Starting phenix.real_space_refine on Thu Jul 2 16:26:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bht_16069/07_2026/8bht_16069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bht_16069/07_2026/8bht_16069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bht_16069/07_2026/8bht_16069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bht_16069/07_2026/8bht_16069.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8bht_16069/07_2026/8bht_16069.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bht_16069/07_2026/8bht_16069.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bht_16069/07_2026/8bht_16069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bht_16069/07_2026/8bht_16069.cif" } resolution = 3.1 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= 0.005 sd= 0.046 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 6 5.49 5 S 58 5.16 5 C 5854 2.51 5 N 1472 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4425 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 19, 'TRANS': 549} Chain breaks: 3 Chain: "B" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4425 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 19, 'TRANS': 549} Chain breaks: 3 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'ATP': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'ATP': 1, 'CLR': 1, 'R1H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.82, per 1000 atoms: 0.20 Number of scatterers: 9016 At special positions: 0 Unit cell: (92.4, 97.02, 121.44, 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 58 16.00 P 6 15.00 O 1626 8.00 N 1472 7.00 C 5854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 279.5 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 66.6% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 85 through 95 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.540A pdb=" N ALA A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.686A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.643A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 391 through 413 removed outlier: 4.710A pdb=" N SER A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 441 through 444 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 497 removed outlier: 4.965A pdb=" N LEU A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Proline residue: A 480 - end of helix Proline residue: A 485 - end of helix removed outlier: 4.853A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 529 removed outlier: 3.578A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.935A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 4.214A pdb=" N VAL A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 557 " --> pdb=" O GLY A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 552 through 557' Processing helix chain 'A' and resid 558 through 561 Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.373A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.705A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 650 removed outlier: 3.770A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.540A pdb=" N ALA B 174 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 217 through 234 removed outlier: 3.685A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.643A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 391 through 413 removed outlier: 4.711A pdb=" N SER B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 441 through 444 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 497 removed outlier: 4.965A pdb=" N LEU B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Proline residue: B 480 - end of helix Proline residue: B 485 - end of helix removed outlier: 4.852A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 529 removed outlier: 3.577A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 removed outlier: 3.935A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 4.214A pdb=" N VAL B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 557' Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 562 through 567 removed outlier: 4.374A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.705A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 650 removed outlier: 3.770A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 5.391A pdb=" N TYR A 44 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER A 65 " --> pdb=" O TYR A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 78 removed outlier: 3.707A pdb=" N PHE A 240 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 207 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N SER A 241 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 209 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 256 through 260 removed outlier: 3.612A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 44 removed outlier: 5.392A pdb=" N TYR B 44 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER B 65 " --> pdb=" O TYR B 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 75 