Starting phenix.real_space_refine on Wed Mar 12 08:57:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sda_40350/03_2025/8sda_40350.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sda_40350/03_2025/8sda_40350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sda_40350/03_2025/8sda_40350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sda_40350/03_2025/8sda_40350.map" model { file = "/net/cci-nas-00/data/ceres_data/8sda_40350/03_2025/8sda_40350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sda_40350/03_2025/8sda_40350.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 7 5.49 5 S 36 5.16 5 C 4963 2.51 5 N 1117 2.21 5 O 1287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7414 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1825 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1823 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1744 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1749 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {' K': 3, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' K': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 5.69, per 1000 atoms: 0.77 Number of scatterers: 7414 At special positions: 0 Unit cell: (96.28, 96.28, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 36 16.00 P 7 15.00 O 1287 8.00 N 1117 7.00 C 4963 6.00 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.709A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 4.047A pdb=" N THR A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 247 removed outlier: 3.682A pdb=" N VAL A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.569A pdb=" N PHE A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 276 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 323 through 350 Processing helix chain 'A' and resid 359 through 373 removed outlier: 4.173A pdb=" N TRP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.694A pdb=" N ILE A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 428 removed outlier: 3.567A pdb=" N ILE A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.521A pdb=" N LYS B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 224 through 247 Processing helix chain 'B' and resid 250 through 256 removed outlier: 3.560A pdb=" N PHE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 276 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 300 through 308 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 323 through 349 removed outlier: 3.520A pdb=" N LEU B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 372 removed outlier: 4.157A pdb=" N TRP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 400 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.735A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 181 through 206 removed outlier: 4.002A pdb=" N THR D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 250 through 256 removed outlier: 3.596A pdb=" N GLY D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 275 Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 289 through 299 Processing helix chain 'D' and resid 300 through 308 Processing helix chain 'D' and resid 310 through 349 removed outlier: 4.220A pdb=" N ARG D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 372 removed outlier: 4.113A pdb=" N TRP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 403 removed outlier: 3.692A pdb=" N ALA D 402 " --> pdb=" O VAL D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 427 removed outlier: 4.368A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 224 through 247 removed outlier: 3.858A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 247 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 256 removed outlier: 4.013A pdb=" N PHE C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 276 removed outlier: 3.740A pdb=" N ILE C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 300 through 308 Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.524A pdb=" N GLN C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 349 removed outlier: 3.585A pdb=" N GLY C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 372 removed outlier: 4.116A pdb=" N TRP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TRP C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 372 " --> pdb=" O THR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 403 Processing helix chain 'C' and