Starting phenix.real_space_refine on Thu May 22 17:47:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psz_17865/05_2025/8psz_17865_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psz_17865/05_2025/8psz_17865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8psz_17865/05_2025/8psz_17865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psz_17865/05_2025/8psz_17865.map" model { file = "/net/cci-nas-00/data/ceres_data/8psz_17865/05_2025/8psz_17865_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psz_17865/05_2025/8psz_17865_trim.cif" } resolution = 2.42 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 56 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 7221 2.51 5 N 2077 2.21 5 O 2481 1.98 5 H 11195 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 23098 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6653 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: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 6652 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 22, 'TRANS': 402} 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: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 7} 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: "D" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 453 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 9} 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} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "V" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 46.840 53.436 18.382 1.00 20.80 S ATOM 4474 SG CYS A 282 44.558 52.018 15.484 1.00 21.12 S ATOM 18191 SG CYS C 233 23.667 63.533 108.687 1.00 68.90 S ATOM 18215 SG CYS C 235 23.744 64.404 104.935 1.00 63.55 S ATOM 16857 SG CYS C 146 12.028 72.706 88.850 1.00 71.81 S ATOM 17045 SG CYS C 159 13.000 75.499 90.912 1.00 66.96 S ATOM 17101 SG CYS C 163 15.366 72.687 90.646 1.00 60.91 S ATOM 17111 SG CYS C 164 14.711 75.039 87.428 1.00 64.71 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: 15.16, per 1000 atoms: 0.66 Number of scatterers: 23098 At special positions: 0 Unit cell: (92.4, 109.2, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 56 15.00 Mg 2 11.99 O 2481 8.00 N 2077 7.00 C 7221 6.00 H 11195 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.11 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 233 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 235 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " Number of angles added : 9 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 15 sheets defined 42.4% alpha, 13.9% beta 15 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 12.16 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 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 311 removed outlier: 3.878A pdb=" N GLN A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.523A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.967A 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: 3.555A 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 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.501A 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 138 removed outlier: 3.648A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.646A 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 Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.728A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.972A 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 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.035A 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 513 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: 3.736A pdb=" N VAL C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 165 removed outlier: 3.549A pdb=" N GLY C 165 " --> pdb=" O ILE C 162 " (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 316 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: 6.627A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.540A 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: 6.302A 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: 6.302A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 159 removed outlier: 7.129A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 224 removed outlier: 6.779A pdb=" N GLY C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 360 through 363 Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 388 removed outlier: 6.623A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 9.75 Time building geometry restraints manager: 7.22 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: 11163 1.03 - 1.23: 52 1.23 - 1.42: 5191 1.42 - 1.62: 6842 1.62 - 1.81: 89 Bond restraints: 23337 Sorted by residual: bond pdb=" O7 A0I B 601 " pdb=" P3 A0I B 601 " ideal model delta sigma weight residual 1.731 1.618 0.113 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C PRO C 234 " pdb=" O PRO C 234 " ideal model delta sigma