Starting phenix.real_space_refine on Tue Mar 3 23:05:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zo8_14843/03_2026/7zo8_14843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zo8_14843/03_2026/7zo8_14843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zo8_14843/03_2026/7zo8_14843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zo8_14843/03_2026/7zo8_14843.map" model { file = "/net/cci-nas-00/data/ceres_data/7zo8_14843/03_2026/7zo8_14843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zo8_14843/03_2026/7zo8_14843.cif" } resolution = 3.6 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= 0.004 sd= 0.120 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 44 5.16 5 C 5678 2.51 5 N 1582 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8952 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4437 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} Conformer: "B" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} bond proxies already assigned to first conformer: 4478 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Restraints were copied for chains: B Time building chain proxies: 4.22, per 1000 atoms: 0.47 Number of scatterers: 8952 At special positions: 0 Unit cell: (74.825, 109.675, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 2 15.00 O 1646 8.00 N 1582 7.00 C 5678 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: 0.64 Conformation dependent library (CDL) restraints added in 717.1 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 71.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 removed outlier: 4.002A pdb=" N TYR A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 17 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 48 removed outlier: 3.762A pdb=" N THR A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 55 through 100 removed outlier: 3.625A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.949A pdb=" N HIS A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 155 removed outlier: 3.616A pdb=" N MET A 134 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 155 through 204 removed outlier: 3.640A pdb=" N GLY A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 235 through 267 removed outlier: 5.257A pdb=" N ASN A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 316 removed outlier: 3.505A pdb=" N PHE A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.890A pdb=" N HIS A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.688A pdb=" N VAL A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 4.253A pdb=" N HIS A 442 " --> pdb=" O HIS A 438 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 removed outlier: 4.379A pdb=" N ALA A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 463 removed outlier: 4.150A pdb=" N ASP A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 463 " --> pdb=" O GLY A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 463' Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.877A pdb=" N LYS A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 570 Processing helix chain 'B' and resid 2 through 17 removed outlier: 4.002A pdb=" N TYR B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 48 removed outlier: 3.761A pdb=" N THR B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 55 through 100 removed outlier: 3.624A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.950A pdb=" N HIS B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 155 removed outlier: 3.616A pdb=" N MET B 134 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 155 through 204 removed outlier: 3.639A pdb=" N GLY B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N HIS B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 235 through 267 removed outlier: 5.257A pdb=" N ASN B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 316 removed outlier: 3.504A pdb=" N PHE B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.889A pdb=" N HIS B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 431 removed outlier: 3.689A pdb=" N VAL B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 4.252A pdb=" N HIS B 442 " --> pdb=" O HIS B 438 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 removed outlier: 4.380A pdb=" N ALA B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 463 removed outlier: 4.150A pdb=" N ASP B 462 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR B 463 " --> pdb=" O GLY B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 459 through 463' Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 473 through 489 Processing helix chain 'B' and resid 503 through 518 removed outlier: 3.877A pdb=" N LYS B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 570 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 5.363A pdb=" N VAL A 354 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 340 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA A 389 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 7.216A pdb=" N VAL A 539 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE A 541 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.363A pdb=" N VAL B 354 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL B 340 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 389 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 411 