Starting phenix.real_space_refine on Fri Dec 27 12:45:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xma_38469/12_2024/8xma_38469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xma_38469/12_2024/8xma_38469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xma_38469/12_2024/8xma_38469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xma_38469/12_2024/8xma_38469.map" model { file = "/net/cci-nas-00/data/ceres_data/8xma_38469/12_2024/8xma_38469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xma_38469/12_2024/8xma_38469.cif" } resolution = 2.65 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= -0.003 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 44 5.16 5 C 3196 2.51 5 N 785 2.21 5 O 825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4858 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2297 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2297 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 291} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2193 SG CYS B 433 28.140 24.694 47.545 1.00105.86 S ATOM 4518 SG CYS A 437 29.976 26.843 21.278 1.00103.74 S ATOM 2291 SG CYS B 446 28.119 34.000 44.671 1.00 90.42 S ATOM 2297 SG CYS B 447 23.736 34.233 45.401 1.00 86.30 S ATOM 4490 SG CYS A 433 37.829 23.700 29.217 1.00103.95 S ATOM 2221 SG CYS B 437 34.991 30.521 54.029 1.00107.45 S ATOM 4588 SG CYS A 446 35.783 33.297 30.016 1.00 85.99 S ATOM 4594 SG CYS A 447 39.783 34.078 29.191 1.00 81.80 S Time building chain proxies: 3.78, per 1000 atoms: 0.78 Number of scatterers: 4858 At special positions: 0 Unit cell: (59.648, 108.112, 68.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 44 16.00 O 825 8.00 N 785 7.00 C 3196 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: 1.42 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 387 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 370 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 433 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 413 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 408 " pdb="ZN ZN A 602 " - pdb=" SG CYS B 437 " pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 446 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 447 " pdb=" ZN A 604 " pdb="ZN ZN A 604 " - pdb=" NE2 HIS A 251 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 387 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 370 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 433 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 413 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 408 " pdb="ZN ZN B 602 " - pdb=" SG CYS A 437 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 373 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 446 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 447 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 251 " 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1138 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 69.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'B' and resid 6 through 33 Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.546A pdb=" N PHE B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 61 Processing helix chain 'B' and resid 76 through 106 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 241 through 272 Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.983A pdb=" N LEU B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 314' Processing helix chain 'B' and resid 315 through 344 removed outlier: 3.629A pdb=" N THR B 319 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 352 through 362 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 410 removed outlier: 3.660A pdb=" N THR B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 33 Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.851A pdb=" N LEU A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.747A pdb=" N VAL A 48 " --> pdb=" O MET A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 106 Processing helix chain 'A' and resid 112 through 134 removed outlier: 3.508A pdb=" N VAL