Starting phenix.real_space_refine on Sat Jul 4 19:55:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psz_17865/07_2026/8psz_17865_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psz_17865/07_2026/8psz_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 { model { file = "/net/cci-nas-00/data/ceres_data/8psz_17865/07_2026/8psz_17865_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psz_17865/07_2026/8psz_17865_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8psz_17865/07_2026/8psz_17865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psz_17865/07_2026/8psz_17865.map" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 4.18, per 1000 atoms: 0.18 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: 1.92 Conformation dependent library (CDL) restraints added in 675.5 milliseconds 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: 3.63 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: 4.50 Time building geometry restraints manager: 2.74 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=" C1' U V 9 " pdb=" N1 U V 9 " pdb=" C6 U V 9 " ideal model delta sigma weight residual 121.20 124.00 -2.80 1.40e+00 5.10e-01 3.99e+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: 1.780 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: 0.090 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 26.810 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 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= 0.146 Angle : 0.506 9.351 16675 Z= 0.278 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (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 ARG 0.007 0.000 ARG C 83 TYR 0.012 0.001 TYR C 315 PHE 0.009 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (12142) covalent geometry : angle 0.49345 / 0.28 (16666) hydrogen bonds : bond 0.12888 / 8.87 ( 514) hydrogen bonds : angle 5.58584 / 4.02 ( 1410) metal coordination : bond 0.00840 / 0.42 ( 12) metal coordination : angle 4.80964 / 2.14 ( 9) *********************** 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 : 0.527 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: 1.4897 time to fit residues: 307.9145 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 : 0.591 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN B 44 ASN C 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.086548 restraints weight = 45596.131| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.69 r_work: 0.2822 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12154 Z= 0.119 Angle : 0.504 5.032 16675 Z= 0.269 Chirality : 0.037 0.140 1901 Planarity : 0.005 0.118 1951 Dihedral : 13.177 73.544 2316 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.23), residues: 1351 helix: 1.77 (0.23), residues: 530 sheet: -0.02 (0.40), residues: 145 loop : -0.03 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 176 TYR 0.011 0.001 TYR A 403 PHE 0.010 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (12142) covalent geometry : angle 0.50068 / 0.27 (16666) hydrogen bonds : bond 0.05062 / 3.31 ( 514) hydrogen bonds : angle 4.74546 / 3.45 ( 1410) metal coordination : bond 0.00445 / 0.26 ( 12) metal coordination : angle 2.66674 / 1.20 ( 9) *********************** 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 144 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.6460 (m110) cc_final: 0.6141 (m110) REVERT: A 279 LYS cc_start: 0.8707 (mttt) cc_final: 0.8358 (mttp) REVERT: B 480 GLU cc_start: 0.7785 (tt0) cc_final: 0.7453 (tt0) REVERT: C 77 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8609 (ptt90) REVERT: C 89 GLU cc_start: 0.7408 (mp0) cc_final: 0.7022 (mp0) REVERT: C 109 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7073 (mp10) REVERT: C 196 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6530 (mt-10) REVERT: C 348 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7479 (mppt) REVERT: C 413 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7777 (mtmt) REVERT: C 427 LYS cc_start: 0.7445 (ttmt) cc_final: 0.7130 (tttm) outliers start: 19 outliers final: 10 residues processed: 139 average time/residue: 1.6444 time to fit residues: 242.7581 Evaluate side-chains 131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 278 SER Chi-restraints excluded: chain A residue 332 ARG 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 77 ARG Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 300 VAL 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 41 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.085589 restraints weight = 51867.671| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.79 r_work: 0.2803 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1308 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= 0.126 Angle : 0.483 5.176 16675 Z= 0.257 Chirality : 0.037 0.138 1901 Planarity : 0.004 0.059 1951 Dihedral : 13.013 73.613 2312 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.46 % Allowed : 16.