through 414 removed outlier: 7.215A pdb=" N VAL B 539 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE B 541 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1883 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: 1.18 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1470 1.31 - 1.43: 2282 1.43 - 1.55: 5262 1.55 - 1.68: 4 1.68 - 1.80: 86 Bond restraints: 9104 Sorted by residual: bond pdb=" CB PLC A 601 " pdb=" O3 PLC A 601 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CB PLC B 601 " pdb=" O3 PLC B 601 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C' PLC A 601 " pdb=" O2 PLC A 601 " ideal model delta sigma weight residual 1.332 1.416 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C' PLC B 601 " pdb=" O2 PLC B 601 " ideal model delta sigma weight residual 1.332 1.415 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" N PLC A 601 " pdb=" C5 PLC A 601 " ideal model delta sigma weight residual 1.508 1.450 0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 12250 3.73 - 7.47: 60 7.47 - 11.20: 4 11.20 - 14.93: 0 14.93 - 18.66: 4 Bond angle restraints: 12318 Sorted by residual: angle pdb=" O1P PLC A 601 " pdb=" P PLC A 601 " pdb=" O2P PLC A 601 " ideal model delta sigma weight residual 119.61 100.95 18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" O1P PLC B 601 " pdb=" P PLC B 601 " pdb=" O2P PLC B 601 " ideal model delta sigma weight residual 119.61 101.00 18.61 3.00e+00 1.11e-01 3.85e+01 angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 110.31 -16.69 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3P PLC B 601 " pdb=" P PLC B 601 " pdb=" O4P PLC B 601 " ideal model delta sigma weight residual 93.62 110.28 -16.66 3.00e+00 1.11e-01 3.09e+01 angle pdb=" C ARG A 135 " pdb=" N GLN A 136 " pdb=" CA GLN A 136 " ideal model delta sigma weight residual 120.58 114.67 5.91 1.71e+00 3.42e-01 1.20e+01 ... (remaining 12313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 5159 27.06 - 54.11: 283 54.11 - 81.17: 36 81.17 - 108.23: 6 108.23 - 135.28: 6 Dihedral angle restraints: 5490 sinusoidal: 2184 harmonic: 3306 Sorted by residual: dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ASP A 51 " pdb=" CA ASP A 51 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA SER B 50 " pdb=" C SER B 50 " pdb=" N ASP B 51 " pdb=" CA ASP B 51 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" C3 PLC B 601 " pdb=" C1 PLC B 601 " pdb=" C2 PLC B 601 " pdb=" O3P PLC B 601 " ideal model delta sinusoidal sigma weight residual 67.16 -157.56 -135.28 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 968 0.035 - 0.069: 349 0.069 - 0.104: 79 0.104 - 0.139: 34 0.139 - 0.174: 10 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA PRO A 103 " pdb=" N PRO A 103 " pdb=" C PRO A 103 " pdb=" CB PRO A 103 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA PRO B 103 " pdb=" N PRO B 103 " pdb=" C PRO B 103 " pdb=" CB PRO B 103 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA HIS B 137 " pdb=" N HIS B 137 " pdb=" C HIS B 137 " pdb=" CB HIS B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1437 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 134 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C MET B 134 " -0.061 2.00e-02 2.50e+03 pdb=" O MET B 134 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 135 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 134 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C MET A 134 " 0.061 2.00e-02 2.50e+03 pdb=" O MET A 134 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 135 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 359 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.26e+00 pdb=" N PRO B 360 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " 0.032 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1892 2.79 - 3.31: 9249 3.31 - 3.84: 14444 3.84 - 4.37: 15461 4.37 - 4.90: 28189 Nonbonded interactions: 69235 Sorted by model distance: nonbonded pdb=" OG SER A 490 " pdb=" O ILE A 492 " model vdw 2.257 3.040 nonbonded pdb=" OG SER B 490 " pdb=" O ILE B 492 " model vdw 2.258 3.040 nonbonded pdb=" O GLY B 561 " pdb=" OG SER B 564 " model vdw 2.319 3.040 nonbonded pdb=" O GLY A 561 " pdb=" OG SER A 564 " model vdw 2.319 3.040 nonbonded pdb=" NH2 ARG A 423 " pdb=" OE2 GLU B 217 " model vdw 2.346 3.120 ... (remaining 69230 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.900 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.150 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.004 0.087 9104 Z= 0.197 Angle : 0.704 18.665 12318 Z= 0.336 Chirality : 0.041 0.174 1440 Planarity : 0.004 0.057 1572 Dihedral : 16.849 135.282 3350 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.75 % Favored : 94.89 % Rotamer: Outliers : 0.42 % Allowed : 0.21 % Favored : 99.36 % 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: 1.72 (0.26), residues: 1140 helix: 2.12 (0.19), residues: 782 sheet: 0.61 (0.58), residues: 70 loop : -1.58 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 383 TYR 0.007 0.001 TYR A 461 PHE 0.018 0.001 PHE A 195 TRP 0.007 0.001 TRP B 106 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9104) covalent geometry : angle 0.70436 (12318) hydrogen bonds : bond 0.09942 ( 641) hydrogen bonds : angle 4.64892 ( 1883) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0645 time to fit residues: 11.2206 Evaluate side-chains 90 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.203807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.152204 restraints weight = 24825.