through 78 removed outlier: 3.707A pdb=" N PHE B 240 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 207 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N SER B 241 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 209 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.612A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1506 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: 1.61 Time building geometry restraints manager: 1.15 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: 1395 1.31 - 1.43: 2508 1.43 - 1.56: 5199 1.56 - 1.69: 21 1.69 - 1.81: 94 Bond restraints: 9217 Sorted by residual: bond pdb=" C13 R1H B 703 " pdb=" N08 R1H B 703 " ideal model delta sigma weight residual 1.448 1.285 0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.35e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C5 ATP B 701 " pdb=" C6 ATP B 701 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.86e+01 ... (remaining 9212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 12437 3.82 - 7.64: 47 7.64 - 11.46: 10 11.46 - 15.29: 4 15.29 - 19.11: 2 Bond angle restraints: 12500 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 120.76 19.11 1.00e+00 1.00e+00 3.65e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 120.82 19.05 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 122.00 14.83 1.00e+00 1.00e+00 2.20e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 122.01 14.82 1.00e+00 1.00e+00 2.20e+02 angle pdb=" C5 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N3 ATP A 701 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.63e+01 ... (remaining 12495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.22: 5306 33.22 - 66.44: 88 66.44 - 99.66: 10 99.66 - 132.88: 1 132.88 - 166.10: 2 Dihedral angle restraints: 5407 sinusoidal: 2133 harmonic: 3274 Sorted by residual: dihedral pdb=" CA GLN A 181 " pdb=" C GLN A 181 " pdb=" N PHE A 182 " pdb=" CA PHE A 182 " ideal model delta harmonic sigma weight residual 180.00 153.96 26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA GLN B 181 " pdb=" C GLN B 181 " pdb=" N PHE B 182 " pdb=" CA PHE B 182 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" C13 R1H B 703 " pdb=" C14 R1H B 703 " pdb=" C15 R1H B 703 " pdb=" C16 R1H B 703 " ideal model delta sinusoidal sigma weight residual 160.69 -5.41 166.10 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 5404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1308 0.069 - 0.139: 118 0.139 - 0.208: 7 0.208 - 0.277: 3 0.277 - 0.346: 2 Chirality restraints: 1438 Sorted by residual: chirality pdb=" C17 CLR A 702 " pdb=" C13 CLR A 702 " pdb=" C16 CLR A 702 " pdb=" C20 CLR A 702 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C17 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C16 CLR B 702 " pdb=" C20 CLR B 702 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C20 CLR B 702 " pdb=" C17 CLR B 702 " pdb=" C21 CLR B 702 " pdb=" C22 CLR B 702 " both_signs ideal model delta sigma weight residual False 2.59 2.85 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1435 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 484 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 485 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 484 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 485 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 211 " 0.016 5.00e-02 4.00e+02 2.36e-02 8.90e-01 pdb=" N PRO A 212 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.013 5.00e-02 4.00e+02 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2194 2.79 - 3.32: 9082 3.32 - 3.84: 14311 3.84 - 4.37: 17072 4.37 - 4.90: 29834 Nonbonded interactions: 72493 Sorted by model distance: nonbonded pdb=" OD1 ASP A 296 " pdb=" NH2 ARG B 246 " model vdw 2.260 3.120 nonbonded pdb=" N GLU A 611 " pdb=" OE1 GLU A 611 " model vdw 2.370 3.120 nonbonded pdb=" N GLU B 611 " pdb=" OE1 GLU B 611 " model vdw 2.371 3.120 nonbonded pdb=" OG SER A 384 " pdb=" OD1 ASP A 477 " model vdw 2.373 3.040 nonbonded pdb=" OG SER B 384 " pdb=" OD1 ASP B 477 " model vdw 2.373 3.040 ... (remaining 72488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 34 through 702) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.960 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: 0.250 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.850 Find NCS groups from input model: 0.170 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:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.009 0.163 9220 Z= 0.415 Angle : 0.821 19.106 12506 Z= 0.523 Chirality : 0.045 0.346 1438 Planarity : 0.003 0.033 1534 Dihedral : 13.578 166.095 3298 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.32 % Favored : 97.50 % Rotamer: Outliers : 0.41 % Allowed : 5.58 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1122 helix: 1.50 (0.20), residues: 648 sheet: -1.71 (0.65), residues: 60 loop : -1.66 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 147 TYR 0.010 0.001 TYR A 