Starting phenix.real_space_refine on Fri Jun 20 01:15:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psz_17865/06_2025/8psz_17865_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psz_17865/06_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_17865/06_2025/8psz_17865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psz_17865/06_2025/8psz_17865.map" model { file = "/net/cci-nas-00/data/ceres_data/8psz_17865/06_2025/8psz_17865_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psz_17865/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.22, per 1000 atoms: 0.62 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: 5.89 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: 12.31 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: 9.51 Time building geometry restraints manager: 7.17 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: 1.650 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: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 73.490 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: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.680 ------------------------------------------------------------------------------- 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 : 1.599 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: 3.7749 time to fit residues: 777.0985 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 : 2.122 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.084002 restraints weight = 44892.170| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.66 r_work: 0.2778 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- 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 = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 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 3.50733 ( 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 : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.8248 (pptt) cc_final: 0.7981 (pttm) REVERT: A 279 LYS cc_start: 0.8705 (mttt) cc_final: 0.8424 (mttp) REVERT: A 323 ASP cc_start: 0.8455 (t0) cc_final: 0.8233 (t0) REVERT: B 53 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7490 (pptt) REVERT: B 480 GLU cc_start: 0.7934 (tt0) cc_final: 0.7607 (tt0) REVERT: C 77 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8726 (ptt90) REVERT: C 89 GLU cc_start: 0.7339 (mp0) cc_final: 0.7059 (mp0) REVERT: C 109 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7051 (mp10) REVERT: C 290 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7733 (mtm110) REVERT: C 348 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7595 (mppt) REVERT: C 413 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7767 (mttm) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 3.9444 time to fit residues: 609.5948 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 : 1.613 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.115805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.085900 restraints weight = 46012.251| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.68 r_work: 0.2809 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 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 = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12154 Z= 0.117 Angle : 0.491 5.350 16675 Z= 0.257 Chirality : 0.037 0.138 1901 Planarity : 0.004 0.070 1951 Dihedral : 12.916 73.609 2311 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.46 % Allowed : 16.64 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1351 helix: 1.91 (0.23), residues: 523 sheet: -0.08 (0.40), residues: 145 loop : -0.07 (0.23), residues: 683 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 44 TYR 0.013 0.001 TYR A 403 ARG 0.005 0.000 ARG B 487 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 514) hydrogen bonds : angle 4.50302 ( 1410) metal coordination : bond 0.00481 ( 12) metal coordination : angle 2.67757 ( 9) covalent geometry : bond 0.00256 (12142) covalent geometry : angle 0.48749 (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 138 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8676 (mttt) cc_final: 0.8336 (mttp) REVERT: B 53 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7395 (pptt) REVERT: B 480 GLU cc_start: 0.7886 (tt0) cc_final: 0.7543 (tt0) REVERT: C 89 GLU cc_start: 0.7221 (mp0) cc_final: 0.6981 (mp0) REVERT: C 109 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7027 (mp10) REVERT: C 196 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6517 (mt-10) REVERT: C 348 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7542 (mppt) REVERT: C 413 LYS cc_start: 0.8111 (mtpt) cc_final: 0.7737 (mttm) outliers start: 17 outliers final: 7 residues processed: 132 average time/residue: 4.3959 time to fit residues: 611.2675 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 : 1.678 ------------------------------------------------------------------------------- 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: 0.7980 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.115069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.084820 restraints weight = 49385.024| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.74 r_work: 0.2790 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 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 = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1705 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 : 0.508 5.553 16675 Z= 0.266 Chirality : 0.037 0.139 1901 Planarity : 0.004 0.062 1951 Dihedral : 12.824 73.587 2306 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.63 % Allowed : 16.21 % 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: 0.96 (0.22), residues: 1351 helix: 1.88 (0.23), residues: 523 sheet: -0.13 (0.40), residues: 145 loop : -0.11 (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 0.004 0.000 ARG B 487 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 514) hydrogen bonds : angle 4.49229 ( 1410) metal coordination : bond 0.00592 ( 12) metal coordination : angle 2.60071 ( 9) covalent geometry : bond 0.00335 (12142) covalent geometry : angle 0.50472 (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 134 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8689 (mttt) cc_final: 0.8413 (mttp) REVERT: B 53 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7501 (pptt) REVERT: B 180 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.9015 (t) REVERT: B 480 GLU cc_start: 0.7907 (tt0) cc_final: 0.7570 (tt0) REVERT: C 109 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7084 (mp10) REVERT: C 170 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6819 (mtpt) REVERT: C 196 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6474 (mt-10) REVERT: C 348 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7549 (mppt) REVERT: C 427 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7221 (ttmt) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 3.9637 time to fit residues: 543.6636 Evaluate side-chains 128 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 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 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 322 SER 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: 1.9990 chunk 3 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.115028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.084399 restraints weight = 55472.292| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.84 r_work: 0.2783 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1787 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 : 0.508 5.608 16675 Z= 0.267 Chirality : 0.038 0.138 1901 Planarity : 0.004 0.057 1951 Dihedral : 12.774 73.592 2302 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.63 % Allowed : 16.12 % 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: 0.93 (0.22), residues: 1351 helix: 1.87 (0.23), residues: 523 sheet: -0.15 (0.40), residues: 145 loop : -0.14 (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 0.015 0.001 TYR A 403 ARG 0.004 0.000 ARG B 487 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 514) hydrogen bonds : angle 4.47287 ( 1410) metal coordination : bond 0.00600 ( 12) metal coordination : angle 2.54414 ( 9) covalent geometry : bond 0.00333 (12142) covalent geometry : angle 0.50501 (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 133 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8686 (mttt) cc_final: 0.8407 (mttp) REVERT: B 180 SER cc_start: 0.9259 (OUTLIER) cc_final: 0.9012 (t) REVERT: B 480 GLU cc_start: 0.7916 (tt0) cc_final: 0.7593 (tt0) REVERT: B 495 LYS cc_start: 0.7641 (ttpp) cc_final: 0.7390 (tmmt) REVERT: C 109 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7080 (mp10) REVERT: C 170 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6832 (mtpt) REVERT: C 196 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6500 (mt-10) REVERT: C 348 LYS cc_start: 0.8212 (mmtp) cc_final: 0.7562 (mppt) REVERT: C 427 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7193 (ttmt) outliers start: 19 outliers final: 11 residues processed: 128 average time/residue: 4.8272 time to fit residues: 657.1513 Evaluate side-chains 127 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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 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 197 ASP Chi-restraints excluded: chain C residue 300 VAL 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: 3.9990 chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.115395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.084983 restraints weight = 50770.872| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.77 r_work: 0.2793 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 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 = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12154 Z= 0.142 Angle : 0.500 5.571 16675 Z= 0.262 Chirality : 0.037 0.138 1901 Planarity : 0.004 0.055 1951 Dihedral : 12.738 73.587 2302 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.72 % Allowed : 15.95 % 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: 0.96 (0.22), residues: 1351 helix: 1.90 (0.23), residues: 523 sheet: -0.14 (0.40), residues: 145 loop : -0.13 (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 0.012 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 0.04529 ( 514) hydrogen bonds : angle 4.44209 ( 1410) metal coordination : bond 0.00584 ( 12) metal coordination : angle 2.53053 ( 9) covalent geometry : bond 0.00317 (12142) covalent geometry : angle 0.49652 (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 136 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7306 (mt-10) REVERT: A 279 LYS cc_start: 0.8687 (mttt) cc_final: 0.8410 (mttp) REVERT: B 180 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.9009 (t) REVERT: B 480 GLU cc_start: 0.7925 (tt0) cc_final: 0.7578 (tt0) REVERT: B 495 LYS cc_start: 0.7695 (ttpp) cc_final: 0.7464 (tmmt) REVERT: C 109 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7088 (mp10) REVERT: C 196 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6499 (mt-10) REVERT: C 348 LYS cc_start: 0.8199 (mmtp) cc_final: 0.7548 (mppt) REVERT: C 427 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7174 (ttmt) outliers start: 20 outliers final: 14 residues processed: 133 average time/residue: 3.7860 time to fit residues: 535.2494 Evaluate side-chains 126 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 117 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 21 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.086914 restraints weight = 54779.378| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.84 r_work: 0.2827 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1940 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= 0.097 Angle : 0.465 5.399 16675 Z= 0.242 Chirality : 0.036 0.136 1901 Planarity : 0.004 0.053 1951 Dihedral : 12.542 73.572 2302 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.37 % Allowed : 16.38 % 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: 2.10 (0.23), residues: 524 sheet: -0.08 (0.40), residues: 145 loop : -0.03 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 239 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 0.03781 ( 514) hydrogen bonds : angle 4.23791 ( 1410) metal coordination : bond 0.00474 ( 12) metal coordination : angle 2.20490 ( 9) covalent geometry : bond 0.00212 (12142) covalent geometry : angle 0.46222 (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 135 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7404 (mt-10) REVERT: A 279 LYS cc_start: 0.8684 (mttt) cc_final: 0.8343 (mttp) REVERT: B 159 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.8941 (mt) REVERT: B 480 GLU cc_start: 0.7866 (tt0) cc_final: 0.7505 (tt0) REVERT: B 495 LYS cc_start: 0.7693 (ttpp) cc_final: 0.7487 (tmmt) REVERT: C 89 GLU cc_start: 0.7390 (mp0) cc_final: 0.7139 (mp0) REVERT: C 109 GLN cc_start: 0.7496 (mm-40) cc_final: 0.7089 (mp10) REVERT: C 348 LYS cc_start: 0.8124 (mmtp) cc_final: 0.7510 (mppt) REVERT: C 427 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7229 (ttmt) outliers start: 16 outliers final: 9 residues processed: 130 average time/residue: 3.8663 time to fit residues: 534.9499 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 : 1.785 ------------------------------------------------------------------------------- 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 301 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: 2.9990 chunk 100 