weight residual 1.235 1.177 0.058 1.30e-02 5.92e+03 1.98e+01 bond pdb=" N4 A0I B 601 " pdb=" P2 A0I B 601 " ideal model delta sigma weight residual 1.701 1.641 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" O3 A0I B 601 " pdb=" P1 A0I B 601 " ideal model delta sigma weight residual 1.662 1.603 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" N4 A0I B 601 " pdb=" P1 A0I B 601 " ideal model delta sigma weight residual 1.691 1.642 0.049 2.00e-02 2.50e+03 5.88e+00 ... (remaining 23332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 41535 1.62 - 3.25: 539 3.25 - 4.87: 46 4.87 - 6.50: 2 6.50 - 8.12: 1 Bond angle restraints: 42123 Sorted by residual: angle pdb=" O6 A0I B 601 " pdb=" P2 A0I B 601 " pdb=" O7 A0I B 601 " ideal model delta sigma weight residual 112.52 104.40 8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" N PRO C 234 " pdb=" CA PRO C 234 " pdb=" CB PRO C 234 " ideal model delta sigma weight residual 103.25 100.43 2.82 1.05e+00 9.07e-01 7.19e+00 angle pdb=" C LYS A 163 " pdb=" CA LYS A 163 " pdb=" CB LYS A 163 " ideal model delta sigma weight residual 110.42 115.61 -5.19 1.99e+00 2.53e-01 6.79e+00 angle pdb=" CA PRO C 234 " pdb=" C PRO C 234 " pdb=" O PRO C 234 " ideal model delta sigma weight residual 120.60 116.81 3.79 1.82e+00 3.02e-01 4.33e+00 angle pdb=" N ASP C 345 " pdb=" CA ASP C 345 " pdb=" C ASP C 345 " ideal model delta sigma weight residual 114.75 112.49 2.26 1.26e+00 6.30e-01 3.22e+00 ... (remaining 42118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 9721 17.80 - 35.60: 836 35.60 - 53.41: 342 53.41 - 71.21: 120 71.21 - 89.01: 29 Dihedral angle restraints: 11048 sinusoidal: 6454 harmonic: 4594 Sorted by residual: dihedral pdb=" CD ARG B 176 " pdb=" NE ARG B 176 " pdb=" CZ ARG B 176 " pdb=" NH1 ARG B 176 " ideal model delta sinusoidal sigma weight residual 0.00 41.02 -41.02 1 1.00e+01 1.00e-02 2.36e+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 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA SER B 286 " pdb=" C SER B 286 " pdb=" N PHE B 287 " pdb=" CA PHE B 287 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 11045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1586 0.044 - 0.088: 227 0.088 - 0.132: 87 0.132 - 0.176: 0 0.176 - 0.220: 1 Chirality restraints: 1901 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 -2.59 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL C 221 " pdb=" N VAL C 221 " pdb=" C VAL C 221 " pdb=" CB VAL C 221 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-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 4.15e-01 ... (remaining 1898 not shown) Planarity restraints: 3274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 176 " 0.749 9.50e-02 1.11e+02 2.50e-01 6.59e+01 pdb=" NE ARG B 176 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 176 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 176 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 176 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 176 " -0.012 2.00e-02 2.50e+03 pdb="HH12 ARG B 176 " 0.010 2.00e-02 2.50e+03 pdb="HH21 ARG B 176 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG B 176 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 3 " -0.022 2.00e-02 2.50e+03 9.08e-03 2.68e+00 pdb=" N9 A V 3 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A V 3 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 3 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A V 3 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 3 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A V 3 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A V 3 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A V 3 " 0.002 2.00e-02 2.50e+03 pdb=" H2 A V 3 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 162 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.019 5.00e-02 4.00e+02 ... (remaining 3271 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 898 2.16 - 2.77: 43029 2.77 - 3.38: 65847 3.38 - 3.99: 89220 3.99 - 4.60: 135252 Nonbonded interactions: 334246 Sorted by model distance: nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.549 2.450 nonbonded pdb=" H GLY A 239 " pdb=" O ALA A 251 " model vdw 1.582 2.450 nonbonded pdb=" OD1 ASN B 397 " pdb=" HG1 THR B 399 " model vdw 1.590 2.450 nonbonded pdb=" H GLY C 85 " pdb=" OD1 ASP C 110 " model vdw 1.630 2.450 nonbonded pdb=" HG1 THR B 103 " pdb=" O ILE B 125 " model vdw 1.631 2.450 ... (remaining 334241 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 Found NCS groups: ncs_group { reference = (chain 'D' and resid 5 through 17) selection = (chain 'S' and (resid 28 through 34 or resid 36 through 40)) } 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: 4.970 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: 1.190 Extract box with map and model: 0.060 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 74.390 