A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 272 removed outlier: 3.572A pdb=" N ASN A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 315 through 344 removed outlier: 3.596A pdb=" N THR A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 352 through 363 removed outlier: 3.907A pdb=" N VAL A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 removed outlier: 4.090A pdb=" N VAL A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 4.143A pdb=" N GLN A 445 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.643A pdb=" N VAL B 369 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LYS B 389 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS B 387 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 382 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N THR B 416 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ALA B 384 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLN B 418 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA B 386 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU B 420 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE B 388 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 378 removed outlier: 6.744A pdb=" N VAL A 369 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LYS A 389 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 382 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N THR A 416 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 384 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLN A 418 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 386 " --> pdb=" O GLN A 418 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 806 1.32 - 1.45: 1175 1.45 - 1.57: 2910 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 4955 Sorted by residual: bond pdb=" CAX Y01 A 606 " pdb=" OAF Y01 A 606 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.27e+00 bond pdb=" CAX Y01 B 607 " pdb=" OAH Y01 B 607 " ideal model delta sigma weight residual 1.248 1.309 -0.061 2.00e-02 2.50e+03 9.22e+00 bond pdb=" CAX Y01 B 606 " pdb=" OAF Y01 B 606 " ideal model delta sigma weight residual 1.247 1.307 -0.060 2.00e-02 2.50e+03 8.98e+00 bond pdb=" CAX Y01 B 608 " pdb=" OAF Y01 B 608 " ideal model delta sigma weight residual 1.247 1.307 -0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" C GLU B 106 " pdb=" N PRO B 107 " ideal model delta sigma weight residual 1.331 1.366 -0.035 1.31e-02 5.83e+03 7.30e+00 ... (remaining 4950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 6573 1.63 - 3.25: 159 3.25 - 4.88: 19 4.88 - 6.50: 7 6.50 - 8.13: 5 Bond angle restraints: 6763 Sorted by residual: angle pdb=" C GLU B 106 " pdb=" N PRO B 107 " pdb=" CA PRO B 107 " ideal model delta sigma weight residual 119.85 116.67 3.18 1.01e+00 9.80e-01 9.88e+00 angle pdb=" N PRO B 107 " pdb=" CA PRO B 107 " pdb=" C PRO B 107 " ideal model delta sigma weight residual 111.38 116.25 -4.87 1.59e+00 3.96e-01 9.37e+00 angle pdb=" CCM AV0 A 605 " pdb=" CBS AV0 A 605 " pdb=" O1 AV0 A 605 " ideal model delta sigma weight residual 109.17 117.30 -8.13 3.00e+00 1.11e-01 7.34e+00 angle pdb=" CA PRO B 107 " pdb=" C PRO B 107 " pdb=" O PRO B 107 " ideal model delta sigma weight residual 121.67 118.44 3.23 1.22e+00 6.72e-01 7.03e+00 angle pdb=" CAL Y01 A 606 " pdb=" CAX Y01 A 606 " pdb=" OAH Y01 A 606 " ideal model delta sigma weight residual 115.62 123.18 -7.56 3.00e+00 1.11e-01 6.36e+00 ... (remaining 6758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.91: 3003 26.91 - 53.82: 140 53.82 - 80.74: 45 80.74 - 107.65: 29 107.65 - 134.56: 28 Dihedral angle restraints: 3245 sinusoidal: 1504 harmonic: 1741 Sorted by residual: dihedral pdb=" CBQ AV0 A 605 " pdb=" CBS AV0 A 605 " pdb=" CCM AV0 A 605 " pdb=" O1 AV0 A 605 " ideal model delta sinusoidal sigma weight residual 70.26 -155.18 -134.56 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" CCD AV0 A 605 " pdb=" CCS AV0 A 605 " pdb=" OBZ AV0 A 605 " pdb=" CCW AV0 A 605 " ideal model delta sinusoidal sigma weight residual 59.29 -71.44 130.73 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CCD