Starting phenix.real_space_refine on Thu May 22 08:14:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psx_17864/05_2025/8psx_17864_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psx_17864/05_2025/8psx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8psx_17864/05_2025/8psx_17864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psx_17864/05_2025/8psx_17864.map" model { file = "/net/cci-nas-00/data/ceres_data/8psx_17864/05_2025/8psx_17864_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psx_17864/05_2025/8psx_17864_trim.cif" } resolution = 2.96 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= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.15, per 1000 atoms: 0.59 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: 5.70 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=" 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: 9.57 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: 7.83 Time building geometry restraints manager: 6.75 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: 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: 40650 1.95 - 3.90: 326 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=" 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=" CA PRO C 84 " pdb=" N PRO C 84 " pdb=" CD PRO C 84 " ideal model delta sigma weight residual 112.00 107.89 4.11 1.40e+00 5.10e-01 8.61e+00 angle pdb=" N GLY C 405 " pdb=" CA GLY C 405 " pdb=" C GLY C 405 " ideal model delta sigma weight residual 110.56 114.32 -3.76 1.36e+00 5.41e-01 7.66e+00 angle pdb=" N PRO A 132 " pdb=" CD PRO A 132 " pdb=" CG PRO A 132 " ideal model delta sigma weight residual 103.20 99.18 4.02 1.50e+00 4.44e-01 7.18e+00 ... (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: 1489 0.042 - 0.084: 223 0.084 - 0.126: 92 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: 1.740 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: 0.390 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 65.140 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 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:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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= 0.140 Angle : 0.531 13.603 15990 Z= 0.271 Chirality : 0.037 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 (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: 0.82 (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 TRP 0.006 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.012 0.001 PHE C 82 TYR 0.010 0.001 TYR A 403 ARG 0.002 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.13210 ( 494) hydrogen bonds : angle 5.61420 ( 1380) metal coordination : bond 0.00480 ( 12) metal coordination : angle 5.71566 ( 8) covalent geometry : bond 0.00311 (11702) covalent geometry : angle 0.51556 (15982) *********************** 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 : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 151 average time/residue: 2.9761 time to fit residues: 482.6965 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 : 1.822 ------------------------------------------------------------------------------- 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 114 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.135172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.113268 restraints weight = 45399.358| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.59 r_work: 0.2985 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 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 = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11714 Z= 0.222 Angle : 0.599 16.252 15990 Z= 0.307 Chirality : 0.041 0.140 1807 Planarity : 0.005 0.072 1934 Dihedral : 11.343 73.483 2045 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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 (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: 0.46 (0.22), residues: 1352 helix: 1.35 (0.23), residues: 535 sheet: -0.77 (0.36), residues: 154 loop : -0.21 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 77 HIS 0.006 0.001 HIS B 378 PHE 0.016 0.002 PHE B 4 TYR 0.017 0.002 TYR A 403 ARG 0.004 0.001 ARG B 302 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 494) hydrogen bonds : angle 4.65699 ( 1380) metal coordination : bond 0.01060 ( 12) metal coordination : angle 7.04999 ( 8) covalent geometry : bond 0.00517 (11702) covalent geometry : angle 0.57789 (15982) *********************** 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 168 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: A 83 GLU cc_start: 0.5164 (OUTLIER) cc_final: 0.4876 (mm-30) REVERT: C 358 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: C 396 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7048 (mt-10) outliers start: 35 outliers final: 19 residues processed: 158 average time/residue: 2.7594 time to fit residues: 471.5576 Evaluate side-chains 146 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 B residue 444 ASP 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 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 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU 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 95 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.133276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.110667 restraints weight = 49975.600| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.64 r_work: 0.2980 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11714 Z= 0.190 Angle : 0.567 15.498 15990 Z= 0.290 Chirality : 0.039 0.149 1807 Planarity : 0.005 0.062 1934 Dihedral : 11.140 73.507 2030 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.17 % Allowed : 17.57 % Favored : 79.26 % 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: 0.30 (0.22), residues: 1352 helix: 1.26 (0.22), residues: 