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 0.113 12154 Z= 0.138 Angle : 0.506 9.351 16675 Z= 0.257 Chirality : 0.037 0.220 1901 Planarity : 0.008 0.321 1951 Dihedral : 17.754 89.008 4872 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.06 % Allowed : 16.38 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1351 helix: 1.65 (0.23), residues: 525 sheet: 0.20 (0.40), residues: 148 loop : -0.07 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 44 TYR 0.012 0.001 TYR C 315 ARG 0.007 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.12888 ( 514) hydrogen bonds : angle 5.58584 ( 1410) metal coordination : bond 0.00840 ( 12) metal coordination : angle 4.80964 ( 9) covalent geometry : bond 0.00281 (12142) covalent geometry : angle 0.49343 (16666) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8594 (mttt) cc_final: 0.8364 (mttp) REVERT: A 332 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: B 282 ASP cc_start: 0.8477 (p0) cc_final: 0.8276 (p0) REVERT: B 480 GLU cc_start: 0.7593 (tt0) cc_final: 0.7385 (tt0) REVERT: C 77 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8663 (ptt90) REVERT: C 89 GLU cc_start: 0.7603 (mp0) cc_final: 0.7392 (mp0) REVERT: C 109 GLN cc_start: 0.7321 (mm-40) cc_final: 0.7065 (mp10) REVERT: C 348 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7638 (mppt) REVERT: C 351 ILE cc_start: 0.7809 (mm) cc_final: 0.7532 (mm) REVERT: C 413 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7524 (mtmt) REVERT: C 427 LYS cc_start: 0.7300 (ttmt) cc_final: 0.7088 (tttm) outliers start: 24 outliers final: 9 residues processed: 194 average time/residue: 3.6910 time to fit residues: 760.1553 Evaluate side-chains 128 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 200 GLN B 44 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.084001 restraints weight = 44892.195| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.66 r_work: 0.2776 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12154 Z= 0.205 Angle : 0.566 6.082 16675 Z= 0.298 Chirality : 0.040 0.141 1901 Planarity : 0.005 0.076 1951 Dihedral : 13.269 73.618 2316 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.06 % Allowed : 15.78 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1351 helix: 1.66 (0.22), residues: 530 sheet: -0.03 (0.40), residues: 145 loop : -0.07 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.016 0.002 PHE C 44 TYR 0.019 0.002 TYR A 403 ARG 0.004 0.001 ARG B 487 Details of bonding type rmsd hydrogen bonds : bond 0.05431 ( 514) hydrogen bonds : angle 4.73457 ( 1410) metal coordination : bond 0.00883 ( 12) metal coordination : angle 3.50736 ( 9) covalent geometry : bond 0.00460 (12142) covalent geometry : angle 0.56012 (16666) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.8247 (pptt) cc_final: 0.7980 (pttm) REVERT: A 279 LYS cc_start: 0.8703 (mttt) cc_final: 0.8419 (mttp) REVERT: A 323 ASP cc_start: 0.8454 (t0) cc_final: 0.8231 (t0) REVERT: B 53 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7491 (pptt) REVERT: B 480 GLU cc_start: 0.7927 (tt0) cc_final: 0.7598 (tt0) REVERT: C 77 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8722 (ptt90) REVERT: C 89 GLU cc_start: 0.7331 (mp0) cc_final: 0.7049 (mp0) REVERT: C 109 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7041 (mp10) REVERT: C 290 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7729 (mtm110) REVERT: C 348 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7586 (mppt) REVERT: C 413 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7767 (mttm) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 3.9634 time to fit residues: 614.2283 Evaluate side-chains 133 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 278 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 53 LYS 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 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 46 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.116242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.086390 restraints weight = 46053.466| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.69 r_work: 0.2817 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12154 Z= 0.110 Angle : 0.484 5.292 16675 Z= 0.253 Chirality : 0.037 0.138 1901 Planarity : 0.004 0.069 1951 Dihedral : 12.867 73.583 2311 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.46 % Allowed : 16.55 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1351 helix: 1.95 (0.23), residues: 523 sheet: -0.07 (0.40), residues: 145 loop : -0.05 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.005 0.000 ARG B 487 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 514) hydrogen bonds : angle 4.46354 ( 1410) metal coordination : bond 0.00463 ( 12) metal coordination : angle 2.57433 ( 9) covalent geometry : bond 0.00241 (12142) covalent geometry : angle 0.48088 (16666) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8693 (mttt) cc_final: 0.8352 (mttp) REVERT: B 53 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7362 (pptt) REVERT: B 480 GLU cc_start: 0.7871 (tt0) cc_final: 0.7532 (tt0) REVERT: C 89 GLU cc_start: 0.7271 (mp0) cc_final: 0.7035 (mp0) REVERT: C 109 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7066 (mp10) REVERT: C 196 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6503 (mt-10) REVERT: C 348 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7527 (mppt) outliers start: 17 outliers final: 7 residues processed: 133 average time/residue: 4.3410 time to fit residues: 609.3363 Evaluate side-chains 124 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.114600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.084728 restraints weight = 49570.307| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.71 r_work: 0.2789 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12154 Z= 0.150 Angle : 0.506 5.520 16675 Z= 0.265 Chirality : 0.037 0.139 1901 Planarity : 0.004 0.061 1951 Dihedral : 12.814 73.598 2306 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.46 % Allowed : 16.21 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1351 helix: 1.91 (0.23), residues: 523 sheet: -0.15 (0.40), residues: 145 loop : -0.10 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.013 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.007 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 514) hydrogen bonds : angle 4.48233 ( 1410) metal coordination : bond 0.00584 ( 12) metal coordination : angle 2.56657 ( 9) covalent geometry : bond 0.00335 (12142) covalent geometry : angle 0.50214 (16666) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8692 (mttt) cc_final: 0.8413 (mttp) REVERT: B 53 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7478 (pptt) REVERT: B 180 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.9007 (t) REVERT: B 480 GLU cc_start: 0.7896 (tt0) cc_final: 0.7544 (tt0) REVERT: C 109 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7076 (mp10) REVERT: C 170 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6748 (mtpt) REVERT: C 196 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6445 (mt-10) REVERT: C 348 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7507 (mppt) REVERT: C 427 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7206 (ttmt) outliers start: 17 outliers final: 10 residues processed: 130 average time/residue: 3.9679 time to fit residues: 546.3871 Evaluate side-chains 130 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 53 LYS 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 444 ASP Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 427 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3335 r_free = 0.3335 target = 0.113184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.082654 restraints weight = 55500.025| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.83 r_work: 0.2756 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12154 Z= 0.211 Angle : 0.558 6.051 16675 Z= 0.294 Chirality : 0.040 0.161 1901 Planarity : 0.005 0.059 1951 Dihedral : 12.930 73.635 2302 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.97 % Allowed : 15.87 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1351 helix: 1.67 (0.22), residues: 523 sheet: -0.27 (0.41), residues: 133 loop : -0.21 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.017 0.002 PHE C 44 TYR 0.017 0.002 TYR A 403 ARG 0.005 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.05296 ( 514) hydrogen bonds : angle 4.61659 ( 1410) metal coordination : bond 0.00842 ( 12) metal coordination : angle 2.99225 ( 9) covalent geometry : bond 0.00475 (12142) covalent geometry : angle 0.55345 (16666) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8690 (mttt) cc_final: 0.8411 (mttp) REVERT: B 53 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7568 (pptt) REVERT: C 109 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7094 (mp10) REVERT: C 196 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6488 (mt-10) REVERT: C 348 LYS cc_start: 0.8219 (mmtp) cc_final: 0.7575 (mppt) REVERT: C 427 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7045 (ttpp) outliers start: 23 outliers final: 15 residues processed: 134 average time/residue: 3.7585 time to fit residues: 535.2703 Evaluate side-chains 130 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 278 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 53 LYS 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 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 427 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 92 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.084576 restraints weight = 50704.430| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.78 r_work: 0.2787 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12154 Z= 0.142 Angle : 