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.23), residues: 1351 helix: 1.81 (0.23), residues: 530 sheet: -0.06 (0.40), residues: 145 loop : -0.05 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 176 TYR 0.016 0.001 TYR A 403 PHE 0.011 0.001 PHE C 44 TRP 0.008 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (12142) covalent geometry : angle 0.48006 / 0.26 (16666) hydrogen bonds : bond 0.04839 / 3.17 ( 514) hydrogen bonds : angle 4.55363 / 3.30 ( 1410) metal coordination : bond 0.00452 / 0.29 ( 12) metal coordination : angle 2.41032 / 1.06 ( 9) *********************** 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 141 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASN cc_start: 0.6587 (m110) cc_final: 0.6289 (m110) REVERT: B 53 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7399 (pptt) REVERT: B 480 GLU cc_start: 0.7849 (tt0) cc_final: 0.7529 (tt0) REVERT: C 77 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8699 (ptt90) REVERT: C 89 GLU cc_start: 0.7293 (mp0) cc_final: 0.7046 (mp0) REVERT: C 109 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7087 (mp10) REVERT: C 170 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6459 (mtpt) REVERT: C 196 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6570 (mt-10) REVERT: C 348 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7543 (mppt) outliers start: 17 outliers final: 10 residues processed: 136 average time/residue: 1.6328 time to fit residues: 234.9842 Evaluate side-chains 130 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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 386 ILE Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 77 ARG 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.0870 chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.086643 restraints weight = 48280.351| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.74 r_work: 0.2821 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12154 Z= 0.103 Angle : 0.468 5.141 16675 Z= 0.249 Chirality : 0.037 0.138 1901 Planarity : 0.004 0.055 1951 Dihedral : 12.893 73.530 2311 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.23), residues: 1351 helix: 1.89 (0.23), residues: 530 sheet: -0.10 (0.41), residues: 145 loop : -0.04 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 83 TYR 0.013 0.001 TYR A 403 PHE 0.010 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (12142) covalent geometry : angle 0.46610 / 0.25 (16666) hydrogen bonds : bond 0.04299 / 2.78 ( 514) hydrogen bonds : angle 4.43905 / 3.22 ( 1410) metal coordination : bond 0.00338 / 0.20 ( 12) metal coordination : angle 2.06818 / 0.91 ( 9) *********************** 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 133 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8700 (mttt) cc_final: 0.8353 (mttp) REVERT: B 480 GLU cc_start: 0.7833 (tt0) cc_final: 0.7465 (tt0) REVERT: C 77 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8648 (ptt90) REVERT: C 89 GLU cc_start: 0.7199 (mp0) cc_final: 0.6980 (mp0) REVERT: C 109 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7062 (mp10) REVERT: C 170 LYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6387 (mtpt) REVERT: C 196 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6563 (mt-10) REVERT: C 348 LYS cc_start: 0.8111 (mmtp) cc_final: 0.7461 (mppt) outliers start: 17 outliers final: 11 residues processed: 128 average time/residue: 1.6710 time to fit residues: 226.3858 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 : 0.660 ------------------------------------------------------------------------------- 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 42 SER 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 B residue 449 SER Chi-restraints excluded: chain C residue 77 ARG 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 301 SER Chi-restraints excluded: chain C residue 322 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 135 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 109 optimal weight: 0.3980 chunk 104 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.084208 restraints weight = 55835.757| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.86 r_work: 0.2777 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12154 Z= 0.159 Angle : 0.498 5.252 16675 Z= 0.266 Chirality : 0.038 0.136 1901 Planarity : 0.004 0.053 1951 Dihedral : 12.900 73.683 2310 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.14 % Allowed : 15.35 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.23), residues: 1351 helix: 1.83 (0.23), residues: 530 sheet: -0.14 (0.40), residues: 145 loop : -0.13 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 83 TYR 0.017 0.001 TYR A 403 PHE 0.014 0.001 PHE C 44 TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (12142) covalent geometry : angle 0.49478 / 0.27 (16666) hydrogen bonds : bond 0.04825 / 3.15 ( 514) hydrogen bonds : angle 4.48251 / 3.24 ( 1410) metal coordination : bond 0.00604 / 0.40 ( 12) metal coordination : angle 2.41365 / 1.08 ( 9) *********************** 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 141 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8719 (mttt) cc_final: 0.8372 (mttp) REVERT: A 323 ASP cc_start: 0.8224 (t0) cc_final: 0.7977 (t0) REVERT: B 53 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7602 (pptt) REVERT: B 480 GLU cc_start: 0.7885 (tt0) cc_final: 0.7546 (tt0) REVERT: C 89 GLU cc_start: 0.7287 (mp0) cc_final: 0.6983 (mp0) REVERT: C 109 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7081 (mp10) REVERT: C 170 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6623 (mtpp) REVERT: C 196 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: C 348 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7511 (mppt) outliers start: 25 outliers final: 14 residues processed: 136 average time/residue: 1.5660 time to fit residues: 226.3110 Evaluate side-chains 132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 332 ARG 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 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 301 SER Chi-restraints excluded: chain C residue 322 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.085186 restraints weight = 49809.588| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.72 r_work: 0.2800 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12154 Z= 0.129 Angle : 0.482 5.356 16675 Z= 0.256 Chirality : 0.037 0.140 1901 Planarity : 0.004 0.054 1951 Dihedral : 12.775 73.543 2306 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.23), residues: 1351 helix: 1.87 (0.23), residues: 530 sheet: -0.16 (0.40), residues: 145 loop : -0.13 