Starting phenix.real_space_refine on Mon Jul 28 00:15:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nt9_0506/07_2025/6nt9_0506.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nt9_0506/07_2025/6nt9_0506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nt9_0506/07_2025/6nt9_0506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nt9_0506/07_2025/6nt9_0506.map" model { file = "/net/cci-nas-00/data/ceres_data/6nt9_0506/07_2025/6nt9_0506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nt9_0506/07_2025/6nt9_0506.cif" } resolution = 3.3 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= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6314 2.51 5 N 1692 2.21 5 O 1852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9906 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4881 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 585} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 2, 'TRANS': 6} Restraints were copied for chains: D, B Time building chain proxies: 9.22, per 1000 atoms: 0.93 Number of scatterers: 9906 At special positions: 0 Unit cell: (80.25, 114.49, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1852 8.00 N 1692 7.00 C 6314 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: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 55.4% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 50 through 61 removed outlier: 3.751A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.524A pdb=" N VAL A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 108 through 130 removed outlier: 3.684A pdb=" N ASN A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.731A pdb=" N GLY A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.943A pdb=" N LEU A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.836A pdb=" N PHE A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 344 removed outlier: 3.597A pdb=" N PHE A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.776A pdb=" N PHE A 370 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 483 removed outlier: 3.802A pdb=" N SER A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 448 " --> pdb=" O ARG A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 527 removed outlier: 3.882A pdb=" N LYS A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 removed outlier: 3.857A pdb=" N HIS A 538 " --> pdb=" O ALA A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 572 removed outlier: 3.751A pdb=" N LEU A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 572 " --> pdb=" O LYS A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 605 removed outlier: 3.808A pdb=" N TYR A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 658 removed outlier: 4.057A pdb=" N GLU A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 646 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 removed outlier: 3.751A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 99 removed outlier: 3.525A pdb=" N VAL B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 108 through 130 removed outlier: 3.683A pdb=" N ASN B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 232 through 240 removed outlier: 3.731A pdb=" N GLY B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.943A pdb=" N LEU B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Proline residue: B 279 - end of helix Processing helix chain 'B' and resid 294 through 307 removed outlier: 3.835A pdb=" N PHE B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 344 removed outlier: 3.598A pdb=" N PHE B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.775A pdb=" N PHE B 370 " --> pdb=" O ALA B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 483 removed outlier: 3.803A pdb=" N SER B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 527 removed outlier: 3.883A pdb=" N LYS B 504 " --> pdb=" O ASP B 500 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 539 removed outlier: 3.857A pdb=" N HIS B 538 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 572 removed outlier: 3.750A pdb=" N LEU B 555 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 572 " --> pdb=" O LYS B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 605 removed outlier: 3.808A pdb=" N TYR B 591 " --> pdb=" O LYS B 587 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 602 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 658 removed outlier: 4.057A pdb=" N GLU B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS B 646 " --> pdb=" O GLU B 642 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.548A pdb=" N ARG A 25 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 14 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 3 removed outlier: 5.055A pdb=" N LYS A 82 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 72 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.593A pdb=" N SER A 247 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 320 through 326 removed outlier: 9.695A pdb=" N ILE A 379 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N HIS A 312 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL A 381 " --> pdb=" O HIS A 312 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A 314 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 352 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.548A pdb=" N ARG B 25 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 14 " --> pdb=" O ARG B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 3 removed outlier: 5.055A pdb=" N LYS B 82 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 72 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 141 through 145 Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.593A pdb=" N SER B 247 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 320 through 326 removed outlier: 9.695A pdb=" N ILE B 379 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS B 312 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL B 381 " --> pdb=" O HIS B 312 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE B 314 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU B 352 " --> pdb=" O LEU B 359 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1728 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: 2.92 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2878 1.33 - 1.45: 1642 1.45 - 1.57: 5508 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 10104 Sorted by residual: bond pdb=" CB VAL B 381 " pdb=" CG2 VAL B 381 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.82e+00 bond pdb=" CB VAL A 381 " pdb=" CG2 VAL A 381 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.64e+00 bond pdb=" CB ILE B 418 " pdb=" CG2 ILE B 418 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.56e+00 bond pdb=" CB ILE A 418 " pdb=" CG2 ILE A 418 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" CG LEU C 374 " pdb=" CD2 LEU C 374 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.58e+00 ... (remaining 10099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 13210 2.26 - 4.52: 399 4.52 - 6.78: 27 6.78 - 9.04: 2 9.04 - 11.30: 4 Bond angle restraints: 13642 Sorted by residual: angle pdb=" C GLY A 175 " pdb=" N THR A 176 " pdb=" CA THR A 176 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C GLY B 175 " pdb=" N THR B 176 " pdb=" CA THR B 176 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C PRO D 371 " pdb=" N GLN D 372 " pdb=" CA GLN D 372 " ideal model delta sigma weight residual 122.15 133.45 -11.30 3.47e+00 8.31e-02 1.06e+01 angle pdb=" C PRO C 371 " pdb=" N GLN C 372 " pdb=" CA GLN C 372 " ideal model delta sigma weight residual 122.15 133.41 -11.26 3.47e+00 8.31e-02 1.05e+01 angle pdb=" C GLY B 294 " pdb=" N PHE B 295 " pdb=" CA PHE B 295 " ideal model delta sigma weight residual 122.09 116.95 5.14 1.79e+00 3.12e-01 8.23e+00 ... (remaining 13637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 5778 14.55 - 29.10: 232 29.10 - 43.64: 76 43.64 - 58.19: 6 58.19 - 72.74: 6 Dihedral angle restraints: 6098 sinusoidal: 2516 harmonic: 3582 Sorted by residual: dihedral pdb=" CA TRP A 293 " pdb=" C TRP A 293 " pdb=" N GLY A 294 " pdb=" CA GLY A 294 " ideal model delta harmonic sigma weight residual -180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TRP B 293 " pdb=" C TRP B 293 " pdb=" N GLY B 294 " pdb=" CA GLY B 294 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ARG B 308 " pdb=" C ARG B 308 " pdb=" N MET B 309 " pdb=" CA MET B 309 " ideal model delta harmonic sigma