Starting phenix.real_space_refine on Sat Jul 4 16:47:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pt2_17866/07_2026/8pt2_17866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pt2_17866/07_2026/8pt2_17866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pt2_17866/07_2026/8pt2_17866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pt2_17866/07_2026/8pt2_17866.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8pt2_17866/07_2026/8pt2_17866.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pt2_17866/07_2026/8pt2_17866.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pt2_17866/07_2026/8pt2_17866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pt2_17866/07_2026/8pt2_17866.map" } resolution = 2.59 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= 0.001 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 27 5.49 5 S 63 5.16 5 C 6950 2.51 5 N 1972 2.21 5 O 2175 1.98 5 H 10901 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: 22091 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 7900 Classifications: {'peptide': 512} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 490} Chain breaks: 1 Chain: "C" Number of atoms: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6676 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 22, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 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: "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: "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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 46.153 53.513 18.541 1.00 47.15 S ATOM 4473 SG CYS A 282 43.740 52.013 15.789 1.00 59.75 S ATOM 18156 SG CYS C 233 22.092 62.596 107.997 1.00 74.16 S ATOM 18180 SG CYS C 235 22.631 64.040 104.434 1.00 71.02 S ATOM 16822 SG CYS C 146 10.935 72.545 88.479 1.00 81.71 S ATOM 17010 SG CYS C 159 11.925 75.602 90.433 1.00 89.66 S ATOM 17066 SG CYS C 163 14.226 72.636 90.449 1.00 72.58 S ATOM 17076 SG CYS C 164 13.852 74.746 87.284 1.00 73.55 S Time building chain proxies: 3.68, per 1000 atoms: 0.17 Number of scatterers: 22091 At special positions: 0 Unit cell: (92.4, 110.88, 125.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 27 15.00 O 2175 8.00 N 1972 7.00 C 6950 6.00 H 10901 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: 2.04 Conformation dependent library (CDL) restraints added in 562.4 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 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " Number of angles added : 9 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 15 sheets defined 42.1% alpha, 14.2% beta 6 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.515A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.431A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.893A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.565A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 66 through 70 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: 3.654A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.590A 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 216 through 221 removed outlier: 3.552A pdb=" N ILE B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.612A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.733A 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 356 through 372 Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.563A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.069A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.773A pdb=" N VAL C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 281 through 289 Processing helix chain 'C' and resid 303 through 317 removed outlier: 4.168A pdb=" N ARG C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.762A pdb=" N LEU C 354 " --> pdb=" O ASN C 350 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 376 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: 6.726A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.414A 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 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: 6.314A 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: 6.314A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.737A 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: 4.220A 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 80 Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 159 removed outlier: 7.100A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=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: 6.848A 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: 6.669A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 2.76 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: 10869 1.03 - 1.23: 43 1.23 - 1.42: 4830 1.42 - 1.62: 6544 1.62 - 1.81: 86 Bond restraints: 22372 Sorted by residual: bond pdb=" C LEU B 167 " pdb=" O LEU B 167 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.19e-02 7.06e+03 4.71e-01 bond pdb=" CB LYS C 352 " pdb=" CG LYS C 352 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.34e-01 bond pdb=" CB GLU C 181 " pdb=" CG GLU C 181 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.19e-01 bond pdb=" CG PRO C 252 " pdb=" CD PRO C 252 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.96e-01 bond pdb=" CG PRO B 502 " pdb=" CD PRO B 502 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.68e-01 ... (remaining 22367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 36391 0.83 - 1.65: 3643 1.65 - 2.48: 245 2.48 - 3.31: 99 3.31 - 4.13: 30 Bond angle restraints: 40408 Sorted by residual: angle pdb=" N LYS C 199 " pdb=" CA LYS C 199 " pdb=" C LYS C 199 " ideal model delta sigma weight residual 114.09 111.09 3.00 1.55e+00 4.16e-01 3.75e+00 angle pdb=" CG ARG B 487 " pdb=" CD ARG B 487 " pdb=" NE ARG B 487 " ideal model delta sigma weight residual 112.00 116.13 -4.13 2.20e+00 2.07e-01 3.53e+00 angle pdb=" CG ARG A 154 " pdb=" CD ARG A 154 " pdb=" NE ARG A 154 " ideal model delta sigma weight residual 112.00 115.79 -3.79 2.20e+00 2.07e-01 2.96e+00 angle pdb=" CD ARG B 487 " pdb=" NE ARG B 487 " pdb=" CZ ARG B 487 " ideal model delta sigma weight residual 124.40 126.76 -2.36 1.40e+00 5.10e-01 2.84e+00 angle pdb=" CG LYS A 147 " pdb=" CD LYS A 147 " pdb=" CE LYS A 147 " ideal model delta sigma weight residual 111.30 115.17 -3.87 2.30e+00 1.89e-01 2.83e+00 ... (remaining 40403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9331 17.98 - 35.95: 777 35.95 - 53.93: 291 53.93 - 71.90: 81 71.90 - 89.88: 31 Dihedral angle restraints: 10511 sinusoidal: 5931 harmonic: 4580 Sorted by residual: dihedral pdb=" CG ARG B 487 " pdb=" CD ARG B 487 " pdb=" NE ARG B 487 " pdb=" CZ ARG B 487 " ideal model delta sinusoidal sigma weight residual -90.00 -39.92 -50.08 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CB GLU C 115 " pdb=" CG GLU C 115 " pdb=" CD GLU C 115 " pdb=" OE1 GLU C 115 " ideal model delta sinusoidal sigma weight residual 0.00 -89.88 89.88 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 63 " pdb=" CD ARG B 63 " pdb=" NE ARG B 63 " pdb=" CZ ARG B 63 " ideal model delta sinusoidal sigma weight residual 90.00 134.84 -44.84 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 10508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1082 0.025 - 0.051: 480 0.051 - 0.076: 102 0.076 - 0.102: 49 0.102 - 0.127: 52 Chirality restraints: 1765 Sorted by residual: chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 253 " pdb=" N ILE B 253 " pdb=" C ILE B 253 " pdb=" CB ILE B 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1762 not shown) Planarity restraints: 3219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 487 " 0.150 9.50e-02 1.11e+02 5.03e-02 3.04e+00 pdb=" NE ARG B 487 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 487 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 487 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 487 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 487 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG B 487 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 487 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 487 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 501 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO B 502 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 217 " -0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A 218 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.020 5.00e-02 4.00e+02 ... (remaining 3216 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1319 2.19 - 2.80: 44023 2.80 - 3.40: 60985 3.40 - 4.00: 82553 4.00 - 4.60: 125729 Nonbonded interactions: 314609 Sorted by model distance: nonbonded pdb=" OD1 ASN B 397 " pdb=" HG1 THR B 399 " model vdw 1.593 2.450 nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.598 2.450 nonbonded pdb=" H GLY A 239 " pdb=" O ALA A 251 " model vdw 1.628 2.450 nonbonded pdb=" O ALA C 330 " pdb=" HG1 THR C 334 " model vdw 1.662 2.450 nonbonded pdb="HH21 ARG B 145 " pdb="HH11 ARG B 155 " model vdw 1.663 2.100 ... (remaining 314604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 1.690 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: 0.150 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 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 : 0.002 0.028 11483 Z= 0.096 Angle : 0.447 4.134 15638 Z= 0.232 Chirality : 0.036 0.127 1765 Planarity : 0.004 0.065 1918 Dihedral : 17.358 89.878 4414 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.37 % Allowed : 18.13 % Favored : 80.50 % 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: 1.25 (0.23), residues: 1345 helix: 2.08 (0.24), residues: 528 sheet: -0.54 (0.42), residues: 130 loop : 0.20 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 487 TYR 0.010 0.001 TYR A 403 PHE 0.010 0.001 PHE C 175 TRP 0.004 0.001 TRP C 263 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (11471) covalent geometry : angle 0.44567 / 0.23 (15629) hydrogen bonds : bond 0.12071 / 7.64 ( 490) hydrogen bonds : angle 5.35624 / 3.82 ( 1374) metal coordination : bond 0.00242 / 0.12 ( 12) metal coordination : angle 1.42684 / 0.