463 PHE 0.012 0.001 PHE B 39 TRP 0.008 0.001 TRP B 627 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.42 ( 9217) covalent geometry : angle 0.81331 / 0.52 (12500) SS BOND : bond 0.00436 / 0.24 ( 3) SS BOND : angle 5.32402 / 3.04 ( 6) hydrogen bonds : bond 0.13653 / 9.39 ( 518) hydrogen bonds : angle 5.98001 / 4.33 ( 1506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 587 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8530 (mp) REVERT: B 108 ILE cc_start: 0.8258 (pp) cc_final: 0.7937 (mt) outliers start: 4 outliers final: 0 residues processed: 181 average time/residue: 0.0858 time to fit residues: 21.0617 Evaluate side-chains 88 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN B 109 ASN B 126 GLN B 243 HIS B 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.141557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114368 restraints weight = 12456.827| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.18 r_work: 0.3452 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9220 Z= 0.165 Angle : 0.633 10.412 12506 Z= 0.320 Chirality : 0.042 0.196 1438 Planarity : 0.004 0.033 1534 Dihedral : 10.961 164.901 1270 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.17 % Allowed : 9.30 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.25), residues: 1122 helix: 1.97 (0.20), residues: 666 sheet: -1.01 (0.54), residues: 86 loop : -1.60 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 191 TYR 0.014 0.001 TYR B 459 PHE 0.020 0.002 PHE A 293 TRP 0.011 0.001 TRP B 379 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 9217) covalent geometry : angle 0.63137 / 0.32 (12500) SS BOND : bond 0.00245 / 0.14 ( 3) SS BOND : angle 2.10175 / 1.20 ( 6) hydrogen bonds : bond 0.04725 / 3.25 ( 518) hydrogen bonds : angle 4.43498 / 3.24 ( 1506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: B 128 ASP cc_start: 0.6566 (m-30) cc_final: 0.6135 (m-30) REVERT: B 198 MET cc_start: 0.8161 (mtp) cc_final: 0.7861 (mtp) REVERT: B 654 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6936 (m-80) outliers start: 21 outliers final: 11 residues processed: 120 average time/residue: 0.0625 time to fit residues: 11.7356 Evaluate side-chains 82 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN B 244 GLN B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102630 restraints weight = 12482.982| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.71 r_work: 0.3180 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9220 Z= 0.160 Angle : 0.582 8.759 12506 Z= 0.296 Chirality : 0.041 0.180 1438 Planarity : 0.004 0.035 1534 Dihedral : 10.116 152.527 1268 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.89 % Allowed : 10.74 % Favored : 86.36 % 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: 1.08 (0.25), residues: 1122 helix: 2.07 (0.20), residues: 666 sheet: -0.60 (0.57), residues: 86 loop : -1.55 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 191 TYR 0.011 0.001 TYR B 463 PHE 0.010 0.001 PHE B 511 TRP 0.010 0.001 TRP B 379 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 9217) covalent geometry : angle 0.58226 / 0.30 (12500) SS BOND : bond 0.00198 / 0.11 ( 3) SS BOND : angle 0.93367 / 0.49 ( 6) hydrogen bonds : bond 0.04539 / 3.13 ( 518) hydrogen bonds : angle 4.19796 / 3.04 ( 1506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 620 ASP cc_start: 0.8060 (t0) cc_final: 0.7828 (t0) REVERT: B 198 MET cc_start: 0.7514 (mtp) cc_final: 0.7103 (mtp) REVERT: B 654 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6694 (m-80) outliers start: 28 outliers final: 20 residues processed: 104 average time/residue: 0.0672 time to fit residues: 10.8405 Evaluate side-chains 90 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.136496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108479 restraints weight = 12690.393| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.21 r_work: 0.3353 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9220 Z= 0.153 Angle : 0.566 9.012 12506 Z= 0.284 Chirality : 0.040 0.158 1438 Planarity : 0.004 0.037 1534 Dihedral : 9.654 145.729 1268 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.72 % Allowed : 10.95 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1122 helix: 2.21 (0.20), residues: 664 sheet: -0.41 (0.57), residues: 86 loop : -1.51 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.012 0.001 TYR B 336 PHE 0.012 0.001 PHE B 432 TRP 0.010 0.001 TRP B 379 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 9217) covalent geometry : angle 0.56624 / 0.28 (12500) SS BOND : bond 0.00103 / 0.06 ( 3) SS BOND : angle 0.52181 / 0.27 ( 6) hydrogen bonds : bond 0.04358 / 3.01 ( 518) hydrogen bonds : angle 4.09354 / 2.98 ( 1506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: B 127 ASP cc_start: 0.7965 (t0) cc_final: 0.6971 (m-30) REVERT: B 128 ASP cc_start: 0.7019 (m-30) cc_final: 0.6683 (m-30) REVERT: B 654 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7165 (m-80) outliers start: 