resid 403 through 427 removed outlier: 4.594A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1107 1.30 - 1.43: 1874 1.43 - 1.56: 4478 1.56 - 1.68: 26 1.68 - 1.81: 65 Bond restraints: 7550 Sorted by residual: bond pdb=" C21 POV D 602 " pdb=" O21 POV D 602 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C21 POV A 603 " pdb=" O21 POV A 603 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C21 POV A 604 " pdb=" O21 POV A 604 " ideal model delta sigma weight residual 1.330 1.457 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C31 POV A 606 " pdb=" O31 POV A 606 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 POV C 603 " pdb=" O21 POV C 603 " ideal model delta sigma weight residual 1.330 1.444 -0.114 2.00e-02 2.50e+03 3.27e+01 ... (remaining 7545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 9903 2.55 - 5.11: 218 5.11 - 7.66: 67 7.66 - 10.22: 32 10.22 - 12.77: 15 Bond angle restraints: 10235 Sorted by residual: angle pdb=" O13 POV A 601 " pdb=" P POV A 601 " pdb=" O14 POV A 601 " ideal model delta sigma weight residual 121.11 108.34 12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" O11 POV A 602 " pdb=" P POV A 602 " pdb=" O12 POV A 602 " ideal model delta sigma weight residual 97.67 109.76 -12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" O13 POV B 602 " pdb=" P POV B 602 " pdb=" O14 POV B 602 " ideal model delta sigma weight residual 121.11 109.07 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O11 POV D 601 " pdb=" P POV D 601 " pdb=" O12 POV D 601 " ideal model delta sigma weight residual 97.67 109.48 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O11 POV C 602 " pdb=" P POV C 602 " pdb=" O12 POV C 602 " ideal model delta sigma weight residual 97.67 109.43 -11.76 3.00e+00 1.11e-01 1.54e+01 ... (remaining 10230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 4212 26.14 - 52.27: 221 52.27 - 78.41: 33 78.41 - 104.54: 9 104.54 - 130.68: 1 Dihedral angle restraints: 4476 sinusoidal: 1731 harmonic: 2745 Sorted by residual: dihedral pdb=" C3 POV A 601 " pdb=" C31 POV A 601 " pdb=" O31 POV A 601 " pdb=" C32 POV A 601 " ideal model delta sinusoidal sigma weight residual 172.61 41.93 130.68 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CB GLU A 239 " pdb=" CG GLU A 239 " pdb=" CD GLU A 239 " pdb=" OE1 GLU A 239 " ideal model delta sinusoidal sigma weight residual 0.00 -83.23 83.23 1 3.00e+01 1.11e-03 9.41e+00 dihedral pdb=" CA GLU B 349 " pdb=" CB GLU B 349 " pdb=" CG GLU B 349 " pdb=" CD GLU B 349 " ideal model delta sinusoidal sigma weight residual 60.00 115.59 -55.59 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 4473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 996 0.051 - 0.103: 215 0.103 - 0.154: 27 0.154 - 0.205: 5 0.205 - 0.257: 2 Chirality restraints: 1245 Sorted by residual: chirality pdb=" CG LEU D 327 " pdb=" CB LEU D 327 " pdb=" CD1 LEU D 327 " pdb=" CD2 LEU D 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU C 225 " pdb=" N LEU C 225 " pdb=" C LEU C 225 " pdb=" CB LEU C 225 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA HIS C 227 " pdb=" N HIS C 227 " pdb=" C HIS C 227 " pdb=" CB HIS C 227 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 1242 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 406 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C PRO B 406 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO B 406 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 407 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 397 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C GLY D 397 " 0.052 2.00e-02 2.50e+03 pdb=" O GLY D 397 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL D 398 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 207 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 208 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.025 5.00e-02 4.00e+02 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.81: 2086 2.81 - 3.39: 9155 3.39 - 3.97: 13853 3.97 - 4.56: 19809 4.56 - 5.14: 27639 Nonbonded interactions: 72542 Sorted by model distance: nonbonded pdb=" O THR B 319 " pdb=" OG SER B 323 " model vdw 2.225 3.040 nonbonded pdb=" O ILE D 407 " pdb=" ND2 ASN D 411 " model vdw 2.280 3.120 nonbonded pdb=" O TYR A 376 " pdb=" K K A 609 " model vdw 2.320 2.850 nonbonded pdb=" O THR C 372 " pdb=" OG1 THR C 373 " model vdw 2.327 3.040 nonbonded