weight residual 180.00 163.72 16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 6095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1015 0.051 - 0.103: 424 0.103 - 0.154: 81 0.154 - 0.205: 8 0.205 - 0.257: 4 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CB ILE A 73 " pdb=" CA ILE A 73 " pdb=" CG1 ILE A 73 " pdb=" CG2 ILE A 73 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE B 73 " pdb=" CA ILE B 73 " pdb=" CG1 ILE B 73 " pdb=" CG2 ILE B 73 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA THR B 176 " pdb=" N THR B 176 " pdb=" C THR B 176 " pdb=" CB THR B 176 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1529 not shown) Planarity restraints: 1732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 137 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO B 138 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 137 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO A 138 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 325 " -0.019 2.00e-02 2.50e+03 1.86e-02 6.94e+00 pdb=" CG TYR A 325 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 325 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 325 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 325 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 325 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 325 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 325 " -0.002 2.00e-02 2.50e+03 ... (remaining 1729 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2114 2.78 - 3.31: 8637 3.31 - 3.84: 15360 3.84 - 4.37: 17261 4.37 - 4.90: 31485 Nonbonded interactions: 74857 Sorted by model distance: nonbonded pdb=" OE2 GLU B 111 " pdb=" OH TYR B 153 " model vdw 2.250 3.040 nonbonded pdb=" OE2 GLU A 111 " pdb=" OH TYR A 153 " model vdw 2.251 3.040 nonbonded pdb=" NH2 ARG A 357 " pdb=" OD2 ASP B 452 " model vdw 2.274 3.120 nonbonded pdb=" O ASP A 523 " pdb=" OG SER A 527 " model vdw 2.342 3.040 nonbonded pdb=" O ASP B 523 " pdb=" OG SER B 527 " model vdw 2.342 3.040 ... (remaining 74852 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 'C' selection = chain 'D' } 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=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: 0.660 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.330 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.010 0.074 10104 Z= 0.416 Angle : 0.894 11.305 13642 Z= 0.489 Chirality : 0.056 0.257 1532 Planarity : 0.007 0.066 1732 Dihedral : 9.659 72.738 3778 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.18 % Allowed : 1.73 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.20), residues: 1200 helix: -0.77 (0.17), residues: 628 sheet: -1.48 (0.39), residues: 146 loop : -1.98 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 619 HIS 0.015 0.003 HIS B 459 PHE 0.030 0.003 PHE A 585 TYR 0.043 0.003 TYR A 325 ARG 0.014 0.001 ARG B 357 Details of bonding type rmsd hydrogen bonds : bond 0.14260 ( 588) hydrogen bonds : angle 5.44051 ( 1728) covalent geometry : bond 0.01029 (10104) covalent geometry : angle 0.89404 (13642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 1.605 Fit side-chains REVERT: A 13 ASP cc_start: 0.7775 (m-30) cc_final: 0.7526 (m-30) REVERT: A 61 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8243 (mtmm) REVERT: A 234 MET cc_start: 0.7488 (tpt) cc_final: 0.7121 (mmm) REVERT: A 320 THR cc_start: 0.8756 (p) cc_final: 0.8534 (p) REVERT: A 351 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 409 ASP cc_start: 0.8086 (m-30) cc_final: 0.7717 (m-30) REVERT: A 414 MET cc_start: 0.8321 (tmm) cc_final: 0.8027 (ttp) REVERT: A 564 TYR cc_start: 0.8038 (m-10) cc_final: 0.7720 (m-10) REVERT: A 648 GLN cc_start: 0.7530 (tt0) cc_final: 0.7195 (tp40) REVERT: B 53 MET cc_start: 0.7450 (mmm) cc_final: 0.7221 (mmp) REVERT: B 61 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8105 (mtmm) REVERT: B 234 MET cc_start: 0.7409 (tpt) cc_final: 0.7047 (mmm) REVERT: B 374 THR cc_start: 0.9056 (p) cc_final: 0.8813 (m) REVERT: B 376 GLU cc_start: 0.8084 (mp0) cc_final: 0.7712 (mp0) REVERT: B 462 THR cc_start: 0.7978 (m) cc_final: 0.7571 (p) REVERT: B 534 ASP cc_start: 0.8503 (p0) cc_final: 0.8260 (p0) REVERT: B 564 TYR cc_start: 