36 outliers final: 24 residues processed: 107 average time/residue: 0.0600 time to fit residues: 10.1239 Evaluate side-chains 94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.128401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099084 restraints weight = 13096.679| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.36 r_work: 0.3197 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9220 Z= 0.296 Angle : 0.710 12.472 12506 Z= 0.358 Chirality : 0.046 0.160 1438 Planarity : 0.005 0.042 1534 Dihedral : 9.406 138.088 1268 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.03 % Allowed : 11.05 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1122 helix: 1.78 (0.20), residues: 654 sheet: -0.49 (0.56), residues: 84 loop : -1.66 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 378 TYR 0.024 0.002 TYR B 463 PHE 0.029 0.002 PHE A 293 TRP 0.010 0.002 TRP B 379 HIS 0.007 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.30 ( 9217) covalent geometry : angle 0.71004 / 0.36 (12500) SS BOND : bond 0.00114 / 0.07 ( 3) SS BOND : angle 0.55641 / 0.30 ( 6) hydrogen bonds : bond 0.05901 / 4.08 ( 518) hydrogen bonds : angle 4.40936 / 3.19 ( 1506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: B 654 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7985 (m-10) outliers start: 39 outliers final: 25 residues processed: 106 average time/residue: 0.0662 time to fit residues: 10.8744 Evaluate side-chains 88 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.0370 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.134643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105231 restraints weight = 12958.575| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.38 r_work: 0.3288 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9220 Z= 0.124 Angle : 0.561 14.120 12506 Z= 0.279 Chirality : 0.039 0.152 1438 Planarity : 0.004 0.040 1534 Dihedral : 9.002 131.112 1268 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.27 % Allowed : 13.74 % Favored : 83.99 % 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: 1.24 (0.25), residues: 1122 helix: 2.18 (0.20), residues: 668 sheet: -0.33 (0.57), residues: 86 loop : -1.53 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.013 0.001 TYR A 413 PHE 0.017 0.001 PHE A 293 TRP 0.011 0.001 TRP A 379 HIS 0.003 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9217) covalent geometry : angle 0.56088 / 0.28 (12500) SS BOND : bond 0.00201 / 0.11 ( 3) SS BOND : angle 0.24348 / 0.13 ( 6) hydrogen bonds : bond 0.04079 / 2.81 ( 518) hydrogen bonds : angle 4.07723 / 2.98 ( 1506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 127 ASP cc_start: 0.7962 (t0) cc_final: 0.6893 (m-30) outliers start: 22 outliers final: 14 residues processed: 90 average time/residue: 0.0739 time to fit residues: 10.1512 Evaluate side-chains 83 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 543 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 107 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.129340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098219 restraints weight = 12841.295| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.67 r_work: 0.3101 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9220 Z= 0.190 Angle : 0.594 9.930 12506 Z= 0.297 Chirality : 0.041 0.151 1438 Planarity : 0.004 0.041 1534 Dihedral : 8.788 125.281 1268 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.27 % Allowed : 13.02 % Favored : 84.71 % 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: 1.21 (0.25), residues: 1122 helix: 2.17 (0.20), residues: 668 sheet: -0.35 (0.57), residues: 86 loop : -1.57 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.014 0.001 TYR B 336 PHE 0.012 0.001 PHE A 39 TRP 0.010 0.001 TRP B 379 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 ( 9217) covalent geometry : angle 0.59385 / 0.30 (12500) SS BOND : bond 0.00134 / 0.08 ( 3) SS BOND : angle 0.28312 / 0.15 ( 6) hydrogen bonds : bond 0.04657 / 3.22 ( 518) hydrogen bonds : angle 4.09810 / 2.98 ( 1506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.332 Fit side-chains REVERT: B 127 ASP cc_start: 0.7937 (t0) cc_final: 0.6804 (m-30) REVERT: B 370 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8050 (t) outliers start: 22 outliers final: 17 residues processed: 86 average time/residue: 0.0749 time to fit residues: 9.9210 Evaluate side-chains 85 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 543 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 105 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100152 restraints weight = 12683.556| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.53 r_work: 0.3190 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9220 Z= 0.124 Angle : 0.562 10.648 12506 Z= 0.278 Chirality : 0.039 0.233 1438 Planarity : 0.003 0.041 1534 Dihedral : 8.483 118.052 1268 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.17 % Allowed : 13.12 % Favored : 84.71 % 