pdb=" O THR A 372 " pdb=" OG1 THR A 373 " model vdw 2.355 3.040 ... (remaining 72537 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 'A' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 211 or resid 224 through 228 or (resid 229 \ through 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 250 or (resid 251 through 252 and (name N or name CA or name C or name \ O or name CB )) or resid 253 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 or resid 288 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or \ resid 319 through 321 or (resid 322 and (name N or name CA or name C or name O \ or name CB )) or resid 323 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throu \ gh 419 or (resid 420 through 427 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'B' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 211 or resid 224 through 228 or (resid 229 \ through 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 250 or (resid 251 through 252 and (name N or name CA or name C or name \ O or name CB )) or resid 253 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 or resid 288 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or \ resid 323 through 325 or (resid 326 and (name N or name CA or name C or name O \ or name CB )) or resid 327 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throu \ gh 419 or (resid 420 through 427 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'C' and (resid 172 through 211 or resid 224 through 228 or (resid 229 thr \ ough 230 and (name N or name CA or name C or name O or name CB )) or resid 231 t \ hrough 273 or (resid 274 and (name N or name CA or name C or name O or name CB ) \ ) or resid 275 or resid 288 through 409 or (resid 410 and (name N or name CA or \ name C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 427)) selection = (chain 'D' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 175 or (resid 176 through 177 and (name N o \ r name CA or name C or name O or name CB )) or resid 178 through 308 or (resid 3 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 310 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or r \ esid 319 through 427)) } 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: 1.450 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 21.140 Find NCS groups from input model: 0.340 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.008 0.128 7550 Z= 0.507 Angle : 1.113 12.774 10235 Z= 0.501 Chirality : 0.043 0.257 1245 Planarity : 0.005 0.045 1217 Dihedral : 15.987 130.675 2686 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.29), residues: 915 helix: 1.30 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 0.42 (0.53), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 172 HIS 0.004 0.001 HIS C 227 PHE 0.011 0.001 PHE A 194 TYR 0.017 0.001 TYR C 416 ARG 0.009 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.735 Fit side-chains REVERT: D 298 MET cc_start: 0.7594 (ttm) cc_final: 0.6911 (tmm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2417 time to fit residues: 53.3253 Evaluate side-chains 123 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 309 HIS D 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.156259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121989 restraints weight = 9933.762| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.95 r_work: 0.3255 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7550 Z= 0.254 Angle : 0.582 8.468 10235 Z= 0.296 Chirality : 0.040 0.144 1245 Planarity : 0.004 0.033 1217 Dihedral : 13.059 107.386 1160 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.04 % Allowed : 10.85 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.29), residues: 915 helix: 1.81 (0.20), residues: 758 sheet: None (None), residues: 0 loop : 0.43 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 365 HIS 0.004 0.001 HIS B 309 PHE 0.027 0.001 PHE B 415 TYR 0.018 0.001 TYR D 269 ARG 0.004 0.001 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8466 (tp30) cc_final: 0.8247 (tp30) REVERT: B 322 ARG cc_start: 0.8409 (tmm-80) cc_final: 0.8128 (ttp80) REVERT: B 372 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9118 (p) REVERT: D 298 MET cc_start: 0.7820 (ttm) cc_final: 0.7074 (tmm) REVERT: C 414 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8518 (tm-30) outliers start: 15 outliers final: 8 residues