Starting phenix.real_space_refine on Fri Aug 7 15:46:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psx_17864/08_2026/8psx_17864_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psx_17864/08_2026/8psx_17864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8psx_17864/08_2026/8psx_17864_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psx_17864/08_2026/8psx_17864_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8psx_17864/08_2026/8psx_17864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psx_17864/08_2026/8psx_17864.map" } resolution = 2.96 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= 0.002 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 37 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 7046 2.51 5 N 2010 2.21 5 O 2239 1.98 5 H 11003 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22403 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 513, 7925 Classifications: {'peptide': 513} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 513, 7925 Classifications: {'peptide': 513} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 1 bond proxies already assigned to first conformer: 7960 Chain: "C" Number of atoms: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6676 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 22, 'TRANS': 403} Chain breaks: 1 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: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 250 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 3} Chain: "S" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 422 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 411 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Chain breaks: 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'A0I': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 45.999 46.033 18.402 1.00 25.04 S ATOM 4473 SG CYS A 282 43.659 44.596 15.566 1.00 19.11 S ATOM 18214 SG CYS C 233 23.303 55.910 108.964 1.00 84.75 S ATOM 18238 SG CYS C 235 23.645 57.568 105.415 1.00 85.78 S ATOM 16880 SG CYS C 146 12.277 64.309 89.727 1.00 78.45 S ATOM 17068 SG CYS C 159 11.918 67.914 91.277 1.00 82.86 S ATOM 17124 SG CYS C 163 14.801 65.538 91.727 1.00 75.36 S ATOM 17134 SG CYS C 164 14.321 67.369 88.371 1.00 76.72 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AASP B 213 " occ=0.50 ... (22 atoms not shown) pdb=" HB3BASP B 213 " occ=0.50 residue: pdb=" N ATYR B 393 " occ=0.60 ... (40 atoms not shown) pdb=" HH BTYR B 393 " occ=0.40 Time building chain proxies: 3.54, per 1000 atoms: 0.16 Number of scatterers: 22403 At special positions: 0 Unit cell: (91.56, 103.32, 126, 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 63 16.00 P 37 15.00 Mg 2 11.99 O 2239 8.00 N 2010 7.00 C 7046 6.00 H 11003 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: 1.60 Conformation dependent library (CDL) restraints added in 617.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " 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 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " Number of angles added : 8 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 16 sheets defined 42.1% alpha, 14.2% beta 9 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 3.53 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 13 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: 3.559A 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 234 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.422A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.640A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.897A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.681A 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 1 through 5 removed outlier: 3.608A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.658A pdb=" N TYR B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.525A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.568A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.702A 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: 4.154A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.596A 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 435 removed outlier: 3.985A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 23 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 107 Processing helix chain 'C' and resid 145 through 151 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 Processing helix chain 'C' and resid 303 through 317 removed outlier: 4.084A 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 350 through 356 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: 6.741A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.969A 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 removed outlier: 3.622A pdb=" N PHE B 291 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.285A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.285A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 9 removed outlier: 7.231A pdb=" N VAL B 8 " --> pdb=" O GLY B 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 