0.8174 (m-10) cc_final: 0.7695 (m-10) REVERT: B 648 GLN cc_start: 0.7670 (tt0) cc_final: 0.7053 (tp-100) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.2599 time to fit residues: 70.0931 Evaluate side-chains 111 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 312 HIS A 369 HIS ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN A 655 GLN B 81 HIS B 312 HIS B 369 HIS B 581 GLN B 655 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.093142 restraints weight = 13963.364| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.02 r_work: 0.2987 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10104 Z= 0.135 Angle : 0.495 6.738 13642 Z= 0.264 Chirality : 0.040 0.129 1532 Planarity : 0.004 0.037 1732 Dihedral : 3.943 16.443 1318 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.64 % Allowed : 6.10 % Favored : 93.26 % 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: 0.56 (0.24), residues: 1200 helix: 1.89 (0.20), residues: 626 sheet: -1.42 (0.39), residues: 134 loop : -1.28 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 619 HIS 0.009 0.001 HIS A 459 PHE 0.021 0.001 PHE B 470 TYR 0.014 0.001 TYR B 325 ARG 0.003 0.000 ARG B 627 Details of bonding type rmsd hydrogen bonds : bond 0.06521 ( 588) hydrogen bonds : angle 3.95713 ( 1728) covalent geometry : bond 0.00270 (10104) covalent geometry : angle 0.49548 (13642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8978 (mp) REVERT: A 61 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8387 (mtmm) REVERT: A 234 MET cc_start: 0.7496 (tpt) cc_final: 0.7200 (mmm) REVERT: A 337 GLU cc_start: 0.8574 (tt0) cc_final: 0.8300 (mm-30) REVERT: A 351 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7981 (mt-10) REVERT: A 409 ASP cc_start: 0.8496 (m-30) cc_final: 0.8099 (m-30) REVERT: A 648 GLN cc_start: 0.7660 (tt0) cc_final: 0.6990 (tp-100) REVERT: B 53 MET cc_start: 0.7490 (mmm) cc_final: 0.7246 (mmp) REVERT: B 61 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8292 (mtmm) REVERT: B 234 MET cc_start: 0.7364 (tpt) cc_final: 0.7115 (mmm) REVERT: B 376 GLU cc_start: 0.8829 (mp0) cc_final: 0.8475 (mp0) REVERT: B 462 THR cc_start: 0.7940 (m) cc_final: 0.7502 (p) REVERT: B 561 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8210 (mm-30) outliers start: 7 outliers final: 3 residues processed: 143 average time/residue: 0.2145 time to fit residues: 43.7546 Evaluate side-chains 117 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN B 312 HIS ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094132 restraints weight = 14181.730| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.07 r_work: 0.2944 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 0.034 10104 Z= 0.171 Angle : 0.511 6.027 13642 Z= 0.270 Chirality : 0.042 0.141 1532 Planarity : 0.004 0.042 1732 Dihedral : 3.686 14.786 1318 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.37 % Allowed : 7.74 % Favored : 90.89 % 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: 1.36 (0.25), residues: 1200 helix: 2.53 (0.20), residues: 630 sheet: -1.38 (0.40), residues: 136 loop : -0.79 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 619 HIS 0.007 0.001 HIS B 459 PHE 0.018 0.001 PHE A 470 TYR 0.017 0.001 TYR B 325 ARG 0.004 0.000 ARG A 440 Details of bonding type rmsd hydrogen bonds : bond 0.06611 ( 588) hydrogen bonds : angle 3.87680 ( 1728) covalent geometry : bond 0.00396 (10104) covalent geometry : angle 0.51067 (13642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8983 (mp) REVERT: A 61 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8351 (mtmm) REVERT: A 351 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 409 ASP cc_start: 0.8579 (m-30) cc_final: 0.8247 (m-30) REVERT: A 516 GLU cc_start: 0.8260 (tp30) cc_final: 0.7876 (tp30) REVERT: A 648 GLN cc_start: 0.7606 (tt0) cc_final: 0.6916 (tp-100) REVERT: B 37 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8927 (mp) REVERT: B 53 MET cc_start: 0.7396 (mmm) cc_final: 0.7167 (mmp) REVERT: B 61 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8256 (mtmm) REVERT: B 234 MET cc_start: 0.7453 (tpt) cc_final: 0.7215 (mmm) REVERT: B 405 ARG cc_start: 0.7894 (mtp-110) cc_final: 0.7662 (ttm-80) REVERT: B 462 