processed: 163 average time/residue: 0.2282 time to fit residues: 47.9238 Evaluate side-chains 141 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121723 restraints weight = 10158.710| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.95 r_work: 0.3246 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7550 Z= 0.206 Angle : 0.522 6.657 10235 Z= 0.264 Chirality : 0.039 0.134 1245 Planarity : 0.004 0.035 1217 Dihedral : 11.873 98.875 1160 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.17 % Allowed : 13.98 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.28), residues: 915 helix: 2.01 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.52 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.002 0.000 HIS B 309 PHE 0.026 0.001 PHE B 274 TYR 0.012 0.001 TYR B 269 ARG 0.007 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.807 Fit side-chains REVERT: A 418 GLU cc_start: 0.8584 (tp30) cc_final: 0.8258 (tp30) REVERT: D 238 MET cc_start: 0.6834 (tmm) cc_final: 0.6629 (tmm) REVERT: D 298 MET cc_start: 0.7791 (ttm) cc_final: 0.7052 (tmm) outliers start: 16 outliers final: 10 residues processed: 152 average time/residue: 0.2265 time to fit residues: 44.4432 Evaluate side-chains 143 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.151680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118095 restraints weight = 10212.927| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.13 r_work: 0.3167 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7550 Z= 0.335 Angle : 0.577 6.812 10235 Z= 0.292 Chirality : 0.040 0.141 1245 Planarity : 0.004 0.036 1217 Dihedral : 11.717 93.076 1160 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.12 % Allowed : 16.42 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.28), residues: 915 helix: 1.90 (0.19), residues: 751 sheet: None (None), residues: 0 loop : 0.52 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 365 HIS 0.003 0.001 HIS D 309 PHE 0.016 0.001 PHE B 274 TYR 0.013 0.001 TYR B 269 ARG 0.007 0.001 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.826 Fit side-chains REVERT: A 418 GLU cc_start: 0.8569 (tp30) cc_final: 0.8127 (tp30) REVERT: D 238 MET cc_start: 0.6882 (tmm) cc_final: 0.6507 (tmm) REVERT: D 298 MET cc_start: 0.7844 (ttm) cc_final: 0.7010 (tmm) REVERT: C 297 ILE cc_start: 0.8488 (mt) cc_final: 0.8255 (mt) outliers start: 23 outliers final: 13 residues processed: 143 average time/residue: 0.2284 time to fit residues: 42.0849 Evaluate side-chains 136 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.0050 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121785 restraints weight = 10102.010| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.94 r_work: 0.3252 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7550 Z= 0.170 Angle : 0.502 6.919 10235 Z= 0.253 Chirality : 0.038 0.122 1245 Planarity : 0.004 0.035 1217 Dihedral : 10.930 89.635 1160 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.31 % Allowed : 17.50 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.29), residues: 915 helix: 2.13 (0.20), residues: 751 sheet: None (None), residues: 0 loop : 0.56 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 366 HIS 0.002 0.000 HIS D 309 PHE 0.018 0.001 PHE B 274 TYR 0.010 0.001 TYR B 269 ARG 0.007 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.737 Fit side-chains REVERT: A 418 GLU cc_start: 0.8615 (tp30) cc_final: 0.8148 (tp30) REVERT: A 422 GLN cc_start: 0.8099 (mm110) cc_final: 0.7719 (mm110) REVERT: B 309 HIS cc_start: 0.8947 (m90) cc_final: 0.8601 (m90) REVERT: B 372 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9166 (p) REVERT: D 238 MET cc_start: 0.6990 (tmm) cc_final: 0.6537 (tmm) REVERT: D 298 MET cc_start: 0.7859 (ttm) cc_final: 0.7055 (tmm) REVERT: C 238 MET cc_start: 0.7163 (tmm) cc_final: 0.6934 (tmm) outliers start: 17 outliers final: 12 residues processed: 151 average time/residue: 0.2190 time to fit residues: 43.2023 Evaluate side-chains 146 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 65 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.154531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121853 restraints weight = 10226.829| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.51 r_work: 0.3170 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7550 Z= 0.203 Angle : 0.522 6.947 10235 Z= 0.262 Chirality : 0.038 