Starting phenix.real_space_refine on Fri Feb 14 06:04:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nt9_0506/02_2025/6nt9_0506.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nt9_0506/02_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_0506/02_2025/6nt9_0506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nt9_0506/02_2025/6nt9_0506.map" model { file = "/net/cci-nas-00/data/ceres_data/6nt9_0506/02_2025/6nt9_0506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nt9_0506/02_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-5592/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: 9.00, per 1000 atoms: 0.91 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: 2.37 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: 1.14 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: 2.94 Time building geometry restraints manager: 2.74 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: 0.590 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.080 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.150 ------------------------------------------------------------------------------- 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= 0.660 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 *********************** 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 : 1.131 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: 0.2627 time to fit residues: 70.4954 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 : 1.231 ------------------------------------------------------------------------------- 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: 0.2846 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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= 0.174 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 *********************** 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 : 1.199 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8980 (mp) REVERT: A 61 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8388 (mtmm) REVERT: A 234 MET cc_start: 0.7503 (tpt) cc_final: 0.7208 (mmm) REVERT: A 337 GLU cc_start: 0.8578 (tt0) cc_final: 0.8302 (mm-30) REVERT: A 351 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 409 ASP cc_start: 0.8493 (m-30) cc_final: 0.8098 (m-30) REVERT: A 648 GLN cc_start: 0.7664 (tt0) cc_final: 0.6996 (tp-100) REVERT: B 53 MET cc_start: 0.7499 (mmm) cc_final: 0.7256 (mmp) REVERT: B 61 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8293 (mtmm) REVERT: B 234 MET cc_start: 0.7370 (tpt) cc_final: 0.7121 (mmm) REVERT: B 376 GLU cc_start: 0.8829 (mp0) cc_final: 0.8475 (mp0) REVERT: B 462 THR cc_start: 0.7941 (m) cc_final: 0.7502 (p) REVERT: B 561 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8212 (mm-30) outliers start: 7 outliers final: 3 residues processed: 143 average time/residue: 0.2145 time to fit residues: 43.7149 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 : 1.293 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.0040 chunk 42 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.3196 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.127514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.099841 restraints weight = 14078.227| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.92 r_work: 0.2793 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10104 Z= 0.240 Angle : 0.500 6.006 13642 Z= 0.264 Chirality : 0.042 0.142 1532 Planarity : 0.004 0.041 1732 Dihedral : 3.659 14.855 1318 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.28 % Allowed : 7.92 % Favored : 90.80 % 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: 1.40 (0.25), residues: 1200 helix: 2.56 (0.20), residues: 630 sheet: -1.37 (0.40), residues: 136 loop : -0.78 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 619 HIS 0.007 0.001 HIS B 459 PHE 0.018 0.001 PHE A 470 TYR 0.015 0.001 TYR B 325 ARG 0.004 0.000 ARG A 357 *********************** 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 132 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.268 Fit side-chains REVERT: A 37 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8844 (mp) REVERT: A 61 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8324 (mtmm) REVERT: A 235 TYR cc_start: 0.8215 (t80) cc_final: 0.8012 (t80) REVERT: A 351 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7922 (mt-10) REVERT: A 409 ASP cc_start: 0.8537 (m-30) cc_final: 0.8195 (m-30) REVERT: A 516 GLU cc_start: 0.8225 (tp30) cc_final: 0.7822 (tp30) REVERT: A 569 ASP cc_start: 0.7013 (m-30) cc_final: 0.6665 (m-30) REVERT: A 648 GLN cc_start: 0.7559 (tt0) cc_final: 0.6892 (tp-100) REVERT: B 37 