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.605 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 15 residues processed: 124 average time/residue: 1.5939 time to fit residues: 211.0460 Evaluate side-chains 124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.084079 restraints weight = 39544.529| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.79 r_work: 0.2819 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.0479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11483 Z= 0.124 Angle : 0.471 3.927 15638 Z= 0.247 Chirality : 0.037 0.134 1765 Planarity : 0.004 0.039 1918 Dihedral : 10.321 77.706 1867 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.63 % Allowed : 17.01 % Favored : 81.36 % 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: 1.27 (0.23), residues: 1345 helix: 2.21 (0.23), residues: 525 sheet: -0.48 (0.41), residues: 128 loop : 0.10 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 487 TYR 0.014 0.001 TYR A 403 PHE 0.013 0.001 PHE C 175 TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11471) covalent geometry : angle 0.46934 / 0.25 (15629) hydrogen bonds : bond 0.04258 / 2.67 ( 490) hydrogen bonds : angle 4.33900 / 3.18 ( 1374) metal coordination : bond 0.00352 / 0.18 ( 12) metal coordination : angle 1.48812 / 0.75 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 92 VAL cc_start: 0.7895 (p) cc_final: 0.7694 (m) REVERT: B 155 ARG cc_start: 0.6368 (mpp80) cc_final: 0.6094 (mpp80) outliers start: 19 outliers final: 14 residues processed: 125 average time/residue: 1.5169 time to fit residues: 203.1289 Evaluate side-chains 121 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 301 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 19 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 44 ASN B 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.083681 restraints weight = 39784.281| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.79 r_work: 0.2807 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11483 Z= 0.147 Angle : 0.484 4.022 15638 Z= 0.254 Chirality : 0.038 0.133 1765 Planarity : 0.004 0.043 1918 Dihedral : 10.163 81.799 1857 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.15 % Allowed : 16.07 % Favored : 81.79 % 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: 1.11 (0.23), residues: 1345 helix: 1.99 (0.23), residues: 533 sheet: -0.48 (0.41), residues: 128 loop : 0.04 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 487 TYR 0.014 0.001 TYR A 403 PHE 0.015 0.001 PHE C 175 TRP 0.005 0.001 TRP C 263 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11471) covalent geometry : angle 0.48225 / 0.25 (15629) hydrogen bonds : bond 0.04387 / 2.75 ( 490) hydrogen bonds : angle 4.23444 / 3.10 ( 1374) metal coordination : bond 0.00584 / 0.32 ( 12) metal coordination : angle 1.72549 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 108 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8683 (tt) outliers start: 25 outliers final: 17 residues processed: 135 average time/residue: 1.3743 time to fit residues: 198.9245 Evaluate side-chains 126 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 301 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.082779 restraints weight = 39867.877| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.77 r_work: 0.2800 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11483 Z= 0.158 Angle : 0.496 4.557 15638 Z= 0.260 Chirality : 0.038 0.135 1765 Planarity : 0.004 0.046 1918 Dihedral : 10.169 84.594 1855 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.15 % Allowed : 16.58 % Favored : 81.27 % 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: 1.04 (0.23), residues: 1345 helix: 1.90 (0.23), residues: 534 sheet: -0.51 (0.41), residues: 128 loop : 0.03 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 487 TYR 0.014 0.001 TYR A 403 PHE 0.015 0.001 PHE C 175 TRP 0.005 0.001 TRP C 263 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (11471) covalent geometry : angle 0.49402 / 0.26 (15629) hydrogen bonds : bond 0.04417 / 2.77 ( 490) hydrogen bonds : angle 4.23100 / 3.10 ( 1374) metal coordination : bond 0.00604 / 0.33 ( 12) metal coordination : angle 1.74285 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.7941 (p) cc_final: 0.7724 (m) REVERT: B 148 GLU cc_start: 0.8075 (tt0) cc_final: 0.7548 (mt-10) REVERT: C 108 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8729 (tt) REVERT: C 356 SER cc_start: 0.8079 (OUTLIER) cc_final: 0.7844 (t) outliers start: 25 outliers final: 15 residues processed: 131 average time/residue: 1.4015 time to fit residues: 197.0791 Evaluate side-chains 126 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 131 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.082326 restraints weight = 39626.611| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.76 r_work: 0.2786 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11483 Z= 0.184 Angle : 0.516 4.185 15638 Z= 0.272 Chirality : 0.039 0.137 1765 Planarity : 0.004 0.047 1918 Dihedral : 10.134 86.835 1852 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.32 % Allowed : 16.41 % Favored : 81.27 % 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 (0.22), residues: 1345 helix: 1.82 (0.23), residues: 527 sheet: -0.48 (0.42), residues: 128 loop : -0.07 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 487 TYR 0.015 0.001 TYR A 403 PHE 0.016 0.001 PHE C 