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.014 0.001 TYR A 403 PHE 0.012 0.001 PHE C 44 TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (12142) covalent geometry : angle 0.47908 / 0.26 (16666) hydrogen bonds : bond 0.04523 / 2.93 ( 514) hydrogen bonds : angle 4.43134 / 3.21 ( 1410) metal coordination : bond 0.00525 / 0.32 ( 12) metal coordination : angle 2.25084 / 1.00 ( 9) *********************** 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: 19 poor density : 117 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8664 (mttt) cc_final: 0.8324 (mttp) REVERT: B 53 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7539 (pptt) REVERT: B 480 GLU cc_start: 0.7869 (tt0) cc_final: 0.7497 (tt0) REVERT: B 495 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7423 (tmmt) REVERT: C 89 GLU cc_start: 0.7283 (mp0) cc_final: 0.7011 (mp0) REVERT: C 109 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7066 (mp10) REVERT: C 170 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6671 (mtpp) REVERT: C 196 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6537 (mt-10) REVERT: C 348 LYS cc_start: 0.8152 (mmtp) cc_final: 0.7505 (mppt) outliers start: 19 outliers final: 13 residues processed: 132 average time/residue: 1.5702 time to fit residues: 220.2783 Evaluate side-chains 130 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 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 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 358 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.085423 restraints weight = 43987.842| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.65 r_work: 0.2802 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 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 = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1645 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= 0.147 Angle : 0.490 5.393 16675 Z= 0.262 Chirality : 0.038 0.138 1901 Planarity : 0.004 0.051 1951 Dihedral : 12.736 73.607 2302 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.54 % Allowed : 15.87 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.23), residues: 1351 helix: 1.85 (0.23), residues: 530 sheet: -0.15 (0.40), residues: 145 loop : -0.15 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 83 TYR 0.015 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (12142) covalent geometry : angle 0.48724 / 0.26 (16666) hydrogen bonds : bond 0.04647 / 3.03 ( 514) hydrogen bonds : angle 4.43838 / 3.21 ( 1410) metal coordination : bond 0.00554 / 0.36 ( 12) metal coordination : angle 2.35281 / 1.05 ( 9) *********************** 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 131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8667 (mttt) cc_final: 0.8390 (mttp) REVERT: B 53 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7533 (pptt) REVERT: B 480 GLU cc_start: 0.7876 (tt0) cc_final: 0.7531 (tt0) REVERT: C 89 GLU cc_start: 0.7290 (mp0) cc_final: 0.7029 (mp0) REVERT: C 109 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7070 (mp10) REVERT: C 170 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6752 (mtpp) REVERT: C 196 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6474 (mt-10) REVERT: C 348 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7501 (mppt) outliers start: 18 outliers final: 13 residues processed: 127 average time/residue: 1.6341 time to fit residues: 220.6253 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 : 0.596 ------------------------------------------------------------------------------- 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 B residue 449 SER 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 301 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.084051 restraints weight = 51262.758| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.78 r_work: 0.2777 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 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 = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1742 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= 0.172 Angle : 0.514 5.546 16675 Z= 0.275 Chirality : 0.038 0.136 1901 Planarity : 0.005 0.055 1951 Dihedral : 12.803 73.641 2302 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.37 % Allowed : 16.04 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1351 helix: 1.76 (0.23), residues: 530 sheet: -0.18 (0.40), residues: 145 loop : -0.20 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 83 TYR 0.016 0.002 TYR A 403 PHE 0.016 0.002 PHE C 44 TRP 0.009 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (12142) covalent geometry : angle 0.51037 / 0.27 (16666) hydrogen bonds : bond 0.04948 / 3.23 ( 514) hydrogen bonds : angle 4.50221 / 3.25 ( 1410) metal coordination : bond 0.00711 / 0.45 ( 12) metal coordination : angle 2.54156 / 1.16 ( 9) *********************** 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 132 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8679 (mttt) cc_final: 0.8399 (mttp) REVERT: B 53 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7568 (pptt) REVERT: B 480 GLU cc_start: 0.7932 (tt0) cc_final: 0.7611 (tt0) REVERT: C 89 GLU cc_start: 0.7274 (mp0) cc_final: 0.6999 (mp0) REVERT: C 109 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7093 (mp10) REVERT: C 170 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6939 (mtpt) REVERT: C 196 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6488 (mt-10) REVERT: C 348 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7522 (mppt) outliers start: 16 outliers final: 13 residues processed: 128 average time/residue: 1.6888 time to fit residues: 229.8471 Evaluate side-chains 130 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 B residue 449 SER 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 