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8782 (mp) REVERT: B 53 MET cc_start: 0.7367 (mmm) cc_final: 0.7127 (mmp) REVERT: B 61 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8228 (mtmm) REVERT: B 234 MET cc_start: 0.7236 (tpt) cc_final: 0.7002 (mmm) REVERT: B 249 VAL cc_start: 0.8957 (t) cc_final: 0.8728 (p) REVERT: B 462 THR cc_start: 0.7854 (m) cc_final: 0.7318 (p) outliers start: 14 outliers final: 9 residues processed: 124 average time/residue: 0.2136 time to fit residues: 38.6679 Evaluate side-chains 118 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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: 0.0470 chunk 72 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.094818 restraints weight = 14118.415| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.00 r_work: 0.2766 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10104 Z= 0.263 Angle : 0.501 7.073 13642 Z= 0.265 Chirality : 0.042 0.140 1532 Planarity : 0.004 0.043 1732 Dihedral : 3.596 13.930 1318 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.64 % Allowed : 8.38 % Favored : 89.98 % 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: 1.67 (0.25), residues: 1200 helix: 2.75 (0.20), residues: 632 sheet: -1.31 (0.41), residues: 136 loop : -0.60 (0.30), residues: 432 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 0.016 0.001 TYR A 325 ARG 0.003 0.000 ARG A 440 *********************** 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 138 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.280 Fit side-chains REVERT: A 37 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8804 (mp) REVERT: A 61 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8324 (mtmm) REVERT: A 351 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7976 (mt-10) REVERT: A 409 ASP cc_start: 0.8516 (m-30) cc_final: 0.8126 (m-30) REVERT: A 569 ASP cc_start: 0.7160 (m-30) cc_final: 0.6830 (m-30) REVERT: A 648 GLN cc_start: 0.7529 (tt0) cc_final: 0.6744 (tp-100) REVERT: B 37 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8771 (mp) REVERT: B 53 MET cc_start: 0.7462 (mmm) cc_final: 0.7218 (mmp) REVERT: B 61 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8242 (mtmm) REVERT: B 234 MET cc_start: 0.7176 (tpt) cc_final: 0.6895 (mmm) REVERT: B 249 VAL cc_start: 0.8989 (t) cc_final: 0.8782 (p) REVERT: B 376 GLU cc_start: 0.8706 (mp0) cc_final: 0.8422 (mp0) REVERT: B 405 ARG cc_start: 0.7821 (mtp-110) cc_final: 0.7516 (ttm-80) REVERT: B 561 GLU cc_start: 0.8025 (tp30) cc_final: 0.7822 (tm-30) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 0.2324 time to fit residues: 43.3828 Evaluate side-chains 122 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 459 HIS 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 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: 3.9990 chunk 113 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.093445 restraints weight = 14197.567| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.08 r_work: 0.2893 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10104 Z= 0.289 Angle : 0.511 6.205 13642 Z= 0.270 Chirality : 0.043 0.142 1532 Planarity : 0.004 0.044 1732 Dihedral : 3.600 13.558 1318 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.55 % Allowed : 8.93 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1200 helix: 2.77 (0.20), residues: 634 sheet: -1.30 (0.41), residues: 136 loop : -0.52 (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 A 459 PHE 0.016 0.001 PHE A 470 TYR 0.016 0.001 TYR A 325 ARG 0.004 0.000 ARG B 440 *********************** 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 135 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.080 Fit side-chains REVERT: A 37 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8914 (mp) REVERT: A 61 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8262 (mtmm) REVERT: A 351 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8004 (mt-10) REVERT: A 376 GLU cc_start: 0.8712 (mp0) cc_final: 0.8450 (mp0) REVERT: A 409 ASP cc_start: 0.8564 (m-30) cc_final: 0.8169 (m-30) REVERT: A 516 GLU cc_start: 0.8253 (tp30) cc_final: 0.7841 (tp30) REVERT: A 648 GLN cc_start: 0.7495 (tt0) cc_final: 0.6799 (tp-100) REVERT: B 37 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8903 (mp) REVERT: B 53 MET cc_start: 0.7435 (mmm) cc_final: 0.7203 (mmp) REVERT: B 61 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8281 (mtmm) REVERT: B 376 GLU cc_start: 0.8718 (mp0) cc_final: 0.8488 (mp0) REVERT: B 523 ASP cc_start: 0.8045 (t70) cc_final: 0.7645 (t0) outliers start: 17 outliers final: 14 residues processed: 129 average time/residue: 0.2028 time to