6911 (tt0) REVERT: A 160 GLU cc_start: 0.8218 (mp0) cc_final: 0.7901 (mp0) REVERT: C 359 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8306 (mpt90) outliers start: 34 outliers final: 20 residues processed: 138 average time/residue: 3.0425 time to fit residues: 450.6673 Evaluate side-chains 127 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.682 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 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 278 SER 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 31 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 124 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 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 = 0.3297 r_free = 0.3297 target = 0.117973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.096336 restraints weight = 37406.972| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.25 r_work: 0.2883 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1203 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= 0.118 Angle : 0.494 6.751 15809 Z= 0.258 Chirality : 0.038 0.145 1780 Planarity : 0.004 0.048 1933 Dihedral : 12.629 163.091 1931 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Rotamer: Outliers : 2.05 % Allowed : 21.30 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1355 helix: 1.77 (0.23), residues: 523 sheet: -0.12 (0.46), residues: 116 loop : -0.13 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.003 0.000 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 479) hydrogen bonds : angle 4.29967 ( 1326) metal coordination : bond 0.00345 ( 12) metal coordination : angle 1.50185 ( 9) covalent geometry : bond 0.00272 (11587) covalent geometry : angle 0.49324 (15800) *********************** 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 138 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8224 (mp0) cc_final: 0.7945 (mp0) outliers start: 24 outliers final: 20 residues processed: 135 average time/residue: 3.0606 time to fit residues: 443.3165 Evaluate side-chains 125 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 278 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 118 VAL 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 273 THR Chi-restraints excluded: chain C residue 278 SER 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 61 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.095822 restraints weight = 37277.942| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.24 r_work: 0.2864 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1232 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= 0.158 Angle : 0.524 7.399 15809 Z= 0.274 Chirality : 0.039 0.146 1780 Planarity : 0.005 0.050 1933 Dihedral : 12.792 162.351 1931 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.56 % Rotamer: Outliers : 2.14 % Allowed : 20.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1355 helix: 1.68 (0.23), residues: 521 sheet: -0.18 (0.46), residues: 116 loop : -0.17 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.013 0.001 PHE B 377 TYR 0.014 0.001 TYR A 403 ARG 0.004 0.000 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 479) hydrogen bonds : angle 4.37847 ( 1326) metal coordination : bond 0.00505 ( 12) metal coordination : angle 1.60898 ( 9) covalent geometry : bond 0.00370 (11587) covalent geometry : angle 0.52242 (15800) *********************** 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 128 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6896 (tt0) REVERT: A 160 GLU cc_start: 0.8229 (mp0) cc_final: 0.7927 (mp0) outliers start: 25 outliers final: 20 residues processed: 126 average time/residue: 3.1997 time to fit residues: 432.2482 Evaluate side-chains 126 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 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 278 SER 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 75 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 115 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.118115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096556 restraints weight = 37421.626| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.24 r_work: 0.2874 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1235 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= 0.131 Angle : 0.503 6.930 15809 Z= 0.262 Chirality : 0.038 0.144 1780 Planarity : 0.004 0.049 1933 Dihedral : 12.682 162.555 1931 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.77 % Favored : 98.15 % Rotamer: Outliers : 2.14 % Allowed : 20.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1355 helix: 1.74 (0.23), residues: 523 sheet: -0.11 (0.46), residues: 116 loop : -0.11 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.013 0.001 TYR A 403 ARG 0.004 0.000 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 479) hydrogen bonds : angle 4.31580 ( 1326) metal coordination : bond 0.00387 ( 12) metal coordination : angle 1.51041 ( 9) covalent geometry : bond 0.00302 (11587) covalent geometry : angle 0.50148 (15800) ********************** 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: 25 poor density : 109 time to evaluate : 1.809 Fit side-chains REVERT: A 85 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6878 (tt0) REVERT: A 160 GLU cc_start: 0.8232 (mp0) cc_final: 0.7948 (mp0) outliers start: 25 outliers final: 21 residues processed: 130 average time/residue: 3.1807 time to fit residues: 443.1146 Evaluate side-chains 129 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 118 VAL 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 278 SER 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 35 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 97 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.117920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.096312 restraints weight = 37405.496| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.25 r_work: 0.2879 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1222 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= 0.121 Angle : 0.496 6.808 15809 Z= 0.258 Chirality : 0.038 0.143 1780 Planarity : 0.004 0.048 1933 Dihedral : 12.622 162.573 1931 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Rotamer: Outliers : 2.05 % Allowed : 20.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1355 helix: 1.79 (0.23), residues: 523 sheet: -0.10 (0.46), residues: 116 loop : -0.09 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 174 PHE 0.011 0.001 PHE C 175 TYR 0.013 0.001 TYR A 403 ARG 0.004 0.000 ARG C 267 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 479) hydrogen bonds : angle 4.28507 ( 1326) metal coordination : bond 0.00365 ( 12) metal coordination : angle 1.42472 ( 9) covalent geometry : bond 0.00279 (11587) covalent geometry : angle 0.49450 (15800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15721.97 seconds wall clock time: 270 minutes 21.00 seconds (16221.00 seconds total)