AV0 A 605 " pdb=" CCS AV0 A 605 " pdb=" OBZ AV0 A 605 " pdb=" OCB AV0 A 605 " ideal model delta sinusoidal sigma weight residual 298.59 168.89 129.70 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 3242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 645 0.045 - 0.090: 173 0.090 - 0.135: 34 0.135 - 0.181: 2 0.181 - 0.226: 3 Chirality restraints: 857 Sorted by residual: chirality pdb=" CA PRO B 107 " pdb=" N PRO B 107 " pdb=" C PRO B 107 " pdb=" CB PRO B 107 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CCW AV0 A 605 " pdb=" CCS AV0 A 605 " pdb=" CCU AV0 A 605 " pdb=" OAV AV0 A 605 " both_signs ideal model delta sigma weight residual False -2.29 -2.50 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CCV AV0 B 605 " pdb=" CCR AV0 B 605 " pdb=" CCT AV0 B 605 " pdb=" OAU AV0 B 605 " both_signs ideal model delta sigma weight residual False -2.30 -2.50 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 854 not shown) Planarity restraints: 790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 112 " -0.035 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO A 113 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 269 " -0.011 2.00e-02 2.50e+03 1.15e-02 2.32e+00 pdb=" CG PHE A 269 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 269 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 269 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 269 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 269 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 269 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 106 " -0.019 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO B 107 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " -0.017 5.00e-02 4.00e+02 ... (remaining 787 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 45 2.55 - 3.13: 3742 3.13 - 3.72: 7700 3.72 - 4.31: 9972 4.31 - 4.90: 17135 Nonbonded interactions: 38594 Sorted by model distance: nonbonded pdb=" OD1 ASP B 47 " pdb="ZN ZN B 604 " model vdw 1.957 2.230 nonbonded pdb=" OE2 GLU A 420 " pdb="ZN ZN A 601 " model vdw 1.981 2.230 nonbonded pdb=" OE2 GLU B 420 " pdb="ZN ZN B 601 " model vdw 1.983 2.230 nonbonded pdb=" OE2 GLU B 371 " pdb="ZN ZN B 603 " model vdw 1.983 2.230 nonbonded pdb=" OD2 ASP A 255 " pdb="ZN ZN A 604 " model vdw 1.987 2.230 ... (remaining 38589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 136 or resid 240 through 447 or resid 601 throug \ h 606)) selection = (chain 'B' and (resid 6 through 136 or resid 240 through 353 or (resid 354 and ( \ name N or name CA or name C or name O or name CB )) or resid 355 through 404 or \ (resid 405 and (name N or name CA or name C or name O or name CB )) or resid 406 \ through 447 or resid 601 through 606)) } 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.890 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4955 Z= 0.291 Angle : 0.627 8.127 6763 Z= 0.302 Chirality : 0.042 0.226 857 Planarity : 0.004 0.054 790 Dihedral : 23.456 134.561 2107 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 3.44 (0.35), residues: 585 helix: 3.18 (0.25), residues: 387 sheet: 1.28 (0.88), residues: 46 loop : 0.12 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 312 HIS 0.003 0.001 HIS B 135 PHE 0.026 0.001 PHE A 269 TYR 0.006 0.001 TYR B 270 ARG 0.006 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.573 Fit side-chains REVERT: B 381 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7598 (mtp85) REVERT: A 63 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.8064 (mtt180) REVERT: A 65 HIS cc_start: 0.7182 (m90) cc_final: 0.6942 (p-80) REVERT: A 78 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7143 (mt-10) REVERT: A 108 HIS cc_start: 0.7109 (m-70) cc_final: 0.6523 (m90) REVERT: A 129 LEU cc_start: 0.7822 (tt) cc_final: 0.7498 (mp) REVERT: A 246 ARG cc_start: 0.7504 (tpt170) cc_final: 0.6364 (ttp80) REVERT: A 380 SER cc_start: 0.8366 (t) cc_final: 0.8136 (p) REVERT: A 434 GLU cc_start: 0.7275 (mp0) cc_final: 0.6949 (mp0) outliers start: 0 outliers final: 1 residues processed: 136 average time/residue: 