0.506 5.609 16675 Z= 0.265 Chirality : 0.037 0.138 1901 Planarity : 0.004 0.055 1951 Dihedral : 12.779 73.577 2302 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.54 % Allowed : 16.21 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1351 helix: 1.83 (0.23), residues: 523 sheet: -0.17 (0.40), residues: 145 loop : -0.16 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.011 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.005 0.000 ARG B 487 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 514) hydrogen bonds : angle 4.46821 ( 1410) metal coordination : bond 0.00639 ( 12) metal coordination : angle 2.46651 ( 9) covalent geometry : bond 0.00316 (12142) covalent geometry : angle 0.50322 (16666) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8690 (mttt) cc_final: 0.8411 (mttp) REVERT: B 180 SER cc_start: 0.9252 (OUTLIER) cc_final: 0.9016 (t) REVERT: C 89 GLU cc_start: 0.7349 (mp0) cc_final: 0.7104 (mp0) REVERT: C 109 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7080 (mp10) REVERT: C 196 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: C 348 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7560 (mppt) REVERT: C 427 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7145 (ttmt) outliers start: 18 outliers final: 12 residues processed: 128 average time/residue: 3.7801 time to fit residues: 513.4148 Evaluate side-chains 125 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 42 SER 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 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 427 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 117 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.085412 restraints weight = 54706.009| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.84 r_work: 0.2803 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12154 Z= 0.110 Angle : 0.477 5.497 16675 Z= 0.250 Chirality : 0.036 0.137 1901 Planarity : 0.004 0.053 1951 Dihedral : 12.628 73.569 2302 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.72 % Allowed : 16.04 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1351 helix: 1.98 (0.23), residues: 524 sheet: -0.12 (0.40), residues: 145 loop : -0.08 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.005 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 514) hydrogen bonds : angle 4.32076 ( 1410) metal coordination : bond 0.00506 ( 12) metal coordination : angle 2.13135 ( 9) covalent geometry : bond 0.00242 (12142) covalent geometry : angle 0.47496 (16666) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8690 (mttt) cc_final: 0.8409 (mttp) REVERT: B 159 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.8929 (mt) REVERT: B 180 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.9019 (t) REVERT: B 480 GLU cc_start: 0.7878 (tt0) cc_final: 0.7484 (tt0) REVERT: B 495 LYS cc_start: 0.7620 (ttpp) cc_final: 0.7379 (tmmt) REVERT: C 89 GLU cc_start: 0.7352 (mp0) cc_final: 0.7074 (mp0) REVERT: C 109 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7081 (mp10) REVERT: C 348 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7569 (mppt) REVERT: C 427 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7124 (ttmt) outliers start: 20 outliers final: 13 residues processed: 131 average time/residue: 3.9379 time to fit residues: 549.6269 Evaluate side-chains 131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 42 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 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 427 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 102 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.117054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.086754 restraints weight = 50271.085| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.77 r_work: 0.2825 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12154 Z= 0.099 Angle : 0.467 5.382 16675 Z= 0.243 Chirality : 0.036 0.137 1901 Planarity : 0.004 0.076 1951 Dihedral : 12.518 73.547 2302 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.20 % Allowed : 16.55 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1351 helix: 2.11 (0.23), residues: 524 sheet: -0.09 (0.40), residues: 145 loop : -0.04 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 514) hydrogen bonds : angle 4.23221 ( 1410) metal coordination : bond 0.00427 ( 12) metal coordination : angle 2.02538 ( 9) covalent geometry : bond 0.00220 (12142) covalent geometry : angle 0.46446 (16666) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8673 (mttt) cc_final: 0.8331 (mttp) REVERT: B 159 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.8934 (mt) REVERT: B 480 GLU cc_start: 0.7862 (tt0) cc_final: 0.7492 (tt0) REVERT: B 495 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7457 (tmmt) REVERT: C 109 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7084 (mp10) REVERT: C 348 LYS cc_start: 0.8102 (mmtp) cc_final: 0.7499 (mppt) REVERT: C 427 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7206 (ttmt) outliers start: 14 outliers final: 10 residues processed: 132 average time/residue: 3.7795 time to fit residues: 530.0782 Evaluate side-chains 127 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 427 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.085485 restraints weight = 48539.909| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.74 r_work: 0.2805 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12154 Z= 0.135 Angle : 0.493 5.431 16675 Z= 0.258 Chirality : 0.037 0.135 1901 Planarity : 0.004 0.074 1951 Dihedral : 12.585 73.576 2301 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.03 % Allowed : 16.81 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1351 helix: 2.00 (0.23), residues: 524 sheet: -0.15 (0.40), residues: 145 loop : -0.08 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.012 0.001 PHE C 44 TYR 0.014 0.001 TYR A 403 ARG 0.008 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 514) hydrogen bonds : angle 4.31441 ( 1410) metal coordination : bond 0.00540 ( 12) metal coordination : angle 2.23921 ( 9) covalent geometry : bond 0.00302 (12142) covalent geometry : angle 0.49051 (16666) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8672 (mttt) cc_final: 0.8332 (mttp) REVERT: B 159 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.8927 (mt) REVERT: B 480 GLU cc_start: 0.7874 (tt0) cc_final: 0.7481 (tt0) REVERT: B 495 LYS cc_start: 0.7700 (ttpp) cc_final: 0.7483 (tmmt) REVERT: C 109 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7076 (mp10) REVERT: C 348 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7581 (mppt) REVERT: C 427 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7207 (ttmt) outliers start: 12 outliers final: 10 residues processed: 124 average time/residue: 3.7782 time to fit residues: 500.2899 Evaluate side-chains 124 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 427 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 125 optimal weight: 0.0050 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.116798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.086131 restraints weight = 54645.041| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.84 r_work: 0.2814 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12154 Z= 0.107 Angle : 0.475 5.281 16675 Z= 0.248 Chirality : 0.036 0.137 1901 Planarity : 0.004 0.072 1951 Dihedral : 12.509 73.549 2301 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.94 % Allowed : 16.81 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1351 helix: 2.09 (0.23), residues: 524 sheet: -0.00 (0.41), residues: 143 loop : -0.04 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.007 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 514) hydrogen bonds : angle 4.23077 ( 1410) metal coordination : bond 0.00496 ( 12) metal coordination : angle 2.05156 ( 9) covalent geometry : bond 0.00238 (12142) covalent geometry : angle 0.47310 (16666) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8677 (mttt) cc_final: 0.8334 (mttp) REVERT: B 159 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.8913 (mt) REVERT: B 495 LYS cc_start: 0.7703 (ttpp) cc_final: 0.7489 (tmmt) REVERT: C 109 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7068 (mp10) REVERT: C 348 LYS cc_start: 0.8108 (mmtp) cc_final: 0.7536 (mppt) REVERT: C 427 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7207 (ttmt) outliers start: 11 outliers final: 8 residues processed: 122 average time/residue: 3.8387 time to fit residues: 497.0703 Evaluate side-chains 121 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 427 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 21 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 100 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.085787 restraints weight = 51116.305| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.79 r_work: 0.2810 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12154 Z= 0.121 Angle : 0.485 5.339 16675 Z= 0.254 Chirality : 0.037 0.136 1901 Planarity : 0.004 0.072 1951 Dihedral : 12.515 73.567 2300 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.94 % Allowed : 16.90 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1351 helix: 2.05 (0.23), residues: 524 sheet: -0.03 (0.40), residues: 143 loop : -0.07 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.010 0.001 PHE C 175 TYR 0.013 0.001 TYR A 403 ARG 0.012 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 514) hydrogen bonds : angle 4.26042 ( 1410) metal coordination : bond 0.00513 ( 12) metal coordination : angle 2.16235 ( 9) covalent geometry : bond 0.00269 (12142) covalent geometry : angle 0.48253 (16666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20601.22 seconds wall clock time: 352 minutes 5.99 seconds (21125.99 seconds total)