535 sheet: -0.86 (0.36), residues: 154 loop : -0.34 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 239 HIS 0.005 0.001 HIS B 378 PHE 0.014 0.002 PHE B 4 TYR 0.015 0.002 TYR A 403 ARG 0.003 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.04762 ( 494) hydrogen bonds : angle 4.50941 ( 1380) metal coordination : bond 0.00756 ( 12) metal coordination : angle 6.69408 ( 8) covalent geometry : bond 0.00441 (11702) covalent geometry : angle 0.54659 (15982) *********************** 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 167 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.903 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: 0.7344 (tm-30) REVERT: A 83 GLU cc_start: 0.5126 (OUTLIER) cc_final: 0.4901 (mt-10) REVERT: A 87 GLN cc_start: 0.7355 (tt0) cc_final: 0.6929 (tm-30) REVERT: B 427 ASP cc_start: 0.7808 (t0) cc_final: 0.7211 (t0) REVERT: C 317 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.7119 (ptt180) REVERT: C 358 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: C 396 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7068 (mt-10) outliers start: 37 outliers final: 22 residues processed: 162 average time/residue: 3.0147 time to fit residues: 524.2211 Evaluate side-chains 155 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 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 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 86 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 325 ILE 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 74 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.134626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.112315 restraints weight = 49161.856| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.60 r_work: 0.2996 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11714 Z= 0.150 Angle : 0.530 14.041 15990 Z= 0.271 Chirality : 0.038 0.149 1807 Planarity : 0.004 0.057 1934 Dihedral : 10.870 73.480 2029 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.83 % Allowed : 17.74 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.22), residues: 1352 helix: 1.39 (0.23), residues: 535 sheet: -0.85 (0.37), residues: 156 loop : -0.26 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 239 HIS 0.005 0.001 HIS B 378 PHE 0.011 0.001 PHE B 4 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 494) hydrogen bonds : angle 4.36586 ( 1380) metal coordination : bond 0.00629 ( 12) metal coordination : angle 6.04147 ( 8) covalent geometry : bond 0.00347 (11702) covalent geometry : angle 0.51296 (15982) *********************** 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 171 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: A 31 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8372 (m) REVERT: A 83 GLU cc_start: 0.5155 (OUTLIER) cc_final: 0.4928 (mm-30) REVERT: A 87 GLN cc_start: 0.7333 (tt0) cc_final: 0.6894 (tm-30) REVERT: B 427 ASP cc_start: 0.7808 (t0) cc_final: 0.7188 (t0) REVERT: C 358 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6838 (mp0) outliers start: 33 outliers final: 15 residues processed: 162 average time/residue: 3.0908 time to fit residues: 536.2894 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 : 1.701 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL 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 39 ARG 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 199 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 358 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 0.0770 chunk 124 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.136640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.114314 restraints weight = 48813.200| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.60 r_work: 0.3018 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- 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 = 0.24 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 = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11714 Z= 0.097 Angle : 0.477 11.674 15990 Z= 0.244 Chirality : 0.037 0.148 1807 Planarity : 0.004 0.052 1934 Dihedral : 10.465 73.501 2026 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.23 % Allowed : 18.51 % Favored : 79.26 % 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: 0.83 (0.23), residues: 1352 helix: 1.80 (0.23), residues: 534 sheet: -0.60 (0.38), residues: 154 loop : -0.12 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.008 0.001 PHE B 158 TYR 0.011 0.001 TYR A 403 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 494) hydrogen bonds : angle 4.10743 ( 1380) metal coordination : bond 0.00425 ( 12) metal coordination : angle 4.87738 ( 8) covalent geometry : bond 0.00222 (11702) covalent geometry : angle 0.46418 (15982) *********************** 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 164 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLN cc_start: 0.7191 (tt0) cc_final: 0.6764 (tm-30) REVERT: B 266 MET cc_start: 0.7995 (tpp) cc_final: 0.6942 (tpt) REVERT: B 427 ASP cc_start: 0.7773 (t0) cc_final: 0.7089 (t0) REVERT: C 35 ASP cc_start: 0.7251 (m-30) cc_final: 0.7033 (m-30) REVERT: C 358 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6729 (mp0) outliers start: 26 outliers final: 11 residues processed: 156 average time/residue: 3.1471 time to fit residues: 525.9974 Evaluate side-chains 140 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU 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 187 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 38 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.134197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.111821 restraints weight = 48869.559| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.61 r_work: 0.3001 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11714 Z= 0.137 Angle : 0.506 11.543 15990 Z= 0.259 