THR cc_start: 0.7935 (m) cc_final: 0.7383 (p) outliers start: 15 outliers final: 9 residues processed: 125 average time/residue: 0.3000 time to fit residues: 54.2544 Evaluate side-chains 120 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 0.0030 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS C 372 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097451 restraints weight = 14077.164| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.98 r_work: 0.2911 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10104 Z= 0.192 Angle : 0.519 7.073 13642 Z= 0.274 Chirality : 0.043 0.141 1532 Planarity : 0.004 0.045 1732 Dihedral : 3.658 14.001 1318 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.46 % Allowed : 8.38 % Favored : 90.16 % 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: 1.59 (0.25), residues: 1200 helix: 2.72 (0.20), residues: 630 sheet: -1.37 (0.40), residues: 136 loop : -0.66 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 619 HIS 0.006 0.001 HIS B 459 PHE 0.016 0.001 PHE A 470 TYR 0.018 0.001 TYR B 325 ARG 0.004 0.000 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.06697 ( 588) hydrogen bonds : angle 3.88764 ( 1728) covalent geometry : bond 0.00456 (10104) covalent geometry : angle 0.51852 (13642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.174 Fit side-chains REVERT: A 37 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8947 (mp) REVERT: A 61 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8324 (mtmm) REVERT: A 351 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 376 GLU cc_start: 0.8716 (mp0) cc_final: 0.8455 (mp0) REVERT: A 409 ASP cc_start: 0.8561 (m-30) cc_final: 0.8194 (m-30) REVERT: A 516 GLU cc_start: 0.8234 (tp30) cc_final: 0.7792 (tp30) REVERT: A 569 ASP cc_start: 0.7325 (m-30) cc_final: 0.6998 (m-30) REVERT: A 648 GLN cc_start: 0.7564 (tt0) cc_final: 0.6885 (tp-100) REVERT: B 37 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8919 (mp) REVERT: B 53 MET cc_start: 0.7462 (mmm) cc_final: 0.7229 (mmp) REVERT: B 61 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8281 (mtmm) REVERT: B 234 MET cc_start: 0.7265 (tpt) cc_final: 0.7024 (mmm) REVERT: B 376 GLU cc_start: 0.8726 (mp0) cc_final: 0.8473 (mp0) REVERT: B 405 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7668 (ttm-80) outliers start: 16 outliers final: 11 residues processed: 130 average time/residue: 0.2702 time to fit residues: 50.6998 Evaluate side-chains 123 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.100598 restraints weight = 14085.020| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.01 r_work: 0.2964 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10104 Z= 0.143 Angle : 0.472 6.049 13642 Z= 0.250 Chirality : 0.041 0.135 1532 Planarity : 0.003 0.042 1732 Dihedral : 3.475 13.459 1318 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.46 % Allowed : 8.93 % Favored : 89.62 % 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: 1.89 (0.25), residues: 1200 helix: 2.93 (0.20), residues: 632 sheet: -1.27 (0.41), residues: 136 loop : -0.47 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 619 HIS 0.005 0.001 HIS B 459 PHE 0.016 0.001 PHE A 470 TYR 0.010 0.001 TYR B 325 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.06101 ( 588) hydrogen bonds : angle 3.73225 ( 1728) covalent geometry : bond 0.00322 (10104) covalent geometry : angle 0.47246 (13642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.640 Fit side-chains REVERT: A 37 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8958 (mp) REVERT: A 61 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8326 (mtmm) REVERT: A 351 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 376 GLU cc_start: 0.8698 (mp0) cc_final: 0.8462 (mp0) REVERT: A 409 ASP cc_start: 0.8528 (m-30) cc_final: 0.8123 (m-30) REVERT: A 639 ASP cc_start: 0.8409 (t0) cc_final: 0.8182 (t0) REVERT: A 648 GLN cc_start: 0.7515 (tt0) cc_final: 0.6805 (tp-100) REVERT: B 37 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8944 (mp) REVERT: B 53 MET cc_start: 0.7425 (mmm) cc_final: 0.7198 (mmp) REVERT: B 61 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8281 (mtmm) REVERT: B 319 MET cc_start: 0.9039 (ttt) cc_final: 