155 through 159 removed outlier: 7.100A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB2, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 224 removed outlier: 6.876A pdb=" N GLY C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 300 through 301 removed outlier: 4.831A pdb=" N THR C 362 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 383 through 388 removed outlier: 6.543A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 2.32 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: 10971 1.03 - 1.23: 49 1.23 - 1.42: 4962 1.42 - 1.62: 6634 1.62 - 1.81: 89 Bond restraints: 22705 Sorted by residual: bond pdb=" O7 A0I B 601 " pdb=" P3 A0I B 601 " ideal model delta sigma weight residual 1.731 1.619 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" N4 A0I B 601 " pdb=" P2 A0I B 601 " ideal model delta sigma weight residual 1.701 1.639 0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" O3 A0I B 601 " pdb=" P1 A0I B 601 " ideal model delta sigma weight residual 1.662 1.602 0.060 2.00e-02 2.50e+03 9.15e+00 bond pdb=" N4 A0I B 601 " pdb=" P1 A0I B 601 " ideal model delta sigma weight residual 1.691 1.640 0.051 2.00e-02 2.50e+03 6.46e+00 bond pdb=" C7 A0I B 601 " pdb=" O12 A0I B 601 " ideal model delta sigma weight residual 1.383 1.422 -0.039 2.00e-02 2.50e+03 3.87e+00 ... (remaining 22700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 40593 1.95 - 3.90: 383 3.90 - 5.85: 15 5.85 - 7.80: 2 7.80 - 9.75: 2 Bond angle restraints: 40995 Sorted by residual: angle pdb=" C LYS A 163 " pdb=" CA LYS A 163 " pdb=" CB LYS A 163 " ideal model delta sigma weight residual 116.54 111.92 4.62 1.15e+00 7.56e-01 1.61e+01 angle pdb=" O5' A S 32 " pdb=" C5' A S 32 " pdb=" C4' A S 32 " ideal model delta sigma weight residual 109.40 112.47 -3.07 8.00e-01 1.56e+00 1.47e+01 angle pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" CD PRO A 132 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.33e+01 angle pdb=" O5' A S 33 " pdb=" C5' A S 33 " pdb=" C4' A S 33 " ideal model delta sigma weight residual 109.40 112.07 -2.67 8.00e-01 1.56e+00 1.11e+01 angle pdb=" O5' A P 14 " pdb=" C5' A P 14 " pdb=" C4' A P 14 " ideal model delta sigma weight residual 109.40 112.03 -2.63 8.00e-01 1.56e+00 1.08e+01 ... (remaining 40990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9449 17.70 - 35.41: 832 35.41 - 53.11: 324 53.11 - 70.82: 95 70.82 - 88.52: 27 Dihedral angle restraints: 10727 sinusoidal: 6131 harmonic: 4596 Sorted by residual: dihedral pdb=" CA ALA A 77 " pdb=" C ALA A 77 " pdb=" N THR A 78 " pdb=" CA THR A 78 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ARG B 394 " pdb=" C ARG B 394 " pdb=" N TYR B 395 " pdb=" CA TYR B 395 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LEU B 265 " pdb=" C LEU B 265 " pdb=" N MET B 266 " pdb=" CA MET B 266 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 10724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1453 0.042 - 0.084: 224 0.084 - 0.126: 127 0.126 - 0.168: 2 0.168 - 0.210: 1 Chirality restraints: 1807 Sorted by residual: chirality pdb=" C7 A0I B 601 " pdb=" C6 A0I B 601 " pdb=" C8 A0I B 601 " pdb=" O12 A0I B 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.58 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA VAL C 195 " pdb=" N VAL C 195 " pdb=" C VAL C 195 " pdb=" CB VAL C 195 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL A 252 " pdb=" N VAL A 252 " pdb=" C VAL A 252 " pdb=" CB VAL A 252 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1804 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 83 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO C 84 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 427 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C ASP B 427 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP B 427 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS B 428 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 131 " 0.033 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 132 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.027 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1910 2.21 - 2.81: 45994 2.81 - 3.41: 60929 3.41 - 4.00: 84242 4.00 - 4.60: 126377 Nonbonded interactions: 319452 Sorted by model distance: nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.618 2.450 nonbonded pdb="HH22 ARG A 201 " pdb=" O LYS A 263 " model vdw 1.622 2.450 nonbonded pdb="HE22 GLN B 57 " pdb=" OP1 U P 5 " model vdw 1.632 2.450 nonbonded pdb=" OE2 GLU B 148 " pdb=" HE ARG B 155 " model vdw 1.646 2.450 nonbonded pdb=" O LEU C 80 " pdb=" HZ1 LYS C 126 " model vdw 1.654 2.450 ... (remaining 319447 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=0.40 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: 1.560 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 0.112 11714 Z= 0.152 Angle : 0.554 13.603 15990 Z= 0.322 Chirality : 0.039 0.210 1807 Planarity : 0.004 0.114 1934 Dihedral : 17.612 88.522 4590 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.71 % Allowed : 19.19 