Chirality : 0.037 0.148 1807 Planarity : 0.004 0.050 1934 Dihedral : 10.389 73.427 2019 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.97 % Allowed : 19.11 % Favored : 78.92 % 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: 0.76 (0.23), residues: 1352 helix: 1.72 (0.23), residues: 534 sheet: -0.71 (0.38), residues: 156 loop : -0.12 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.005 0.001 HIS B 378 PHE 0.011 0.001 PHE B 4 TYR 0.013 0.001 TYR A 403 ARG 0.007 0.000 ARG C 290 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 494) hydrogen bonds : angle 4.17038 ( 1380) metal coordination : bond 0.00581 ( 12) metal coordination : angle 4.99044 ( 8) covalent geometry : bond 0.00320 (11702) covalent geometry : angle 0.49362 (15982) *********************** 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 161 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8360 (m) REVERT: A 83 GLU cc_start: 0.5112 (OUTLIER) cc_final: 0.4832 (mm-30) REVERT: A 87 GLN cc_start: 0.7183 (tt0) cc_final: 0.6726 (tm-30) REVERT: B 266 MET cc_start: 0.8009 (tpp) cc_final: 0.7054 (tpt) REVERT: B 427 ASP cc_start: 0.7773 (t0) cc_final: 0.7068 (t0) REVERT: C 35 ASP cc_start: 0.7287 (m-30) cc_final: 0.7075 (m-30) outliers start: 23 outliers final: 17 residues processed: 157 average time/residue: 3.0658 time to fit residues: 515.2510 Evaluate side-chains 152 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain B residue 180 SER 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 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 102 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.136041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.113852 restraints weight = 50168.998| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.61 r_work: 0.3011 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11714 Z= 0.131 Angle : 0.501 11.030 15990 Z= 0.257 Chirality : 0.037 0.149 1807 Planarity : 0.004 0.051 1934 Dihedral : 10.368 73.453 2019 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.14 % Allowed : 18.68 % 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 (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: 0.75 (0.23), residues: 1352 helix: 1.72 (0.23), residues: 534 sheet: -0.69 (0.39), residues: 156 loop : -0.15 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.004 0.001 HIS B 378 PHE 0.009 0.001 PHE B 4 TYR 0.013 0.001 TYR A 403 ARG 0.007 0.000 ARG C 290 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 494) hydrogen bonds : angle 4.15721 ( 1380) metal coordination : bond 0.00532 ( 12) metal coordination : angle 4.78169 ( 8) covalent geometry : bond 0.00304 (11702) covalent geometry : angle 0.48971 (15982) *********************** 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 161 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8362 (m) REVERT: A 83 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.4888 (mt-10) REVERT: A 87 GLN cc_start: 0.7226 (tt0) cc_final: 0.6765 (tm-30) REVERT: B 266 MET cc_start: 0.7998 (tpp) cc_final: 0.7091 (tpt) REVERT: B 427 ASP cc_start: 0.7728 (t0) cc_final: 0.7041 (t0) REVERT: C 35 ASP cc_start: 0.7275 (m-30) cc_final: 0.7068 (m-30) REVERT: C 186 TYR cc_start: 0.6736 (t80) cc_final: 0.6519 (t80) outliers start: 25 outliers final: 17 residues processed: 156 average time/residue: 2.9943 time to fit residues: 503.8091 Evaluate side-chains 149 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU 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 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 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.134562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.112596 restraints weight = 55193.945| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.58 r_work: 0.2992 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- 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 = 0.23 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 = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11714 Z= 0.136 Angle : 0.520 14.890 15990 Z= 0.261 Chirality : 0.038 0.149 1807 Planarity : 0.005 0.084 1934 Dihedral : 10.388 73.445 2018 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.14 % Allowed : 19.02 % 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 (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 (0.23), residues: 1352 helix: 1.69 (0.23), residues: 534 sheet: -0.69 (0.39), residues: 156 loop : -0.15 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.004 0.001 HIS B 378 PHE 0.010 0.001 PHE B 4 TYR 0.013 0.001 TYR A 403 ARG 0.011 0.000 ARG C 290 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 494) hydrogen bonds : angle 4.17431 ( 1380) metal coordination : bond 0.00557 ( 12) metal coordination : angle 7.03745 ( 8) covalent geometry : bond 0.00317 (11702) covalent geometry : angle 0.49575 (15982) *********************** 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 155 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8381 (m) REVERT: A 83 GLU cc_start: 0.5127 (OUTLIER) cc_final: 0.4878 (mm-30) REVERT: A 87 GLN cc_start: 0.7266 (tt0) cc_final: 0.6765 (tm-30) REVERT: B 266 MET cc_start: 0.7996 (tpp) cc_final: 0.7091 (tpt) REVERT: B 427 ASP cc_start: 0.7726 (t0) cc_final: 0.7031 (t0) REVERT: C 358 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: C 396 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7112 (mt-10) outliers start: 25 outliers final: 18 residues processed: 151 average time/residue: 2.8908 time to fit residues: 468.9171 Evaluate side-chains 156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU 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 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 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS 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 396 