1.3933 time to fit residues: 195.7383 Evaluate side-chains 89 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN B 135 HIS A 108 HIS A 127 ASN A 440 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4955 Z= 0.251 Angle : 0.596 8.222 6763 Z= 0.281 Chirality : 0.042 0.266 857 Planarity : 0.004 0.051 790 Dihedral : 14.735 131.335 1115 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.28 % Allowed : 12.63 % Favored : 83.10 % 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: 3.56 (0.35), residues: 585 helix: 3.11 (0.25), residues: 393 sheet: 1.40 (0.88), residues: 45 loop : 0.51 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 312 HIS 0.005 0.001 HIS B 135 PHE 0.011 0.001 PHE B 21 TYR 0.016 0.002 TYR B 396 ARG 0.005 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.517 Fit side-chains REVERT: B 78 GLU cc_start: 0.7941 (pm20) cc_final: 0.7716 (pp20) REVERT: B 401 LYS cc_start: 0.7786 (mttm) cc_final: 0.7585 (mptm) REVERT: B 445 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6709 (tm-30) REVERT: A 37 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7546 (ttm) REVERT: A 65 HIS cc_start: 0.7431 (m90) cc_final: 0.7043 (p-80) REVERT: A 78 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7297 (mt-10) REVERT: A 108 HIS cc_start: 0.7131 (m90) cc_final: 0.6852 (m-70) REVERT: A 129 LEU cc_start: 0.7903 (tt) cc_final: 0.7691 (mp) outliers start: 21 outliers final: 5 residues processed: 103 average time/residue: 1.2366 time to fit residues: 132.4242 Evaluate side-chains 92 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 135 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4955 Z= 0.188 Angle : 0.512 5.798 6763 Z= 0.246 Chirality : 0.038 0.248 857 Planarity : 0.003 0.044 790 Dihedral : 11.895 137.988 1113 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.65 % Allowed : 16.29 % Favored : 81.06 % 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: 3.67 (0.35), residues: 585 helix: 3.23 (0.25), residues: 392 sheet: 1.07 (0.91), residues: 47 loop : 0.60 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 312 HIS 0.006 0.001 HIS B 135 PHE 0.007 0.001 PHE B 104 TYR 0.018 0.002 TYR B 396 ARG 0.003 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.519 Fit side-chains REVERT: B 368 GLU cc_start: 0.7963 (pp20) cc_final: 0.7689 (pp20) REVERT: A 65 HIS cc_start: 0.7408 (m90) cc_final: 0.7005 (p-80) outliers start: 13 outliers final: 6 residues processed: 84 average time/residue: 1.1460 time to fit residues: 100.4894 Evaluate side-chains 85 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4955 Z= 0.199 Angle : 0.483 4.968 6763 Z= 0.238 Chirality : 0.038 0.197 857 Planarity : 0.003 0.040 790 Dihedral : 11.588 139.127 1113 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.46 % Allowed : 16.90 % Favored : 79.63 % 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: 3.65 (0.35), residues: 585 helix: 3.23 (0.24), residues: 392 sheet: 1.02 (0.89), residues: 48 loop : 0.57 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 312 HIS 0.005 0.001 HIS B 135 PHE 0.006 0.001 PHE B 21 TYR 0.018 0.002 TYR B 396 ARG 0.003 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.548 Fit side-chains REVERT: B 368 GLU cc_start: 0.7976 (pp20) cc_final: 0.7534 (pp20) REVERT: B 401 LYS cc_start: 0.7648 (mptm) cc_final: 0.7269 (mptp) REVERT: B 445 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: A 65 HIS cc_start: 0.7323 (m90) cc_final: 0.7049 (p-80) outliers start: 17 outliers final: 7 residues processed: 88 average time/residue: 1.1266 time to fit residues: 103.5214 Evaluate side-chains 87 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4955 Z= 0.235 Angle : 0.497 5.017 6763 Z= 0.248 Chirality : 0.039 0.131 857 Planarity : 0.003 0.038 790 Dihedral : 11.424 140.423 1113 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.05 % Allowed : 18.53 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.51 (0.35), residues: 585 helix: 3.15 (0.24), residues: 392 sheet: 0.60 (0.88), residues: 49 loop : 0.57 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 