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.23), residues: 1352 helix: 1.62 (0.23), residues: 534 sheet: -0.70 (0.37), residues: 163 loop : 0.08 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.010 0.001 TYR A 403 PHE 0.012 0.001 PHE C 82 TRP 0.006 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (11702) covalent geometry : angle 0.53933 / 0.32 (15982) hydrogen bonds : bond 0.13210 / 8.07 ( 494) hydrogen bonds : angle 5.61420 / 3.93 ( 1380) metal coordination : bond 0.00480 / 0.26 ( 12) metal coordination : angle 5.71566 / 2.86 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 151 average time/residue: 1.1916 time to fit residues: 194.1858 Evaluate side-chains 143 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 LYS 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: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.135321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.112498 restraints weight = 51705.400| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.70 r_work: 0.2985 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11714 Z= 0.188 Angle : 0.560 15.520 15990 Z= 0.289 Chirality : 0.039 0.157 1807 Planarity : 0.005 0.076 1934 Dihedral : 11.247 73.510 2045 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.00 % Allowed : 17.91 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1352 helix: 1.51 (0.22), residues: 534 sheet: -0.81 (0.37), residues: 158 loop : -0.07 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 83 TYR 0.014 0.002 TYR A 403 PHE 0.013 0.001 PHE B 4 TRP 0.006 0.001 TRP B 77 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (11702) covalent geometry : angle 0.54131 / 0.29 (15982) hydrogen bonds : bond 0.05300 / 3.29 ( 494) hydrogen bonds : angle 4.72890 / 3.35 ( 1380) metal coordination : bond 0.00726 / 0.41 ( 12) metal coordination : angle 6.48298 / 3.24 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: B 427 ASP cc_start: 0.7848 (t0) cc_final: 0.7301 (t0) REVERT: C 358 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: C 396 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7041 (mt-10) outliers start: 35 outliers final: 22 residues processed: 161 average time/residue: 1.1010 time to fit residues: 192.0022 Evaluate side-chains 156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.113106 restraints weight = 52597.248| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.69 r_work: 0.2994 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11714 Z= 0.154 Angle : 0.528 14.789 15990 Z= 0.271 Chirality : 0.038 0.148 1807 Planarity : 0.004 0.063 1934 Dihedral : 11.047 73.426 2040 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.66 % Allowed : 18.17 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1352 helix: 1.51 (0.22), residues: 535 sheet: -0.74 (0.38), residues: 151 loop : -0.15 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 39 TYR 0.014 0.001 TYR A 403 PHE 0.011 0.001 PHE B 4 TRP 0.006 0.001 TRP C 239 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (11702) covalent geometry : angle 0.50978 / 0.27 (15982) hydrogen bonds : bond 0.04790 / 2.96 ( 494) hydrogen bonds : angle 4.54027 / 3.22 ( 1380) metal coordination : bond 0.00659 / 0.37 ( 12) metal coordination : angle 6.11308 / 3.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: A 83 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.4943 (mm-30) REVERT: B 427 ASP cc_start: 0.7840 (t0) cc_final: 0.7212 (t0) REVERT: C 358 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: C 396 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7044 (mt-10) outliers start: 31 outliers final: 17 residues processed: 159 average time/residue: 1.0385 time to fit residues: 179.1644 Evaluate side-chains 146 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 72 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 195 ASN B 44 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.135435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.112532 restraints weight = 54383.057| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.84 r_work: 0.2980 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11714 Z= 0.174 Angle : 0.540 14.669 15990 Z= 0.278 Chirality : 0.039 0.150 1807 Planarity : 0.004 0.058 1934 Dihedral : 10.932 73.432 2033 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.08 % Allowed : 17.82 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1352 helix: 1.44 (0.22), residues: 535 sheet: -0.83 (0.37), residues: 156 loop : -0.20 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 155 TYR 0.015 0.002 TYR A 403 PHE 0.013 0.001 PHE B 4 TRP 0.006 0.001 TRP B 77 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (11702) covalent geometry : angle 0.52212 / 0.28 (15982) hydrogen bonds : bond 0.04642 / 2.88 ( 494) hydrogen bonds : angle 4.47257 / 3.17 ( 1380) metal coordination : bond 0.00784 / 0.48 ( 12) metal coordination : angle 6.16322 / 3.09 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: A 31 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8362 (m) REVERT: B 427 ASP cc_start: 0.7864 (t0) cc_final: 0.7217 (t0) REVERT: C 93 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6726 (m-30) REVERT: C 358 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: C 396 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7070 (mt-10) outliers start: 36 outliers final: 21 residues processed: 159 average time/residue: 1.1596 time to fit residues: 199.4727 Evaluate side-chains 154 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.112069 restraints weight = 45470.033| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.54 r_work: 0.2993 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11714 Z= 0.159 Angle : 0.529 14.268 15990 Z= 0.272 Chirality : 0.038 0.150 1807 Planarity : 0.005 0.063 1934 Dihedral : 10.864 73.422 2027 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.00 % Allowed : 17.99 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1352 helix: 1.43 (0.22), residues: 535 sheet: -0.83 (0.38), residues: 156 loop : -0.21 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 302 TYR 0.014 0.002 TYR A 403 PHE 0.012 0.001 PHE B 4 TRP 0.006 0.001 TRP C 239 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (11702) covalent geometry : angle 0.51176 / 0.27 (15982) hydrogen bonds : bond 0.04505 / 2.80 ( 494) hydrogen bonds : angle 4.42417 / 3.13 ( 1380) metal coordination : bond 0.00693 / 0.39 ( 12) metal coordination : angle 5.98972 / 3.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: A 31 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8344 (m) REVERT: A 87 GLN cc_start: 0.7401 (tt0) cc_final: 0.6970 (tm-30) REVERT: B 427 ASP cc_start: 0.7796 (t0) cc_final: 0.7120 (t0) REVERT: C 396 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6997 (mt-10) outliers start: 35 outliers final: 23 residues processed: 156 average time/residue: 1.2882 time to fit residues: 217.3789 Evaluate side-chains 155 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.135167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.112010 restraints weight = 54905.257| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.74 r_work: 0.2999 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11714 Z= 0.106 Angle : 0.492 13.227 15990 Z= 0.253 Chirality : 0.037 0.150 1807 Planarity : 0.004 0.050 1934 Dihedral : 10.654 73.410 2027 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.83 % Allowed : 18.34 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1352 helix: 1.63 (0.23), residues: 535 sheet: -0.73 (0.40), residues: 151 loop : -0.10 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.011 0.001 TYR A 403 PHE 0.008 0.001 PHE C 44 TRP 0.005 0.001 TRP C 209 HIS 0.011 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (11702) covalent geometry : angle 0.47728 / 0.25 (15982) hydrogen bonds : bond 0.03952 / 2.45 ( 494) hydrogen bonds : angle 4.28595 / 3.04 ( 1380) metal coordination : bond 0.00513 / 0.25 ( 12) metal coordination : angle 5.40173 / 2.73 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8380 (m) REVERT: B 427 ASP cc_start: 0.7816 (t0) cc_final: 0.7122 (t0) outliers start: 33 outliers final: 16 residues processed: 153 average time/residue: 1.1804 time to fit residues: 195.3495 Evaluate side-chains 145 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.133837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.111481 restraints weight = 49903.434| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.71 r_work: 0.2964 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11714 Z= 0.180 Angle : 0.551 17.600 15990 Z= 0.278 Chirality : 0.039 0.147 1807 Planarity : 0.004 0.049 1934 Dihedral : 10.696 73.484 2023 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.23 % Allowed : 18.77 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1352 helix: 1.43 (0.22), residues: 535 sheet: -0.78 (0.39), residues: 156 loop : -0.23 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.016 0.002 TYR A 403 PHE 0.015 0.001 PHE B 4 TRP 0.007 0.001 TRP B 77 HIS 0.005 0.001 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (11702) covalent geometry : angle 0.51960 / 0.28 (15982) hydrogen bonds : bond 0.04470 / 2.80 ( 494) hydrogen bonds : angle 4.34455 / 3.07 ( 1380) metal coordination : bond 0.00773 / 0.46 ( 12) metal coordination : angle 8.27630 / 3.99 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8392 (m) REVERT: B 427 ASP cc_start: 0.7764 (t0) cc_final: 0.7090 (t0) outliers start: 26 outliers final: 18 residues processed: 147 average time/residue: 1.2238 time to fit residues: 193.8380 Evaluate side-chains 147 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 346 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.133928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.110494 restraints weight = 60703.271| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.82 r_work: 0.2968 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11714 Z= 0.164 Angle : 0.544 17.005 15990 Z= 0.274 Chirality : 0.038 0.149 1807 Planarity : 0.004 0.050 1934 Dihedral : 10.721 73.425 2023 