175 TRP 0.006 0.001 TRP C 263 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (11471) covalent geometry : angle 0.51378 / 0.27 (15629) hydrogen bonds : bond 0.04706 / 2.95 ( 490) hydrogen bonds : angle 4.28392 / 3.14 ( 1374) metal coordination : bond 0.00728 / 0.43 ( 12) metal coordination : angle 1.88222 / 0.96 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7693 (mmt90) REVERT: B 148 GLU cc_start: 0.8091 (tt0) cc_final: 0.7583 (mt-10) REVERT: C 356 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7887 (t) REVERT: C 389 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7687 (mpt-90) outliers start: 27 outliers final: 20 residues processed: 134 average time/residue: 1.3516 time to fit residues: 193.9359 Evaluate side-chains 133 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 389 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.081755 restraints weight = 39073.904| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.74 r_work: 0.2775 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11483 Z= 0.200 Angle : 0.531 4.222 15638 Z= 0.281 Chirality : 0.039 0.139 1765 Planarity : 0.005 0.047 1918 Dihedral : 10.209 88.267 1852 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.58 % Allowed : 16.49 % Favored : 80.93 % 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: 0.74 (0.22), residues: 1345 helix: 1.67 (0.22), residues: 534 sheet: -0.53 (0.41), residues: 128 loop : -0.19 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 487 TYR 0.015 0.001 TYR A 403 PHE 0.017 0.001 PHE C 175 TRP 0.007 0.001 TRP C 263 HIS 0.006 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (11471) covalent geometry : angle 0.52922 / 0.28 (15629) hydrogen bonds : bond 0.04838 / 3.04 ( 490) hydrogen bonds : angle 4.32992 / 3.17 ( 1374) metal coordination : bond 0.00802 / 0.46 ( 12) metal coordination : angle 1.90533 / 0.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.7881 (p) cc_final: 0.7680 (m) REVERT: A 141 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7723 (mmt90) REVERT: B 148 GLU cc_start: 0.8067 (tt0) cc_final: 0.7582 (mt-10) REVERT: C 110 ASP cc_start: 0.7200 (m-30) cc_final: 0.6922 (m-30) REVERT: C 356 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7917 (t) REVERT: C 389 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7689 (mpt-90) outliers start: 30 outliers final: 22 residues processed: 130 average time/residue: 1.4786 time to fit residues: 206.0829 Evaluate side-chains 131 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 389 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.082510 restraints weight = 38675.685| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.73 r_work: 0.2787 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11483 Z= 0.165 Angle : 0.506 4.137 15638 Z= 0.267 Chirality : 0.038 0.137 1765 Planarity : 0.004 0.052 1918 Dihedral : 10.186 87.894 1852 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.41 % Allowed : 16.84 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1345 helix: 1.77 (0.22), residues: 533 sheet: -0.47 (0.42), residues: 128 loop : -0.18 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 487 TYR 0.014 0.001 TYR A 403 PHE 0.015 0.001 PHE C 175 TRP 0.006 0.001 TRP C 263 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (11471) covalent geometry : angle 0.50438 / 0.27 (15629) hydrogen bonds : bond 0.04507 / 2.82 ( 490) hydrogen bonds : angle 4.25152 / 3.11 ( 1374) metal coordination : bond 0.00589 / 0.31 ( 12) metal coordination : angle 1.76721 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7708 (mmt90) REVERT: B 148 GLU cc_start: 0.8070 (tt0) cc_final: 0.7600 (mt-10) REVERT: C 108 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8722 (tt) REVERT: C 110 ASP cc_start: 0.7144 (m-30) cc_final: 0.6935 (m-30) REVERT: C 356 SER cc_start: 0.8170 (OUTLIER) cc_final: 0.7914 (t) REVERT: C 389 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7711 (mpt-90) outliers start: 28 outliers final: 20 residues processed: 129 average time/residue: 1.5597 time to fit residues: 215.1394 Evaluate side-chains 131 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 389 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 1.9990 chunk 129 optimal weight: 0.0980 chunk 107 optimal weight: 0.0060 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.084976 restraints weight = 39449.911| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.76 r_work: 0.2830 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11483 Z= 0.091 Angle : 0.464 5.940 15638 Z= 0.241 Chirality : 0.037 0.136 1765 Planarity : 0.004 0.061 1918 Dihedral : 10.012 85.907 1852 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.29 % Allowed : 18.21 % Favored : 80.50 % 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: 1.20 (0.23), residues: 1345 helix: 2.15 (0.23), residues: 527 sheet: -0.32 (0.43), residues: 126 loop : 0.01 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 487 TYR 0.011 0.001 TYR A 403 PHE 0.009 0.001 PHE C 175 TRP 0.006 0.001 TRP C 239 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (11471) covalent geometry : angle 0.46238 / 0.24 (15629) hydrogen bonds : bond 0.03571 / 2.22 ( 490) hydrogen bonds : angle 4.02685 / 2.96 ( 1374) metal coordination : bond 0.00347 / 0.23 ( 12) metal coordination : angle 1.42191 / 0.70 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.7876 (p) cc_final: 0.7661 (m) REVERT: B 148 GLU cc_start: 0.8063 (tt0) cc_final: 0.7593 (mt-10) REVERT: C 108 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8722 (tt) REVERT: C 110 ASP cc_start: 0.7176 (m-30) cc_final: 0.6940 (m-30) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 1.5004 time to fit residues: 203.5084 Evaluate side-chains 124 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 151 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 6 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.083499 restraints weight = 39512.668| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.77 r_work: 0.2807 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11483 Z= 0.133 Angle : 0.482 5.756 15638 Z= 0.252 Chirality : 0.037 0.137 1765 Planarity : 0.004 0.059 1918 Dihedral : 9.888 86.916 1848 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.55 % Allowed : 17.96 % Favored : 80.50 % 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: 1.08 (0.23), residues: 1345 helix: 1.97 (0.23), residues: 534 sheet: -0.19 (0.40), residues: 148 loop : -0.04 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 487 TYR 0.013 0.001 TYR A 403 PHE 0.014 0.001 PHE C 175 TRP 0.005 0.001 TRP C 263 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (11471) covalent geometry : angle 0.48106 / 0.25 (15629) hydrogen bonds : bond 0.04052 / 2.53 ( 490) hydrogen bonds : angle 4.09141 / 3.01 ( 1374) metal coordination : bond 0.00461 / 0.24 ( 12) metal coordination : angle 1.57277 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.7843 (p) cc_final: 0.7630 (m) REVERT: A 141 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7683 (mmt90) REVERT: B 148 GLU cc_start: 0.8055 (tt0) cc_final: 0.7597 (mt-10) REVERT: C 83 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7426 (mtm-85) REVERT: C 108 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8744 (tt) REVERT: C 110 ASP cc_start: 0.7199 (m-30) cc_final: 0.6960 (m-30) outliers start: 18 outliers final: 14 residues processed: 124 average time/residue: 1.4875 time to fit residues: 196.8518 Evaluate side-chains 125 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 151 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 119 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 0.0030 chunk 98 optimal weight: 0.3980 chunk 127 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.085574 restraints weight = 39565.395| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.76 r_work: 0.2841 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11483 Z= 0.090 Angle : 0.456 6.242 15638 Z= 0.236 Chirality : 0.037 0.136 1765 Planarity : 0.004 0.066 1918 Dihedral : 9.766 85.564 1848 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.86 % Allowed : 18.81 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.30 (0.23), residues: 1345 helix: 2.17 (0.23), residues: 534 sheet: -0.10 (0.40), residues: 146 loop : 0.08 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 487 TYR 0.011 0.001 TYR A 403 PHE 0.009 0.001 PHE C 175 TRP 0.006 0.001 TRP C 239 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (11471) covalent geometry : angle 0.45529 / 0.24 (15629) hydrogen bonds : bond 0.03426 / 2.13 ( 490) hydrogen bonds : angle 3.93977 / 2.91 ( 1374) metal coordination : bond 0.00288 / 0.17 ( 12) metal coordination : angle 1.34687 / 0.67 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 148 GLU cc_start: 0.8052 (tt0) cc_final: 0.7591 (mt-10) REVERT: C 108 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8725 (tt) REVERT: C 110 ASP cc_start: 0.7144 (m-30) cc_final: 0.6902 (m-30) outliers start: 10 outliers final: 8 residues processed: 118 average time/residue: 1.5834 time to fit residues: 199.6250 Evaluate side-chains 117 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 33 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.084237 restraints weight = 38906.174| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.78 r_work: 0.2816 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11483 Z= 0.118 Angle : 0.471 5.069 15638 Z= 0.245 Chirality : 0.037 0.137 1765 Planarity : 0.004 0.062 1918 Dihedral : 9.784 86.554 1846 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.12 % Allowed : 18.64 % Favored : 80.24 % 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: 1.18 (0.23), residues: 1345 helix: 2.07 (0.23), residues: 534 sheet: -0.17 (0.41), residues: 148 loop : 0.01 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 487 TYR 0.013 0.001 TYR A 403 PHE 0.013 0.001 PHE C 175 TRP 0.005 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11471) covalent geometry : angle 0.46984 / 0.25 (15629) hydrogen bonds : bond 0.03810 / 2.37 ( 490) hydrogen bonds : angle 4.00324 / 2.94 ( 1374) metal coordination : bond 0.00377 / 0.19 ( 12) metal coordination : angle 1.48344 / 0.74 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6944.33 seconds wall clock time: 118 minutes 12.36 seconds (7092.36 seconds total)