0.8838 (ttm) REVERT: B 376 GLU cc_start: 0.8717 (mp0) cc_final: 0.8470 (mp0) REVERT: B 409 ASP cc_start: 0.8480 (m-30) cc_final: 0.8043 (m-30) REVERT: B 523 ASP cc_start: 0.8094 (t70) cc_final: 0.7682 (t0) outliers start: 16 outliers final: 13 residues processed: 133 average time/residue: 0.2602 time to fit residues: 51.4948 Evaluate side-chains 125 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 293 TRP Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094249 restraints weight = 14152.789| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.11 r_work: 0.2888 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10104 Z= 0.161 Angle : 0.484 5.868 13642 Z= 0.254 Chirality : 0.041 0.139 1532 Planarity : 0.003 0.044 1732 Dihedral : 3.465 13.551 1318 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.28 % Allowed : 9.56 % Favored : 88.16 % 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: 1.97 (0.25), residues: 1200 helix: 3.01 (0.20), residues: 634 sheet: -1.31 (0.41), residues: 136 loop : -0.44 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.005 0.001 HIS B 459 PHE 0.015 0.001 PHE A 470 TYR 0.010 0.001 TYR A 325 ARG 0.002 0.000 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.06241 ( 588) hydrogen bonds : angle 3.75381 ( 1728) covalent geometry : bond 0.00376 (10104) covalent geometry : angle 0.48406 (13642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.210 Fit side-chains REVERT: A 37 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8906 (mp) REVERT: A 61 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8315 (mtmm) REVERT: A 351 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8030 (mt-10) REVERT: A 376 GLU cc_start: 0.8700 (mp0) cc_final: 0.8469 (mp0) REVERT: A 409 ASP cc_start: 0.8542 (m-30) cc_final: 0.8102 (m-30) REVERT: A 512 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6865 (tt0) REVERT: A 516 GLU cc_start: 0.8205 (tp30) cc_final: 0.7803 (tp30) REVERT: A 639 ASP cc_start: 0.8336 (t0) cc_final: 0.8101 (t0) REVERT: B 37 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8906 (mp) REVERT: B 53 MET cc_start: 0.7506 (mmm) cc_final: 0.7252 (mmp) REVERT: B 61 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8251 (mtmm) REVERT: B 376 GLU cc_start: 0.8757 (mp0) cc_final: 0.8510 (mp0) REVERT: B 405 ARG cc_start: 0.7875 (mtp-110) cc_final: 0.7622 (ttm-80) REVERT: B 523 ASP cc_start: 0.8076 (t70) cc_final: 0.7688 (t0) outliers start: 25 outliers final: 16 residues processed: 132 average time/residue: 0.1976 time to fit residues: 37.8656 Evaluate side-chains 130 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 293 TRP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 293 TRP Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.0070 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 312 HIS A 512 GLN C 372 GLN B 133 HIS D 372 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.097670 restraints weight = 14149.492| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.10 r_work: 0.2955 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10104 Z= 0.112 Angle : 0.444 6.790 13642 Z= 0.233 Chirality : 0.039 0.127 1532 Planarity : 0.003 0.044 1732 Dihedral : 3.255 12.793 1318 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.82 % Allowed : 9.74 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.25), residues: 1200 helix: 3.32 (0.20), residues: 634 sheet: -1.15 (0.41), residues: 136 loop : -0.29 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.008 0.001 HIS A 459 PHE 0.016 0.001 PHE A 470 TYR 0.008 0.001 TYR B 153 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.05415 ( 588) hydrogen bonds : angle 3.56064 ( 1728) covalent geometry : bond 0.00229 (10104) covalent geometry : angle 0.44394 (13642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.178 Fit side-chains REVERT: A 61 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8356 (mtmm) REVERT: A 376 GLU cc_start: 0.8716 (mp0) cc_final: 0.8470 (mp0) REVERT: A 459 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6765 (t70) REVERT: A 516 GLU cc_start: 0.8020 (tp30) cc_final: 0.7712 (tp30) REVERT: A 639 ASP cc_start: 0.8261 (t0) cc_final: 0.8024 (t0) REVERT: B 37 