312 HIS 0.005 0.001 HIS B 135 PHE 0.008 0.001 PHE B 21 TYR 0.020 0.002 TYR B 396 ARG 0.003 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.570 Fit side-chains REVERT: B 10 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7249 (mtt90) REVERT: B 78 GLU cc_start: 0.7863 (pp20) cc_final: 0.7529 (pp20) REVERT: B 445 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: A 65 HIS cc_start: 0.7523 (m90) cc_final: 0.7052 (p-80) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 1.3221 time to fit residues: 122.6426 Evaluate side-chains 85 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 0.0870 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4955 Z= 0.171 Angle : 0.458 5.143 6763 Z= 0.228 Chirality : 0.037 0.138 857 Planarity : 0.003 0.037 790 Dihedral : 11.317 141.450 1113 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.85 % Allowed : 20.16 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.35), residues: 585 helix: 3.32 (0.24), residues: 392 sheet: 0.39 (0.86), residues: 51 loop : 0.56 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 312 HIS 0.004 0.000 HIS B 135 PHE 0.005 0.001 PHE B 104 TYR 0.016 0.001 TYR B 396 ARG 0.002 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.529 Fit side-chains REVERT: B 78 GLU cc_start: 0.7820 (pp20) cc_final: 0.7522 (pp20) REVERT: B 401 LYS cc_start: 0.7647 (mptm) cc_final: 0.7382 (mptm) REVERT: A 65 HIS cc_start: 0.7512 (m90) cc_final: 0.7034 (p-80) REVERT: A 368 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8279 (pp20) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 1.1258 time to fit residues: 103.3510 Evaluate side-chains 86 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 57 optimal weight: 0.1980 chunk 36 optimal weight: 0.0060 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4955 Z= 0.135 Angle : 0.424 4.908 6763 Z= 0.213 Chirality : 0.036 0.145 857 Planarity : 0.003 0.036 790 Dihedral : 11.046 142.512 1113 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.65 % Allowed : 19.96 % Favored : 77.39 % 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: 3.90 (0.35), residues: 585 helix: 3.51 (0.24), residues: 392 sheet: 0.67 (0.88), residues: 50 loop : 0.55 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 312 HIS 0.002 0.000 HIS B 135 PHE 0.014 0.001 PHE B 88 TYR 0.013 0.001 TYR B 396 ARG 0.002 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.548 Fit side-chains REVERT: B 78 GLU cc_start: 0.7822 (pp20) cc_final: 0.7424 (pp20) REVERT: B 368 GLU cc_start: 0.7999 (pp20) cc_final: 0.7722 (pp20) REVERT: B 405 ASP cc_start: 0.7925 (m-30) cc_final: 0.7583 (p0) REVERT: A 65 HIS cc_start: 0.7376 (m90) cc_final: 0.7126 (p-80) REVERT: A 69 LYS cc_start: 0.8229 (tptp) cc_final: 0.7972 (tptm) REVERT: A 246 ARG cc_start: 0.7325 (tpt170) cc_final: 0.6219 (ttp80) REVERT: A 368 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8231 (pp20) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 1.3259 time to fit residues: 120.0831 Evaluate side-chains 85 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.0020 chunk 5 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4955 Z= 0.163 Angle : 0.438 4.893 6763 Z= 0.220 Chirality : 0.037 0.137 857 Planarity : 0.003 0.036 790 Dihedral : 10.971 141.995 1113 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.26 % Allowed : 19.35 % Favored : 77.39 % 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: 3.89 (0.35), residues: 585 helix: 3.50 (0.24), residues: 392 sheet: 0.60 (0.88), residues: 50 loop : 0.58 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 312 HIS 0.003 0.000 HIS B 135 PHE 0.007 0.001 PHE B 88 TYR 0.014 0.001 TYR B 396 ARG 0.002 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.531 Fit side-chains REVERT: B 78 GLU cc_start: 0.7859 (pp20) cc_final: 0.7484 (pp20) REVERT: B 368 GLU cc_start: 0.8084 (pp20) cc_final: 0.7684 (pp20) REVERT: B 401 LYS cc_start: 0.7582 (mptm) cc_final: 0.7362 (mptm) REVERT: A 65 HIS cc_start: 0.7436 (m90) cc_final: 0.7079 (p-80) REVERT: A 69 LYS cc_start: 0.8225 (tptp) cc_final: 0.7963 (tptm) REVERT: A 246 ARG cc_start: 0.7364 (tpt170) cc_final: 0.6237 (ttp80) REVERT: A 368 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8270 (pp20) outliers start: 16 outliers final: 8 residues processed: 91 average time/residue: 1.2915 time to fit residues: 122.7320 Evaluate side-chains 89 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4955 Z= 0.180 Angle : 0.460 5.905 6763 Z= 0.230 Chirality : 0.037 0.133 857 Planarity : 0.003 0.036 790 Dihedral : 10.905 141.296 1113 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.65 % Allowed : 19.55 % Favored : 77.80 % 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: 3.82 (0.35), residues: 585 helix: 3.42 (0.24), residues: 392 sheet: 0.58 (0.87), residues: 50 loop : 0.62 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 312 HIS 0.003 0.000 HIS B 135 PHE 0.008 0.001 PHE B 88 TYR 0.016 0.001 TYR B 396 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.934 Fit side-chains REVERT: B 78 GLU cc_start: 0.7862 (pp20) cc_final: 0.7567 (pp20) REVERT: B 368 GLU cc_start: 0.8080 (pp20) cc_final: 0.7726 (pp20) REVERT: B 401 LYS cc_start: 0.7614 (mptm) cc_final: 0.7395 (mptm) REVERT: B 405 ASP cc_start: 0.8002 (m-30) cc_final: 0.7618 (p0) REVERT: A 65 HIS cc_start: 0.7454 (m90) cc_final: 0.7040 (p-80) REVERT: A 69 LYS cc_start: 0.8233 (tptp) cc_final: 0.7970 (tptm) REVERT: A 246 ARG cc_start: 0.7374 (tpt170) cc_final: 0.6261 (ttp80) REVERT: A 368 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8301 (pp20) outliers start: 13 outliers final: 7 residues processed: 90 average time/residue: 1.3852 time to fit residues: 130.1450 Evaluate side-chains 90 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 368 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4955 Z= 0.186 Angle : 0.457 4.902 6763 Z= 0.231 Chirality : 0.037 0.144 857 Planarity : 0.003 0.035 790 Dihedral : 10.856 140.697 1113 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.04 % Allowed : 20.37 % Favored : 77.60 % 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: 3.82 (0.35), residues: 585 helix: 3.41 (0.24), residues: 392 sheet: 0.59 (0.87), residues: 50 loop : 0.66 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 312 HIS 0.003 0.000 HIS B 135 PHE 0.007 0.001 PHE B 88 TYR 0.017 0.001 TYR B 396 ARG 0.002 0.000 ARG A 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.502 Fit side-chains REVERT: B 78 GLU cc_start: 0.7821 (pp20) cc_final: 0.7589 (pp20) REVERT: B 368 GLU cc_start: 0.8108 (pp20) cc_final: 0.7721 (pp20) REVERT: B 401 LYS cc_start: 0.7634 (mptm) cc_final: 0.7398 (mptm) REVERT: B 405 ASP cc_start: 0.7938 (m-30) cc_final: 0.7519 (p0) REVERT: A 65 HIS cc_start: 0.7455 (m90) cc_final: 0.7041 (p-80) REVERT: A 69 LYS cc_start: 0.8233 (tptp) cc_final: 0.7967 (tptm) REVERT: A 368 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8321 (pp20) outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 1.1941 time to fit residues: 108.2040 Evaluate side-chains 89 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 368 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 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 = 0.3808 r_free = 0.3808 target = 0.152859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113068 restraints weight = 4260.803| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.07 r_work: 0.3165 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4955 Z= 0.163 Angle : 0.453 5.052 6763 Z= 0.226 Chirality : 0.037 0.144 857 Planarity : 0.003 0.035 790 Dihedral : 10.757 140.485 1113 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.04 % Allowed : 19.96 % Favored : 78.00 % 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: 3.85 (0.35), residues: 585 helix: 3.44 (0.24), residues: 392 sheet: 0.67 (0.88), residues: 50 loop : 0.62 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 312 HIS 0.003 0.000 HIS B 135 PHE 0.008 0.001 PHE B 88 TYR 0.016 0.001 TYR B 396 ARG 0.002 0.000 ARG B 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2450.81 seconds wall clock time: 44 minutes 49.15 seconds (2689.15 seconds total)