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.149845 restraints weight = 26499.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.151422 restraints weight = 11539.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.150691 restraints weight = 10980.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.150892 restraints weight = 9013.074| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 9104 Z= 0.416 Angle : 0.836 13.307 12318 Z= 0.439 Chirality : 0.052 0.237 1440 Planarity : 0.006 0.077 1572 Dihedral : 13.164 133.610 1320 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.58 % Favored : 94.89 % Rotamer: Outliers : 1.27 % Allowed : 8.49 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.84 (0.25), residues: 1140 helix: 1.38 (0.19), residues: 784 sheet: 0.67 (0.57), residues: 70 loop : -1.78 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 135 TYR 0.025 0.002 TYR A 263 PHE 0.024 0.003 PHE B 278 TRP 0.009 0.003 TRP A 8 HIS 0.011 0.002 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.01042 ( 9104) covalent geometry : angle 0.83570 (12318) hydrogen bonds : bond 0.08003 ( 641) hydrogen bonds : angle 4.74388 ( 1883) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.332 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 96 average time/residue: 0.0633 time to fit residues: 9.4783 Evaluate side-chains 98 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 453 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 30.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.205471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.158680 restraints weight = 21034.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.157822 restraints weight = 29953.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156205 restraints weight = 7875.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156205 restraints weight = 4064.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156205 restraints weight = 4064.604| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9104 Z= 0.154 Angle : 0.589 8.726 12318 Z= 0.308 Chirality : 0.042 0.177 1440 Planarity : 0.004 0.037 1572 Dihedral : 12.368 118.505 1320 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.84 % Favored : 94.81 % Rotamer: Outliers : 0.85 % Allowed : 10.51 % Favored : 88.64 % 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: 1.35 (0.26), residues: 1140 helix: 1.85 (0.19), residues: 782 sheet: 0.66 (0.56), residues: 70 loop : -1.80 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 423 TYR 0.023 0.001 TYR B 263 PHE 0.019 0.001 PHE A 195 TRP 0.006 0.001 TRP B 62 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9104) covalent geometry : angle 0.58928 (12318) hydrogen bonds : bond 0.05798 ( 641) hydrogen bonds : angle 4.26526 ( 1883) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.269 Fit side-chains REVERT: B 393 MET cc_start: 0.6933 (tpp) cc_final: 0.6720 (tpp) outliers start: 4 outliers final: 3 residues processed: 95 average time/residue: 0.0703 time to fit residues: 10.3296 Evaluate side-chains 90 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 453 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 53 optimal weight: 0.0770 chunk 91 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.201379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.147292 restraints weight = 29664.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.148163 restraints weight = 34685.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.146327 restraints weight = 13546.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.146820 restraints weight = 11694.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.147742 restraints weight = 8330.643| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9104 Z= 0.148 Angle : 0.572 9.744 12318 Z= 0.295 Chirality : 0.041 0.173 1440 Planarity : 0.004 0.037 1572 Dihedral : 11.123 99.764 1320 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.31 % Favored : 95.33 % Rotamer: Outliers : 1.17 % Allowed : 12.42 % Favored : 86.41 % 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: 1.51 (0.26), residues: 1140 helix: 1.98 (0.19), residues: 782 sheet: 0.70 (0.56), residues: 70 loop : -1.76 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 288 TYR 0.006 0.001 TYR B 13 PHE 0.017 0.001 PHE B 195 TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9104) covalent geometry : angle 0.57174 (12318) hydrogen bonds : bond 0.05489 ( 641) hydrogen bonds : angle 4.18356 ( 1883) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.304 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 96 average time/residue: 0.0670 time to fit residues: 10.0224 Evaluate side-chains 91 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 453 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.204044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.153844 restraints weight = 18863.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.149496 restraints weight = 25325.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.149706 restraints weight = 9146.