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8919 (mp) REVERT: B 53 MET cc_start: 0.7474 (mmm) cc_final: 0.7209 (mmp) REVERT: B 61 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8217 (mtmm) REVERT: B 65 LYS cc_start: 0.8854 (ptmt) cc_final: 0.8576 (pttt) REVERT: B 376 GLU cc_start: 0.8726 (mp0) cc_final: 0.8466 (mp0) REVERT: B 523 ASP cc_start: 0.8022 (t70) cc_final: 0.7669 (t0) outliers start: 20 outliers final: 15 residues processed: 134 average time/residue: 0.1940 time to fit residues: 38.3057 Evaluate side-chains 127 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 293 TRP Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 372 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098883 restraints weight = 14300.422| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.02 r_work: 0.2786 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10104 Z= 0.159 Angle : 0.488 6.615 13642 Z= 0.255 Chirality : 0.041 0.139 1532 Planarity : 0.003 0.045 1732 Dihedral : 3.342 12.627 1318 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.09 % Allowed : 9.84 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.25), residues: 1200 helix: 3.26 (0.20), residues: 634 sheet: -1.25 (0.41), residues: 136 loop : -0.24 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 619 HIS 0.008 0.001 HIS A 459 PHE 0.016 0.001 PHE A 470 TYR 0.009 0.001 TYR A 325 ARG 0.002 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.06042 ( 588) hydrogen bonds : angle 3.66986 ( 1728) covalent geometry : bond 0.00372 (10104) covalent geometry : angle 0.48830 (13642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.220 Fit side-chains REVERT: A 37 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8828 (mp) REVERT: A 61 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8254 (mtmm) REVERT: A 319 MET cc_start: 0.9009 (ttt) cc_final: 0.8771 (ttt) REVERT: A 376 GLU cc_start: 0.8669 (mp0) cc_final: 0.8417 (mp0) REVERT: A 459 HIS cc_start: 0.6923 (OUTLIER) cc_final: 0.6649 (t70) REVERT: A 639 ASP cc_start: 0.8173 (t0) cc_final: 0.7932 (t0) REVERT: B 37 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8796 (mp) REVERT: B 53 MET cc_start: 0.7568 (mmm) cc_final: 0.7307 (mmp) REVERT: B 61 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8190 (mtmm) REVERT: B 376 GLU cc_start: 0.8720 (mp0) cc_final: 0.8455 (mp0) REVERT: B 523 ASP cc_start: 0.8004 (t70) cc_final: 0.7624 (t0) outliers start: 23 outliers final: 20 residues processed: 125 average time/residue: 0.1929 time to fit residues: 35.7582 Evaluate side-chains 126 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 293 TRP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 293 TRP Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 94 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 512 GLN ** 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 = 0.3498 r_free = 0.3498 target = 0.127278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098828 restraints weight = 14302.068| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.01 r_work: 0.2779 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10104 Z= 0.163 Angle : 0.492 6.300 13642 Z= 0.258 Chirality : 0.041 0.140 1532 Planarity : 0.003 0.045 1732 Dihedral : 3.388 12.684 1318 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.28 % Allowed : 10.11 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.25), residues: 1200 helix: 3.23 (0.20), residues: 634 sheet: -1.19 (0.42), residues: 140 loop : -0.28 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 9 HIS 0.008 0.001 HIS A 459 PHE 0.017 0.001 PHE A 470 TYR 0.010 0.001 TYR A 325 ARG 0.002 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.06149 ( 588) hydrogen bonds : angle 3.71958 ( 1728) covalent geometry : bond 0.00382 (10104) covalent geometry : angle 0.49207 (13642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.293 Fit side-chains REVERT: A 37 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8815 (mp) REVERT: A 61 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8242 (mtmm) REVERT: A 319 MET cc_start: 0.9040 (ttt) cc_final: 0.8792 (ttt) REVERT: A 376 GLU cc_start: 0.8655 (mp0) cc_final: 0.8400 (mp0) REVERT: A 459 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.6657 (t70) REVERT: A 639 ASP cc_start: 0.8166 (t0) cc_final: 0.7919 (t0) REVERT: B 37 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8796 (mp) REVERT: B 53 MET cc_start: 0.7580 (mmm) cc_final: 0.7324 (mmp) REVERT: B 61 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8189 (mtmm) REVERT: B 319 MET cc_start: 0.9054 (ttt) cc_final: 0.8841 (ttt) REVERT: B 376 GLU cc_start: 0.8705 (mp0) cc_final: 0.8444 (mp0) REVERT: B 409 ASP cc_start: 0.8533 (m-30) cc_final: 0.8069 (m-30) REVERT: B 523 ASP cc_start: 0.8033 (t70) cc_final: 0.7662 (t0) outliers start: 25 outliers final: 21 residues processed: 121 average time/residue: 0.2775 time to fit residues: 50.7839 Evaluate side-chains 127 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 293 TRP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 293 TRP Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 512 GLN ** 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 = 0.3481 r_free = 0.3481 target = 0.126461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097224 restraints weight = 14194.702| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.04 r_work: 0.2871 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10104 Z= 0.115 Angle : 0.443 5.992 13642 Z= 0.232 Chirality : 0.039 0.128 1532 Planarity : 0.003 0.043 1732 Dihedral : 3.185 12.305 1318 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.73 % Allowed : 10.84 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.25), residues: 1200 helix: 3.44 (0.20), residues: 634 sheet: -1.16 (0.42), residues: 136 loop : -0.09 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 619 HIS 0.008 0.001 HIS A 459 PHE 0.016 0.001 PHE A 470 TYR 0.009 0.001 TYR B 564 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.05316 ( 588) hydrogen bonds : angle 3.50373 ( 1728) covalent geometry : bond 0.00242 (10104) covalent geometry : angle 0.44342 (13642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.219 Fit side-chains REVERT: A 37 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8836 (mp) REVERT: A 59 LEU cc_start: 0.8557 (mp) cc_final: 0.8199 (tt) REVERT: A 61 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8278 (mtmm) REVERT: A 376 GLU cc_start: 0.8660 (mp0) cc_final: 0.8406 (mp0) REVERT: A 598 MET cc_start: 0.8923 (tpp) cc_final: 0.8693 (mmm) REVERT: B 37 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8833 (mp) REVERT: B 53 MET cc_start: 0.7549 (mmm) cc_final: 0.7293 (mmp) REVERT: B 61 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8181 (mtmm) REVERT: B 65 LYS cc_start: 0.8898 (ptmt) cc_final: 0.8552 (pttt) REVERT: B 523 ASP cc_start: 0.7867 (t70) cc_final: 0.7536 (t0) outliers start: 19 outliers final: 16 residues processed: 121 average time/residue: 0.1990 time to fit residues: 35.5942 Evaluate side-chains 119 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 293 TRP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 293 TRP Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.0870 chunk 48 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 512 GLN ** 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 = 0.3490 r_free = 0.3490 target = 0.126910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097170 restraints weight = 14105.512| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.02 r_work: 0.2947 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10104 Z= 0.127 Angle : 0.459 5.634 13642 Z= 0.241 Chirality : 0.040 0.137 1532 Planarity : 0.003 0.042 1732 Dihedral : 3.201 12.094 1318 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.00 % Allowed : 10.56 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.25), residues: 1200 helix: 3.43 (0.20), residues: 634 sheet: -1.16 (0.42), residues: 136 loop : -0.02 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 619 HIS 0.006 0.001 HIS A 459 PHE 0.016 0.001 PHE A 470 TYR 0.008 0.001 TYR B 153 ARG 0.001 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.05482 ( 588) hydrogen bonds : angle 3.53887 ( 1728) covalent geometry : bond 0.00279 (10104) covalent geometry : angle 0.45866 (13642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5357.21 seconds wall clock time: 96 minutes 16.47 seconds (5776.47 seconds total)