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 127 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 103 optimal weight: 0.2980 chunk 120 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.136087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.114070 restraints weight = 48570.282| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.58 r_work: 0.3016 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11714 Z= 0.130 Angle : 0.513 14.067 15990 Z= 0.259 Chirality : 0.037 0.150 1807 Planarity : 0.005 0.086 1934 Dihedral : 10.367 73.459 2018 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.06 % Allowed : 19.11 % 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 (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: 0.76 (0.23), residues: 1352 helix: 1.73 (0.23), residues: 534 sheet: -0.68 (0.39), residues: 156 loop : -0.14 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.004 0.001 HIS B 378 PHE 0.009 0.001 PHE B 4 TYR 0.015 0.001 TYR C 186 ARG 0.012 0.000 ARG C 290 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 494) hydrogen bonds : angle 4.15884 ( 1380) metal coordination : bond 0.00523 ( 12) metal coordination : angle 6.51548 ( 8) covalent geometry : bond 0.00301 (11702) covalent geometry : angle 0.49153 (15982) *********************** 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 155 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.5071 (OUTLIER) cc_final: 0.4859 (mm-30) REVERT: A 87 GLN cc_start: 0.7240 (tt0) cc_final: 0.6774 (tm-30) REVERT: B 84 ARG cc_start: 0.6391 (mtm110) cc_final: 0.6119 (mtm180) REVERT: B 266 MET cc_start: 0.7987 (tpp) cc_final: 0.7090 (tpt) REVERT: B 427 ASP cc_start: 0.7721 (t0) cc_final: 0.7037 (t0) REVERT: C 290 ARG cc_start: 0.7653 (ttp-110) cc_final: 0.7380 (ttm110) REVERT: C 358 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6497 (mp0) REVERT: C 396 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7092 (mt-10) outliers start: 24 outliers final: 18 residues processed: 151 average time/residue: 3.0153 time to fit residues: 488.6287 Evaluate side-chains 152 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU 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 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 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS 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 396 GLU 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 81 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.133234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.110332 restraints weight = 54555.567| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.72 r_work: 0.2951 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11714 Z= 0.188 Angle : 0.561 14.667 15990 Z= 0.285 Chirality : 0.039 0.150 1807 Planarity : 0.005 0.079 1934 Dihedral : 10.612 73.378 2018 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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 (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: 0.53 (0.22), residues: 1352 helix: 1.49 (0.23), residues: 534 sheet: -0.80 (0.38), residues: 156 loop : -0.22 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 77 HIS 0.006 0.001 HIS B 378 PHE 0.014 0.001 PHE B 4 TYR 0.015 0.002 TYR A 403 ARG 0.012 0.001 ARG C 290 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 494) hydrogen bonds : angle 4.31716 ( 1380) metal coordination : bond 0.00794 ( 12) metal coordination : angle 6.99822 ( 8) covalent geometry : bond 0.00440 (11702) covalent geometry : angle 0.53836 (15982) ********************** 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 155 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8401 (m) REVERT: A 87 GLN cc_start: 0.7232 (tt0) cc_final: 0.6708 (tm-30) REVERT: B 84 ARG cc_start: 0.6459 (mtm110) cc_final: 0.6172 (mtm180) REVERT: B 266 MET cc_start: 0.8022 (tpp) cc_final: 0.7205 (tpt) REVERT: B 427 ASP cc_start: 0.7783 (t0) cc_final: 0.7089 (t0) REVERT: C 358 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: C 396 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7169 (mt-10) outliers start: 23 outliers final: 19 residues processed: 151 average time/residue: 2.9319 time to fit residues: 476.2825 Evaluate side-chains 149 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR 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 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 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS 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 396 GLU 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 67 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 47 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.136947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.114303 restraints weight = 53789.027| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.73 r_work: 0.3004 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11714 Z= 0.119 Angle : 0.511 13.914 15990 Z= 0.259 Chirality : 0.037 0.149 1807 Planarity : 0.005 0.097 1934 Dihedral : 10.402 73.439 2018 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.89 % Allowed : 19.19 % Favored : 78.92 % 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 (0.23), residues: 1352 helix: 1.66 (0.23), residues: 534 sheet: -0.73 (0.39), residues: 156 loop : -0.11 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS C 276 PHE 0.008 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.013 0.000 ARG C 290 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 494) hydrogen bonds : angle 4.17976 ( 1380) metal coordination : bond 0.00464 ( 12) metal coordination : angle 6.30110 ( 8) covalent geometry : bond 0.00276 (11702) covalent geometry : angle 0.49143 (15982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15130.28 seconds wall clock time: 258 minutes 46.92 seconds (15526.92 seconds total)