Starting phenix.real_space_refine on Thu Feb 13 16:05:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zo8_14843/02_2025/7zo8_14843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zo8_14843/02_2025/7zo8_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_14843/02_2025/7zo8_14843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zo8_14843/02_2025/7zo8_14843.map" model { file = "/net/cci-nas-00/data/ceres_data/7zo8_14843/02_2025/7zo8_14843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zo8_14843/02_2025/7zo8_14843.cif" } resolution = 3.6 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= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 9.98, per 1000 atoms: 1.11 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: 2.35 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 0.83 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: 2.31 Time building geometry restraints manager: 2.65 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: 0.05 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: 0.840 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.020 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- 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= 0.273 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 (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: 1.72 (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 TRP 0.007 0.001 TRP B 106 HIS 0.005 0.001 HIS B 137 PHE 0.018 0.001 PHE A 195 TYR 0.007 0.001 TYR A 461 ARG 0.007 0.000 ARG B 383 *********************** 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 : 0.938 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1661 time to fit residues: 28.0921 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 : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.204485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.153896 restraints weight = 28800.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.149255 restraints weight = 32648.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.143910 restraints weight = 19097.116| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9104 Z= 0.322 Angle : 0.624 8.378 12318 Z= 0.328 Chirality : 0.043 0.182 1440 Planarity : 0.004 0.040 1572 Dihedral : 12.409 130.319 1320 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.49 % Favored : 95.16 % Rotamer: Outliers : 0.85 % Allowed : 7.32 % Favored : 91.83 % 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: 1.51 (0.26), residues: 1140 helix: 1.94 (0.19), residues: 788 sheet: 0.76 (0.57), residues: 70 loop : -1.71 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 238 HIS 0.007 0.001 HIS A 137 PHE 0.017 0.001 PHE A 195 TYR 0.023 0.001 TYR A 263 ARG 0.003 0.000 ARG A 383 *********************** 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: 4 poor density : 99 time to evaluate : 0.999 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 100 average time/residue: 0.1658 time to fit residues: 25.5731 Evaluate side-chains 97 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 422 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 75 optimal weight: 0.0000 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 47 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.205353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.149473 restraints weight = 24431.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.149503 restraints weight = 30997.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.142953 restraints weight = 14011.267| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9104 Z= 0.233 Angle : 0.579 9.341 12318 Z= 0.300 Chirality : 0.041 0.169 1440 Planarity : 0.004 0.036 1572 Dihedral : 11.481 114.625 1320 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.75 % Favored : 94.89 % Rotamer: Outliers : 1.06 % Allowed : 9.24 % Favored : 89.70 % 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: 1.60 (0.26), residues: 1140 helix: 2.04 (0.19), residues: 782 sheet: 0.73 (0.56), residues: 70 loop : -1.70 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 238 HIS 0.005 0.001 HIS B 137 PHE 0.017 0.001 PHE B 195 TYR 0.023 0.001 TYR A 263 ARG 0.004 0.000 ARG A 383 *********************** 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 101 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.017 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 95 average time/residue: 0.1786 time to fit residues: 25.8968 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 : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL 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 414 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 99 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.207487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.152377 restraints weight = 23229.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.155217 restraints weight = 29666.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.154038 restraints weight = 13940.594| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9104 Z= 0.188 Angle : 0.540 8.462 12318 Z= 0.279 Chirality : 0.040 0.170 1440 Planarity : 0.004 0.037 1572 Dihedral : 10.087 88.595 1320 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 1.06 % Allowed : 9.87 % Favored : 89.07 % 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: 1.74 (0.26), residues: 1140 helix: 2.18 (0.19), residues: 782 sheet: 0.68 (0.56), residues: 70 loop : -1.72 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 106 HIS 0.004 0.001 HIS A 137 PHE 0.017 0.001 PHE A 195 TYR 0.023 0.001 TYR A 263 ARG 0.001 0.000 ARG B 247 *********************** 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 107 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.906 Fit side-chains REVERT: A 263 TYR cc_start: 0.8272 (t80) cc_final: 0.8051 (t80) outliers start: 6 outliers final: 4 residues processed: 104 average time/residue: 0.1750 time to fit residues: 28.1678 Evaluate side-chains 95 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 0.7980 chunk 76 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 104 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.208137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.162624 restraints weight = 22451.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.161345 restraints weight = 30444.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.159647 restraints weight = 8265.846| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9104 Z= 0.186 Angle : 0.540 7.770 12318 Z= 0.276 Chirality : 0.040 0.162 1440 Planarity : 0.004 0.036 1572 Dihedral : 9.350 71.546 1320 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.06 % Allowed : 11.89 % Favored : 87.05 % 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: 1.81 (0.26), residues: 1140 helix: 2.20 (0.19), residues: 784 sheet: 0.84 (0.59), residues: 70 loop : -1.66 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 238 HIS 0.004 0.001 HIS A 137 PHE 0.016 0.001 PHE B 195 TYR 0.024 0.001 TYR B 263 ARG 0.002 0.000 ARG B 271 *********************** 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 104 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 99 average time/residue: 0.1713 time to fit residues: 25.5414 Evaluate side-chains 99 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 414 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.205722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.159393 restraints weight = 21468.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.156202 restraints weight = 27478.