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: 1.45 (0.26), residues: 1122 helix: 2.34 (0.20), residues: 670 sheet: -0.23 (0.58), residues: 86 loop : -1.45 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.013 0.001 TYR B 336 PHE 0.011 0.001 PHE B 432 TRP 0.011 0.001 TRP B 379 HIS 0.003 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9217) covalent geometry : angle 0.56246 / 0.28 (12500) SS BOND : bond 0.00208 / 0.12 ( 3) SS BOND : angle 0.22101 / 0.11 ( 6) hydrogen bonds : bond 0.03972 / 2.73 ( 518) hydrogen bonds : angle 3.98941 / 2.91 ( 1506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.325 Fit side-chains REVERT: A 128 ASP cc_start: 0.6675 (m-30) cc_final: 0.6468 (m-30) REVERT: A 339 SER cc_start: 0.8552 (t) cc_final: 0.8248 (p) REVERT: B 127 ASP cc_start: 0.7941 (t0) cc_final: 0.6755 (m-30) outliers start: 21 outliers final: 17 residues processed: 93 average time/residue: 0.0624 time to fit residues: 9.2470 Evaluate side-chains 86 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.130868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100121 restraints weight = 12829.867| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.61 r_work: 0.3138 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9220 Z= 0.145 Angle : 0.579 12.849 12506 Z= 0.283 Chirality : 0.040 0.260 1438 Planarity : 0.004 0.041 1534 Dihedral : 8.190 110.177 1268 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.17 % Allowed : 13.33 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1122 helix: 2.37 (0.20), residues: 670 sheet: -0.24 (0.57), residues: 86 loop : -1.44 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.013 0.001 TYR B 336 PHE 0.011 0.001 PHE B 432 TRP 0.010 0.001 TRP B 379 HIS 0.003 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9217) covalent geometry : angle 0.57877 / 0.28 (12500) SS BOND : bond 0.00129 / 0.07 ( 3) SS BOND : angle 0.22236 / 0.11 ( 6) hydrogen bonds : bond 0.04119 / 2.84 ( 518) hydrogen bonds : angle 4.00953 / 2.92 ( 1506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.326 Fit side-chains REVERT: B 127 ASP cc_start: 0.7921 (t0) cc_final: 0.6763 (m-30) REVERT: B 128 ASP cc_start: 0.7580 (m-30) cc_final: 0.7300 (m-30) outliers start: 21 outliers final: 20 residues processed: 89 average time/residue: 0.0730 time to fit residues: 10.2193 Evaluate side-chains 86 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.099621 restraints weight = 12810.951| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.66 r_work: 0.3119 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9220 Z= 0.165 Angle : 0.607 14.345 12506 Z= 0.296 Chirality : 0.041 0.282 1438 Planarity : 0.004 0.041 1534 Dihedral : 7.927 101.274 1268 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.38 % Allowed : 13.12 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.26), residues: 1122 helix: 2.33 (0.20), residues: 670 sheet: -0.23 (0.57), residues: 86 loop : -1.46 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.015 0.001 TYR B 336 PHE 0.011 0.001 PHE B 432 TRP 0.009 0.001 TRP B 379 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 9217) covalent geometry : angle 0.60716 / 0.30 (12500) SS BOND : bond 0.00135 / 0.08 ( 3) SS BOND : angle 0.21800 / 0.11 ( 6) hydrogen bonds : bond 0.04304 / 2.96 ( 518) hydrogen bonds : angle 4.04226 / 2.94 ( 1506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.359 Fit side-chains REVERT: B 127 ASP cc_start: 0.7950 (t0) cc_final: 0.6793 (m-30) REVERT: B 370 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8110 (t) outliers start: 23 outliers final: 21 residues processed: 87 average time/residue: 0.0749 time to fit residues: 10.0786 Evaluate side-chains 87 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 654 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 chunk 19 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097270 restraints weight = 12540.476| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.68 r_work: 0.3114 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9220 Z= 0.126 Angle : 0.571 14.156 12506 Z= 0.281 Chirality : 0.040 0.276 1438 Planarity : 0.004 0.041 1534 Dihedral : 7.555 86.272 1268 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.17 % Allowed : 13.74 % Favored : 84.09 % 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: 1.58 (0.26), residues: 1122 helix: 2.42 (0.20), residues: 670 sheet: -0.13 (0.57), residues: 86 loop : -1.38 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 246 TYR 0.016 0.001 TYR B 336 PHE 0.011 0.001 PHE B 432 TRP 0.010 0.001 TRP B 379 HIS 0.003 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9217) covalent geometry : angle 0.57117 / 0.28 (12500) SS BOND : bond 0.00148 / 0.08 ( 3) SS BOND : angle 0.18574 / 0.09 ( 6) hydrogen bonds : bond 0.03886 / 2.66 ( 518) hydrogen bonds : angle 3.97420 / 2.89 ( 1506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2005.70 seconds wall clock time: 35 minutes 12.93 seconds (2112.93 seconds total)