fit residues: 38.2295 Evaluate side-chains 126 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 459 HIS 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: 0.8980 chunk 9 optimal weight: 0.0060 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 B 459 HIS D 372 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101833 restraints weight = 14007.220| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.86 r_work: 0.2890 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10104 Z= 0.157 Angle : 0.446 5.718 13642 Z= 0.235 Chirality : 0.040 0.129 1532 Planarity : 0.003 0.042 1732 Dihedral : 3.328 13.348 1318 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.73 % Allowed : 9.74 % Favored : 88.52 % 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: 2.11 (0.25), residues: 1200 helix: 3.13 (0.20), residues: 634 sheet: -1.29 (0.41), residues: 138 loop : -0.36 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 619 HIS 0.006 0.001 HIS B 459 PHE 0.016 0.001 PHE A 470 TYR 0.009 0.001 TYR B 153 ARG 0.002 0.000 ARG A 357 *********************** 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 140 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.166 Fit side-chains REVERT: A 37 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8858 (mp) REVERT: A 61 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8364 (mtmm) REVERT: A 351 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 376 GLU cc_start: 0.8657 (mp0) cc_final: 0.8369 (mp0) REVERT: A 409 ASP cc_start: 0.8517 (m-30) cc_final: 0.8096 (m-30) REVERT: A 512 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6806 (tt0) REVERT: A 516 GLU cc_start: 0.8007 (tp30) cc_final: 0.7703 (tp30) REVERT: B 37 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8827 (mp) REVERT: B 53 MET cc_start: 0.7521 (mmm) cc_final: 0.7259 (mmp) REVERT: B 61 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8226 (mtmm) REVERT: B 65 LYS cc_start: 0.8868 (ptmt) cc_final: 0.8552 (pttt) REVERT: B 376 GLU cc_start: 0.8703 (mp0) cc_final: 0.8431 (mp0) REVERT: B 523 ASP cc_start: 0.8003 (t70) cc_final: 0.7628 (t0) outliers start: 19 outliers final: 12 residues processed: 132 average time/residue: 0.2005 time to fit residues: 38.7239 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 : 1.132 ------------------------------------------------------------------------------- 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 73 ILE Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 408 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1811 > 50: distance: 41 - 65: 8.641 distance: 44 - 62: 12.773 distance: 57 - 62: 15.001 distance: 62 - 63: 8.181 distance: 63 - 64: 18.345 distance: 63 - 66: 20.381 distance: 64 - 65: 16.744 distance: 64 - 69: 19.372 distance: 66 - 67: 14.570 distance: 66 - 68: 12.688 distance: 69 - 70: 7.273 distance: 70 - 71: 8.038 distance: 70 - 73: 15.637 distance: 71 - 72: 15.928 distance: 73 - 74: 15.817 distance: 75 - 76: 3.515 distance: 76 - 77: 11.162 distance: 76 - 79: 16.552 distance: 77 - 78: 23.381 distance: 77 - 86: 22.259 distance: 79 - 80: 13.905 distance: 80 - 81: 18.883 distance: 81 - 82: 8.293 distance: 82 - 83: 12.228 distance: 83 - 84: 15.256 distance: 83 - 85: 16.927 distance: 86 - 87: 16.216 distance: 87 - 88: 23.526 distance: 87 - 90: 9.656 distance: 88 - 89: 39.106 distance: 88 - 95: 29.163 distance: 90 - 91: 12.630 distance: 91 - 92: 13.925 distance: 92 - 93: 23.845 distance: 92 - 94: 15.853 distance: 95 - 96: 8.540 distance: 95 - 101: 14.625 distance: 96 - 97: 8.795 distance: 96 - 99: 16.503 distance: 97 - 98: 15.775 distance: 97 - 102: 11.392 distance: 99 - 100: 24.593 distance: 100 - 101: 37.101 distance: 102 - 103: 17.345 distance: 103 - 104: 11.411 distance: 103 - 106: 17.939 distance: 104 - 105: 19.068 distance: 104 - 110: 10.015 distance: 106 - 107: 22.947 distance: 107 - 108: 39.450 distance: 107 - 109: 15.091 distance: 110 - 111: 4.716 distance: 111 - 112: 17.749 distance: 111 - 114: 9.602 distance: 112 - 113: 30.391 distance: 112 - 118: 5.992 distance: 114 - 115: 5.997 distance: 115 - 116: 23.379 distance: 115 - 117: 12.891 distance: 118 - 119: 11.822 distance: 119 - 120: 9.311 distance: 119 - 122: 14.173 distance: 120 - 121: 10.909 distance: 120 - 125: 6.954 distance: 122 - 123: 8.391 distance: 122 - 124: 11.826 distance: 125 - 126: 10.848 distance: 126 - 127: 9.867 distance: 126 - 129: 8.655 distance: 127 - 128: 27.048 distance: 127 - 133: 21.771 distance: 129 - 130: 21.172 distance: 129 - 131: 12.419 distance: 130 - 132: 21.403 distance: 133 - 134: 39.084 distance: 134 - 135: 48.771 distance: 135 - 136: 37.465 distance: 135 - 137: 34.819