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.114512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.083960 restraints weight = 50140.854| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.77 r_work: 0.2778 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12154 Z= 0.182 Angle : 0.530 5.734 16675 Z= 0.278 Chirality : 0.038 0.137 1901 Planarity : 0.005 0.055 1951 Dihedral : 12.740 73.597 2301 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.37 % Allowed : 16.81 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1351 helix: 1.87 (0.23), residues: 524 sheet: -0.18 (0.40), residues: 145 loop : -0.13 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.016 0.002 PHE C 44 TYR 0.016 0.002 TYR A 403 ARG 0.006 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04857 ( 514) hydrogen bonds : angle 4.46056 ( 1410) metal coordination : bond 0.00693 ( 12) metal coordination : angle 2.72035 ( 9) covalent geometry : bond 0.00410 (12142) covalent geometry : angle 0.52598 (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 131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8673 (mttt) cc_final: 0.8398 (mttp) REVERT: B 159 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.8920 (mt) REVERT: B 480 GLU cc_start: 0.7940 (tt0) cc_final: 0.7589 (tt0) REVERT: B 495 LYS cc_start: 0.7671 (ttpp) cc_final: 0.7457 (tmmt) REVERT: C 109 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7098 (mp10) REVERT: C 348 LYS cc_start: 0.8182 (mmtp) cc_final: 0.7591 (mppt) REVERT: C 427 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7160 (ttmt) outliers start: 16 outliers final: 12 residues processed: 128 average time/residue: 3.7995 time to fit residues: 516.6924 Evaluate side-chains 128 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.114563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.084172 restraints weight = 48330.738| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.73 r_work: 0.2782 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12154 Z= 0.176 Angle : 0.529 5.619 16675 Z= 0.278 Chirality : 0.038 0.137 1901 Planarity : 0.005 0.079 1951 Dihedral : 12.771 73.581 2301 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.20 % Allowed : 16.90 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1351 helix: 1.75 (0.23), residues: 524 sheet: -0.24 (0.40), residues: 145 loop : -0.15 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 PHE 0.015 0.001 PHE C 44 TYR 0.015 0.001 TYR A 403 ARG 0.007 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 514) hydrogen bonds : angle 4.47502 ( 1410) metal coordination : bond 0.00675 ( 12) metal coordination : angle 2.79017 ( 9) covalent geometry : bond 0.00395 (12142) covalent geometry : angle 0.52533 (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 131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.814 Fit side-chains revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8687 (mttt) cc_final: 0.8409 (mttp) REVERT: B 159 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.8927 (mt) REVERT: C 109 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7061 (mp10) REVERT: C 348 LYS cc_start: 0.8181 (mmtp) cc_final: 0.7586 (mppt) REVERT: C 427 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7119 (ttmt) outliers start: 14 outliers final: 12 residues processed: 129 average time/residue: 3.7319 time to fit residues: 515.2921 Evaluate side-chains 129 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.892 ------------------------------------------------------------------------------- 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 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 300 VAL 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: 0.9980 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.116249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.085472 restraints weight = 54372.295| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.84 r_work: 0.2805 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12154 Z= 0.112 Angle : 0.485 5.355 16675 Z= 0.254 Chirality : 0.037 0.139 1901 Planarity : 0.004 0.076 1951 Dihedral : 12.623 73.558 2301 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.03 % Allowed : 17.07 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1351 helix: 1.97 (0.23), residues: 524 sheet: -0.17 (0.40), residues: 145 loop : -0.07 (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 0.010 0.001 PHE C 175 TYR 0.013 0.001 TYR A 403 ARG 0.009 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 514) hydrogen bonds : angle 4.31494 ( 1410) metal coordination : bond 0.00540 ( 12) metal coordination : angle 2.24214 ( 9) covalent geometry : bond 0.00246 (12142) covalent geometry : angle 0.48263 (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 126 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 2.715 Fit side-chains revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8689 (mttt) cc_final: 0.8343 (mttp) REVERT: B 159 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.8934 (mt) REVERT: C 109 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7089 (mp10) REVERT: C 348 LYS cc_start: 0.8167 (mmtp) cc_final: 0.7605 (mppt) REVERT: C 427 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7194 (ttmt) outliers start: 12 outliers final: 10 residues processed: 124 average time/residue: 4.3621 time to fit residues: 575.4774 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 : 1.737 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.7980 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: 0.3980 chunk 132 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 3 optimal weight: 0.0570 overall best weight: 0.8100 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.116530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.085965 restraints weight = 51466.280| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.79 r_work: 0.2814 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12154 Z= 0.111 Angle : 0.479 5.328 16675 Z= 0.250 Chirality : 0.036 0.136 1901 Planarity : 0.005 0.075 1951 Dihedral : 12.550 73.551 2301 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.86 % Allowed : 17.24 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1351 helix: 2.04 (0.23), residues: 524 sheet: -0.16 (0.40), residues: 145 loop : -0.06 (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 0.010 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 0.04005 ( 514) hydrogen bonds : angle 4.26207 ( 1410) metal coordination : bond 0.00508 ( 12) metal coordination : angle 2.23009 ( 9) covalent geometry : bond 0.00247 (12142) covalent geometry : angle 0.47637 (16666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22140.78 seconds wall clock time: 381 minutes 40.58 seconds (22900.58 seconds total)