0.127 1245 Planarity : 0.004 0.035 1217 Dihedral : 10.375 84.602 1160 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.90 % Allowed : 19.00 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.29), residues: 915 helix: 2.11 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.62 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.002 0.000 HIS D 309 PHE 0.020 0.001 PHE B 274 TYR 0.010 0.001 TYR B 269 ARG 0.008 0.001 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.828 Fit side-chains REVERT: A 418 GLU cc_start: 0.8634 (tp30) cc_final: 0.8185 (tp30) REVERT: A 422 GLN cc_start: 0.8146 (mm110) cc_final: 0.7779 (mm110) REVERT: B 309 HIS cc_start: 0.8911 (m90) cc_final: 0.8576 (m90) REVERT: B 372 THR cc_start: 0.9396 (OUTLIER) cc_final: 0.9175 (p) REVERT: D 238 MET cc_start: 0.7062 (tmm) cc_final: 0.6539 (tmm) REVERT: D 298 MET cc_start: 0.7809 (ttm) cc_final: 0.7100 (tmm) REVERT: C 238 MET cc_start: 0.7207 (tmm) cc_final: 0.6961 (tmm) REVERT: C 297 ILE cc_start: 0.8553 (mt) cc_final: 0.8177 (mt) REVERT: C 414 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8346 (tm-30) REVERT: C 416 TYR cc_start: 0.7604 (t80) cc_final: 0.7288 (m-80) outliers start: 14 outliers final: 10 residues processed: 143 average time/residue: 0.2240 time to fit residues: 41.6439 Evaluate side-chains 137 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.154367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120648 restraints weight = 9944.208| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.96 r_work: 0.3229 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7550 Z= 0.211 Angle : 0.526 7.013 10235 Z= 0.263 Chirality : 0.038 0.127 1245 Planarity : 0.004 0.035 1217 Dihedral : 10.039 84.106 1160 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.17 % Allowed : 18.86 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.28), residues: 915 helix: 2.14 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.68 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 365 HIS 0.002 0.000 HIS D 309 PHE 0.022 0.001 PHE B 274 TYR 0.010 0.001 TYR B 269 ARG 0.008 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8633 (tp30) cc_final: 0.8117 (tp30) REVERT: A 422 GLN cc_start: 0.8143 (mm110) cc_final: 0.7776 (mm110) REVERT: B 309 HIS cc_start: 0.8958 (m90) cc_final: 0.8581 (m90) REVERT: B 372 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.9204 (p) REVERT: D 238 MET cc_start: 0.6965 (tmm) cc_final: 0.6418 (tmm) REVERT: D 298 MET cc_start: 0.7898 (ttm) cc_final: 0.7088 (tmm) REVERT: C 238 MET cc_start: 0.7188 (tmm) cc_final: 0.6956 (tmm) REVERT: C 297 ILE cc_start: 0.8503 (mt) cc_final: 0.8146 (mt) REVERT: C 414 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8352 (tm-30) outliers start: 16 outliers final: 10 residues processed: 142 average time/residue: 0.2246 time to fit residues: 41.2219 Evaluate side-chains 138 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 262 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.157030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124201 restraints weight = 10149.947| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.20 r_work: 0.3234 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7550 Z= 0.156 Angle : 0.506 6.989 10235 Z= 0.254 Chirality : 0.037 0.120 1245 Planarity : 0.004 0.035 1217 Dihedral : 9.537 84.704 1160 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.17 % Allowed : 19.00 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.29), residues: 915 helix: 2.24 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.77 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 366 HIS 0.001 0.000 HIS D 309 PHE 0.024 0.001 PHE B 274 TYR 0.008 0.001 TYR B 269 ARG 0.008 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8578 (tp30) cc_final: 0.8147 (tp30) REVERT: A 422 GLN cc_start: 0.8197 (mm110) cc_final: 0.7858 (mm110) REVERT: B 309 HIS cc_start: 0.8842 (m90) cc_final: 0.8593 (m90) REVERT: B 372 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9105 (p) REVERT: D 238 MET cc_start: 0.7101 (tmm) cc_final: 0.6716 (tmm) REVERT: D 298 MET cc_start: 0.7807 (ttm) cc_final: 0.7123 (tmm) REVERT: C 238 MET cc_start: 0.7281 (tmm) cc_final: 0.7054 (tmm) REVERT: C 414 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8264 (tm-30) outliers start: 16 outliers final: 10 residues processed: 144 average time/residue: 0.2182 time