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.149650 restraints weight = 9206.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.149727 restraints weight = 6772.446| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9104 Z= 0.174 Angle : 0.590 8.858 12318 Z= 0.306 Chirality : 0.042 0.185 1440 Planarity : 0.004 0.038 1572 Dihedral : 10.498 97.672 1320 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.06 % Allowed : 12.95 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1140 helix: 2.00 (0.19), residues: 780 sheet: 0.79 (0.58), residues: 70 loop : -1.82 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 288 TYR 0.025 0.001 TYR B 263 PHE 0.017 0.001 PHE B 195 TRP 0.006 0.001 TRP A 106 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9104) covalent geometry : angle 0.59012 (12318) hydrogen bonds : bond 0.05780 ( 641) hydrogen bonds : angle 4.20054 ( 1883) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.326 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 93 average time/residue: 0.0737 time to fit residues: 10.5218 Evaluate side-chains 95 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 453 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 98 optimal weight: 0.0040 chunk 71 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.203904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.147486 restraints weight = 25223.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.149166 restraints weight = 32350.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.148420 restraints weight = 15264.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.148143 restraints weight = 10785.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.149296 restraints weight = 8038.591| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9104 Z= 0.135 Angle : 0.552 8.290 12318 Z= 0.284 Chirality : 0.041 0.195 1440 Planarity : 0.004 0.037 1572 Dihedral : 9.813 87.978 1320 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 1.27 % Allowed : 12.95 % Favored : 85.77 % 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: 1.74 (0.26), residues: 1140 helix: 2.18 (0.19), residues: 780 sheet: 0.98 (0.60), residues: 70 loop : -1.78 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 271 TYR 0.006 0.001 TYR A 7 PHE 0.017 0.001 PHE A 195 TRP 0.006 0.001 TRP A 106 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9104) covalent geometry : angle 0.55206 (12318) hydrogen bonds : bond 0.05165 ( 641) hydrogen bonds : angle 4.09577 ( 1883) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 101 average time/residue: 0.0705 time to fit residues: 10.9988 Evaluate side-chains 97 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 453 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.205026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.151786 restraints weight = 27328.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.143321 restraints weight = 31122.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.136420 restraints weight = 17000.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138076 restraints weight = 13549.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.139386 restraints weight = 8359.240| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9104 Z= 0.161 Angle : 0.576 7.432 12318 Z= 0.296 Chirality : 0.041 0.186 1440 Planarity : 0.004 0.037 1572 Dihedral : 9.382 80.841 1320 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 1.06 % Allowed : 13.16 % Favored : 85.77 % 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: 1.71 (0.26), residues: 1140 helix: 2.15 (0.19), residues: 780 sheet: 0.97 (0.60), residues: 70 loop : -1.78 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 288 TYR 0.025 0.001 TYR A 263 PHE 0.018 0.001 PHE B 195 TRP 0.006 0.001 TRP A 106 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9104) covalent geometry : angle 0.57608 (12318) hydrogen bonds : bond 0.05482 ( 641) hydrogen bonds : angle 4.13080 ( 1883) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.322 Fit side-chains REVERT: A 108 GLN cc_start: 0.8409 (mp10) cc_final: 0.7665 (mp10) REVERT: B 108 GLN cc_start: 0.8411 (mp10) cc_final: 0.7762 (mp10) outliers start: 6 outliers final: 5 residues processed: 93 average time/residue: 0.0628 time to fit residues: 9.2561 Evaluate side-chains 98 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 453 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.206384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.154109 restraints weight = 29803.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.147985 restraints weight = 34485.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.140724 restraints weight = 15988.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.142504 restraints weight = 13783.