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.31 % Allowed : 18.51 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1352 helix: 1.40 (0.22), residues: 535 sheet: -0.84 (0.38), residues: 156 loop : -0.23 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.014 0.002 TYR A 403 PHE 0.012 0.001 PHE B 4 TRP 0.006 0.001 TRP B 77 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (11702) covalent geometry : angle 0.51429 / 0.27 (15982) hydrogen bonds : bond 0.04418 / 2.76 ( 494) hydrogen bonds : angle 4.35222 / 3.08 ( 1380) metal coordination : bond 0.00726 / 0.42 ( 12) metal coordination : angle 7.88812 / 3.83 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8379 (m) REVERT: B 427 ASP cc_start: 0.7806 (t0) cc_final: 0.7132 (t0) REVERT: C 396 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7082 (mt-10) outliers start: 27 outliers final: 20 residues processed: 152 average time/residue: 1.2001 time to fit residues: 196.6786 Evaluate side-chains 147 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.134593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.111972 restraints weight = 53328.318| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.72 r_work: 0.2974 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 0.046 11714 Z= 0.131 Angle : 0.520 16.148 15990 Z= 0.263 Chirality : 0.038 0.150 1807 Planarity : 0.004 0.048 1934 Dihedral : 10.619 73.406 2023 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.80 % Allowed : 19.11 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.22), residues: 1352 helix: 1.51 (0.23), residues: 535 sheet: -0.79 (0.39), residues: 156 loop : -0.17 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.013 0.001 TYR A 403 PHE 0.009 0.001 PHE B 4 TRP 0.006 0.001 TRP A 346 HIS 0.008 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (11702) covalent geometry : angle 0.49353 / 0.26 (15982) hydrogen bonds : bond 0.04148 / 2.58 ( 494) hydrogen bonds : angle 4.28872 / 3.04 ( 1380) metal coordination : bond 0.00566 / 0.28 ( 12) metal coordination : angle 7.32048 / 3.57 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8370 (m) REVERT: A 87 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7038 (mt0) REVERT: B 427 ASP cc_start: 0.7767 (t0) cc_final: 0.7079 (t0) outliers start: 21 outliers final: 18 residues processed: 147 average time/residue: 1.3082 time to fit residues: 208.1938 Evaluate side-chains 146 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.134770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.112546 restraints weight = 46923.131| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.65 r_work: 0.2984 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11714 Z= 0.130 Angle : 0.515 15.653 15990 Z= 0.260 Chirality : 0.037 0.150 1807 Planarity : 0.004 0.068 1934 Dihedral : 10.569 73.433 2023 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.97 % Allowed : 19.02 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1352 helix: 1.55 (0.23), residues: 535 sheet: -0.80 (0.39), residues: 156 loop : -0.14 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 141 TYR 0.013 0.001 TYR A 403 PHE 0.010 0.001 PHE B 4 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11702) covalent geometry : angle 0.49012 / 0.26 (15982) hydrogen bonds : bond 0.04077 / 2.54 ( 494) hydrogen bonds : angle 4.25022 / 3.01 ( 1380) metal coordination : bond 0.00548 / 0.28 ( 12) metal coordination : angle 7.05099 / 3.45 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8371 (m) REVERT: A 87 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7040 (mt0) REVERT: B 427 ASP cc_start: 0.7734 (t0) cc_final: 0.7058 (t0) outliers start: 23 outliers final: 20 residues processed: 148 average time/residue: 1.2822 time to fit residues: 204.4742 Evaluate side-chains 148 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 76 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.134556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.112405 restraints weight = 47951.777| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.68 r_work: 0.2995 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11714 Z= 0.137 Angle : 0.518 15.370 15990 Z= 0.263 Chirality : 0.038 0.149 1807 Planarity : 0.004 0.056 1934 Dihedral : 10.565 73.438 2023 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.14 % Allowed : 18.85 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1352 helix: 1.56 (0.23), residues: 534 sheet: -0.81 (0.39), residues: 156 loop : -0.16 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 141 TYR 0.013 0.001 TYR A 403 PHE 0.010 0.001 PHE B 4 TRP 0.006 0.001 TRP C 239 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11702) covalent geometry : angle 0.49399 / 0.26 (15982) hydrogen bonds : bond 0.04116 / 2.57 ( 494) hydrogen bonds : angle 4.25068 / 3.01 ( 1380) metal coordination : bond 0.00573 / 0.30 ( 12) metal coordination : angle 6.93243 / 3.40 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.45 seconds wall clock time: 109 minutes 52.33 seconds (6592.33 seconds total)