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.157039 restraints weight = 6720.164| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9104 Z= 0.268 Angle : 0.583 7.142 12318 Z= 0.300 Chirality : 0.041 0.178 1440 Planarity : 0.004 0.037 1572 Dihedral : 9.179 69.200 1320 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.14 % Favored : 95.51 % Rotamer: Outliers : 1.49 % Allowed : 11.68 % Favored : 86.84 % 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: 1.72 (0.26), residues: 1140 helix: 2.16 (0.19), residues: 780 sheet: 0.87 (0.59), residues: 70 loop : -1.78 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 106 HIS 0.006 0.001 HIS B 137 PHE 0.016 0.001 PHE A 278 TYR 0.006 0.001 TYR A 461 ARG 0.002 0.000 ARG A 288 *********************** 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 105 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.944 Fit side-chains REVERT: A 108 GLN cc_start: 0.8253 (mp10) cc_final: 0.7641 (mp10) REVERT: A 248 MET cc_start: 0.8333 (mmm) cc_final: 0.7677 (mmm) REVERT: B 108 GLN cc_start: 0.8287 (mp10) cc_final: 0.7664 (mp10) REVERT: B 248 MET cc_start: 0.8320 (mmm) cc_final: 0.7655 (mmm) outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 0.1550 time to fit residues: 24.1428 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 : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL 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 414 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 0.9980 chunk 50 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 chunk 34 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.207736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.158348 restraints weight = 28047.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.151641 restraints weight = 33218.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.146101 restraints weight = 19459.507| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1500 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= 0.206 Angle : 0.553 7.243 12318 Z= 0.282 Chirality : 0.040 0.162 1440 Planarity : 0.004 0.037 1572 Dihedral : 8.819 61.767 1320 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 1.06 % Allowed : 12.21 % Favored : 86.73 % 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: 1.83 (0.26), residues: 1140 helix: 2.26 (0.19), residues: 780 sheet: 0.89 (0.60), residues: 70 loop : -1.77 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 106 HIS 0.004 0.001 HIS B 137 PHE 0.016 0.001 PHE A 195 TYR 0.024 0.001 TYR B 263 ARG 0.001 0.000 ARG B 288 *********************** 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 102 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.049 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 96 average time/residue: 0.1525 time to fit residues: 23.4214 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 : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL 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 414 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.203765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.148283 restraints weight = 25229.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.146397 restraints weight = 33002.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.140776 restraints weight = 14173.397| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- 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 = 0.28 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 = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9104 Z= 0.337 Angle : 0.623 7.929 12318 Z= 0.321 Chirality : 0.043 0.184 1440 Planarity : 0.004 0.041 1572 Dihedral : 8.792 66.673 1320 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 1.38 % Allowed : 12.42 % Favored : 86.20 % 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: 1.63 (0.26), residues: 1140 helix: 2.10 (0.19), residues: 780 sheet: 0.84 (0.60), residues: 70 loop : -1.79 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 106 HIS 0.006 0.001 HIS A 137 PHE 0.018 0.001 PHE B 278 TYR 0.006 0.001 TYR A 461 ARG 0.003 0.000 ARG A 288 *********************** 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 98 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 1.004 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.1535 time to fit residues: 22.4385 Evaluate side-chains 97 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL 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 177 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 422 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.204499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.153838 restraints weight = 18416.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.149437 restraints weight = 26606.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.148978 restraints weight = 11107.919| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9104 Z= 0.291 Angle : 0.620 11.097 12318 Z= 0.313 Chirality : 0.042 0.174 1440 Planarity : 0.004 0.038 1572 Dihedral : 8.715 63.535 1320 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.31 % Favored : 95.33 % Rotamer: Outliers : 1.17 % Allowed : 12.63 % Favored : 86.20 % 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: 1.64 (0.26), residues: 1140 helix: 2.10 (0.19), residues: 780 sheet: 0.84 (0.60), residues: 70 loop : -1.80 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.006 0.001 HIS A 137 PHE 0.017 0.001 PHE A 195 TYR 0.026 0.002 TYR A 263 ARG 0.002 0.000 ARG A 135 *********************** 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 100 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.990 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 93 average time/residue: 0.1630 time to fit residues: 23.7619 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 : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 177 MET 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 414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.0050 chunk 89 optimal weight: 20.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.208763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.162441 restraints weight = 23656.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.161006 restraints weight = 28950.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.159429 restraints weight = 8425.538| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9104 Z= 0.187 Angle : 0.572 10.762 12318 Z= 0.286 Chirality : 0.040 0.178 1440 Planarity : 0.004 0.035 1572 Dihedral : 8.413 59.521 1320 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % 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 (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: 1.93 (0.26), residues: 1140 helix: 2.31 (0.19), residues: 782 sheet: 0.96 (0.61), residues: 70 loop : -1.69 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 106 HIS 0.004 0.001 HIS B 137 PHE 0.015 0.001 PHE A 195 TYR 0.007 0.001 TYR A 7 ARG 0.002 0.000 ARG B 433 ********************** 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 106 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.863 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 101 average time/residue: 0.1715 time to fit residues: 26.4217 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 : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 VAL 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 414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 0.0570 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.208634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.160026 restraints weight = 10718.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.160058 restraints weight = 24580.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.160948 restraints weight = 17455.840| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1750 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= 0.204 Angle : 0.577 10.589 12318 Z= 0.288 Chirality : 0.040 0.166 1440 Planarity : 0.004 0.038 1572 Dihedral : 8.222 59.298 1320 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer: Outliers : 1.17 % Allowed : 13.48 % Favored : 85.35 % 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: 1.96 (0.26), residues: 1140 helix: 2.35 (0.19), residues: 782 sheet: 0.90 (0.60), residues: 70 loop : -1.70 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 106 HIS 0.004 0.001 HIS B 137 PHE 0.015 0.001 PHE B 453 TYR 0.007 0.001 TYR A 13 ARG 0.003 0.000 ARG A 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.96 seconds wall clock time: 51 minutes 1.20 seconds (3061.20 seconds total)