to fit residues: 41.0305 Evaluate side-chains 138 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 262 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.152335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118929 restraints weight = 10100.260| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.39 r_work: 0.3158 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7550 Z= 0.281 Angle : 0.564 7.078 10235 Z= 0.284 Chirality : 0.039 0.134 1245 Planarity : 0.004 0.045 1217 Dihedral : 9.759 83.609 1160 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.04 % Allowed : 20.35 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.28), residues: 915 helix: 2.12 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.95 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.002 0.001 HIS D 309 PHE 0.038 0.001 PHE B 415 TYR 0.011 0.001 TYR B 269 ARG 0.008 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8556 (tp30) cc_final: 0.7953 (tp30) REVERT: A 422 GLN cc_start: 0.8154 (mm110) cc_final: 0.7736 (mm110) REVERT: B 274 PHE cc_start: 0.8014 (t80) cc_final: 0.7801 (t80) REVERT: B 309 HIS cc_start: 0.8872 (m90) cc_final: 0.8519 (m90) REVERT: B 372 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.9189 (p) REVERT: D 238 MET cc_start: 0.6936 (tmm) cc_final: 0.6563 (tmm) REVERT: D 298 MET cc_start: 0.7845 (ttm) cc_final: 0.7028 (tmm) REVERT: C 238 MET cc_start: 0.7079 (tmm) cc_final: 0.6837 (tmm) REVERT: C 242 LEU cc_start: 0.7483 (tp) cc_final: 0.7276 (tp) REVERT: C 297 ILE cc_start: 0.8429 (mt) cc_final: 0.8110 (mt) REVERT: C 414 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8350 (tm-30) outliers start: 15 outliers final: 10 residues processed: 131 average time/residue: 0.2362 time to fit residues: 39.8144 Evaluate side-chains 132 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 87 optimal weight: 0.0870 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.154526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121767 restraints weight = 10036.588| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.29 r_work: 0.3185 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7550 Z= 0.192 Angle : 0.539 7.565 10235 Z= 0.271 Chirality : 0.039 0.222 1245 Planarity : 0.004 0.071 1217 Dihedral : 9.534 84.285 1160 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.49 % Allowed : 21.44 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.29), residues: 915 helix: 2.20 (0.19), residues: 761 sheet: None (None), residues: 0 loop : 0.94 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 365 HIS 0.002 0.000 HIS D 309 PHE 0.031 0.001 PHE B 415 TYR 0.010 0.001 TYR B 269 ARG 0.009 0.001 ARG C 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8596 (tp30) cc_final: 0.7993 (tp30) REVERT: A 422 GLN cc_start: 0.8176 (mm110) cc_final: 0.7775 (mm110) REVERT: B 309 HIS cc_start: 0.8863 (m90) cc_final: 0.8557 (m90) REVERT: B 372 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9153 (p) REVERT: D 238 MET cc_start: 0.6935 (tmm) cc_final: 0.6544 (tmm) REVERT: D 298 MET cc_start: 0.7848 (ttm) cc_final: 0.7094 (tmm) REVERT: C 238 MET cc_start: 0.7207 (tmm) cc_final: 0.6977 (tmm) REVERT: C 297 ILE cc_start: 0.8474 (mt) cc_final: 0.8132 (mt) REVERT: C 414 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8330 (tm-30) outliers start: 11 outliers final: 10 residues processed: 132 average time/residue: 0.2357 time to fit residues: 40.2226 Evaluate side-chains 137 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.154239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121343 restraints weight = 9961.707| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.14 r_work: 0.3203 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7550 Z= 0.198 Angle : 0.538 7.871 10235 Z= 0.270 Chirality : 0.039 0.209 1245 Planarity : 0.004 0.047 1217 Dihedral : 9.381 84.672 1160 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.76 % Allowed : 21.17 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.29), residues: 915 helix: 2.20 (0.19), residues: 761 sheet: None (None), residues: 0 loop : 0.96 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 365 HIS 0.002 0.000 HIS D 309 PHE 0.032 0.001 PHE B 415 TYR 0.010 0.001 TYR B 269 ARG 0.009 0.001 ARG C 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4077.95 seconds wall clock time: 71 minutes 8.69 seconds (4268.69 seconds total)