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.143326 restraints weight = 8832.748| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9104 Z= 0.146 Angle : 0.568 10.828 12318 Z= 0.290 Chirality : 0.041 0.186 1440 Planarity : 0.004 0.037 1572 Dihedral : 8.945 70.105 1320 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 1.06 % Allowed : 13.69 % Favored : 85.24 % 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: 1.77 (0.26), residues: 1140 helix: 2.19 (0.19), residues: 780 sheet: 1.03 (0.60), residues: 70 loop : -1.75 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.005 0.001 TYR A 96 PHE 0.018 0.001 PHE B 195 TRP 0.006 0.001 TRP A 106 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9104) covalent geometry : angle 0.56806 (12318) hydrogen bonds : bond 0.05267 ( 641) hydrogen bonds : angle 4.08971 ( 1883) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.316 Fit side-chains REVERT: A 108 GLN cc_start: 0.8400 (mp10) cc_final: 0.7678 (mp10) REVERT: B 108 GLN cc_start: 0.8377 (mp10) cc_final: 0.7710 (mp10) outliers start: 6 outliers final: 5 residues processed: 97 average time/residue: 0.0720 time to fit residues: 10.8154 Evaluate side-chains 100 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 453 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.206015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.154115 restraints weight = 26130.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.149496 restraints weight = 33058.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.144915 restraints weight = 18033.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.146107 restraints weight = 14988.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.146718 restraints weight = 9585.411| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9104 Z= 0.156 Angle : 0.581 10.403 12318 Z= 0.296 Chirality : 0.041 0.181 1440 Planarity : 0.004 0.037 1572 Dihedral : 8.796 66.036 1320 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.49 % Allowed : 13.38 % Favored : 85.14 % 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: 1.76 (0.26), residues: 1140 helix: 2.18 (0.19), residues: 780 sheet: 0.99 (0.60), residues: 70 loop : -1.75 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 271 TYR 0.025 0.001 TYR B 263 PHE 0.019 0.001 PHE B 195 TRP 0.006 0.001 TRP B 238 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9104) covalent geometry : angle 0.58095 (12318) hydrogen bonds : bond 0.05433 ( 641) hydrogen bonds : angle 4.11289 ( 1883) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8366 (mp10) cc_final: 0.7634 (mp10) outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.0712 time to fit residues: 10.8440 Evaluate side-chains 102 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 453 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.204874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.151832 restraints weight = 25926.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.144229 restraints weight = 31364.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135345 restraints weight = 18701.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.138131 restraints weight = 14484.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.138655 restraints weight = 9186.335| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9104 Z= 0.167 Angle : 0.596 10.708 12318 Z= 0.303 Chirality : 0.042 0.179 1440 Planarity : 0.004 0.038 1572 Dihedral : 8.731 63.199 1320 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.31 % Favored : 95.33 % Rotamer: Outliers : 1.38 % Allowed : 13.38 % Favored : 85.24 % 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: 1.72 (0.26), residues: 1140 helix: 2.16 (0.19), residues: 780 sheet: 0.95 (0.60), residues: 70 loop : -1.77 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 271 TYR 0.005 0.001 TYR A 461 PHE 0.019 0.001 PHE B 195 TRP 0.006 0.001 TRP B 238 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9104) covalent geometry : angle 0.59581 (12318) hydrogen bonds : bond 0.05616 ( 641) hydrogen bonds : angle 4.14833 ( 1883) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.287 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 0.0721 time to fit residues: 10.4268 Evaluate side-chains 100 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 453 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 112 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.207781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.156773 restraints weight = 24353.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151562 restraints weight = 30478.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.146866 restraints weight = 17667.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.149046 restraints weight = 15216.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.148716 restraints weight = 10749.064| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9104 Z= 0.132 Angle : 0.569 10.621 12318 Z= 0.286 Chirality : 0.040 0.185 1440 Planarity : 0.004 0.038 1572 Dihedral : 8.558 56.606 1320 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.06 % Allowed : 14.12 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.86 (0.26), residues: 1140 helix: 2.27 (0.19), residues: 780 sheet: 0.97 (0.60), residues: 70 loop : -1.74 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 433 TYR 0.024 0.001 TYR A 263 PHE 0.017 0.001 PHE A 453 TRP 0.007 0.001 TRP A 106 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9104) covalent geometry : angle 0.56857 (12318) hydrogen bonds : bond 0.05068 ( 641) hydrogen bonds : angle 4.08176 ( 1883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1493.46 seconds wall clock time: 26 minutes 24.06 seconds (1584.06 seconds total)