301 SER Chi-restraints excluded: chain C residue 322 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 0.0000 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.083976 restraints weight = 50530.615| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.78 r_work: 0.2776 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 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 = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1781 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= 0.177 Angle : 0.516 5.687 16675 Z= 0.276 Chirality : 0.039 0.138 1901 Planarity : 0.005 0.051 1951 Dihedral : 12.825 73.574 2302 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.37 % Allowed : 16.12 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.22), residues: 1351 helix: 1.71 (0.23), residues: 530 sheet: -0.22 (0.39), residues: 145 loop : -0.24 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 83 TYR 0.016 0.002 TYR A 403 PHE 0.016 0.002 PHE C 44 TRP 0.009 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (12142) covalent geometry : angle 0.51315 / 0.28 (16666) hydrogen bonds : bond 0.05009 / 3.27 ( 514) hydrogen bonds : angle 4.52412 / 3.26 ( 1410) metal coordination : bond 0.00740 / 0.46 ( 12) metal coordination : angle 2.55341 / 1.14 ( 9) *********************** 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: 16 poor density : 115 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8681 (mttt) cc_final: 0.8405 (mttp) REVERT: A 323 ASP cc_start: 0.8335 (t70) cc_final: 0.8059 (t0) REVERT: B 53 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7542 (pptt) REVERT: B 480 GLU cc_start: 0.7940 (tt0) cc_final: 0.7641 (tt0) REVERT: C 89 GLU cc_start: 0.7244 (mp0) cc_final: 0.6981 (mp0) REVERT: C 109 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7089 (mp10) REVERT: C 170 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7082 (mtpt) REVERT: C 196 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: C 348 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7528 (mppt) outliers start: 16 outliers final: 12 residues processed: 127 average time/residue: 1.6723 time to fit residues: 225.2130 Evaluate side-chains 131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 B residue 449 SER 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 301 SER Chi-restraints excluded: chain C residue 322 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.085868 restraints weight = 41912.151| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.62 r_work: 0.2813 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 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 = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1808 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= 0.120 Angle : 0.482 5.663 16675 Z= 0.257 Chirality : 0.037 0.140 1901 Planarity : 0.004 0.060 1951 Dihedral : 12.740 73.526 2302 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.11 % Allowed : 16.38 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.23), residues: 1351 helix: 1.83 (0.23), residues: 530 sheet: -0.17 (0.40), residues: 145 loop : -0.15 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 83 TYR 0.014 0.001 TYR A 403 PHE 0.011 0.001 PHE C 44 TRP 0.008 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12142) covalent geometry : angle 0.47872 / 0.26 (16666) hydrogen bonds : bond 0.04459 / 2.88 ( 514) hydrogen bonds : angle 4.41742 / 3.20 ( 1410) metal coordination : bond 0.00531 / 0.33 ( 12) metal coordination : angle 2.33047 / 1.04 ( 9) ********************** 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 131 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8672 (mttt) cc_final: 0.8336 (mttp) REVERT: A 323 ASP cc_start: 0.8187 (t70) cc_final: 0.7974 (t0) REVERT: B 480 GLU cc_start: 0.7895 (tt0) cc_final: 0.7594 (tt0) REVERT: C 89 GLU cc_start: 0.7235 (mp0) cc_final: 0.6990 (mp0) REVERT: C 109 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7067 (mp10) REVERT: C 170 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7061 (mtpp) REVERT: C 196 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6502 (mt-10) REVERT: C 348 LYS cc_start: 0.8169 (mmtp) cc_final: 0.7567 (mppt) outliers start: 13 outliers final: 10 residues processed: 127 average time/residue: 1.6131 time to fit residues: 217.7177 Evaluate side-chains 125 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR 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 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 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.086431 restraints weight = 45664.022| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.70 r_work: 0.2821 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 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 = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1840 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= 0.105 Angle : 0.465 5.585 16675 Z= 0.247 Chirality : 0.037 0.138 1901 Planarity : 0.004 0.057 1951 Dihedral : 12.629 73.525 2302 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.03 % Allowed : 16.55 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1351 helix: 1.94 (0.23), residues: 530 sheet: -0.14 (0.40), residues: 145 loop : -0.11 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 83 TYR 0.013 0.001 TYR A 403 PHE 0.009 0.001 PHE C 175 TRP 0.008 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (12142) covalent geometry : angle 0.46285 / 0.25 (16666) hydrogen bonds : bond 0.04133 / 2.66 ( 514) hydrogen bonds : angle 4.31428 / 3.13 ( 1410) metal coordination : bond 0.00460 / 0.32 ( 12) metal coordination : angle 2.14592 / 0.96 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8870.42 seconds wall clock time: 150 minutes 20.88 seconds (9020.88 seconds total)