Starting phenix.real_space_refine on Fri Aug 22 15:19:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xma_38469/08_2025/8xma_38469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xma_38469/08_2025/8xma_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_38469/08_2025/8xma_38469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xma_38469/08_2025/8xma_38469.map" model { file = "/net/cci-nas-00/data/ceres_data/8xma_38469/08_2025/8xma_38469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xma_38469/08_2025/8xma_38469.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3} 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: {'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3, 'GLU: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: 1.56, per 1000 atoms: 0.32 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: 0.47 Conformation dependent library (CDL) restraints added in 193.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.15 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: 0.76 Time building geometry restraints manager: 0.60 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 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 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- 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 : 0.015 0.407 4975 Z= 0.509 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 : 7.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG B 354 TYR 0.006 0.001 TYR B 270 PHE 0.026 0.001 PHE A 269 TRP 0.017 0.001 TRP B 312 HIS 0.003 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 4955) covalent geometry : angle 0.62665 ( 6763) hydrogen bonds : bond 0.11187 ( 323) hydrogen bonds : angle 4.08726 ( 963) metal coordination : bond 0.21927 ( 20) *********************** 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 : 0.213 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: 0.7451 time to fit residues: 104.4540 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 : 0.192 ------------------------------------------------------------------------------- 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 54 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 440 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112311 restraints weight = 4549.991| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.25 r_work: 0.3196 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4975 Z= 0.163 Angle : 0.596 8.280 6763 Z= 0.281 Chirality : 0.041 0.242 857 Planarity : 0.004 0.051 790 Dihedral : 14.753 131.583 1115 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.28 % Allowed : 12.83 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.55 (0.35), residues: 585 helix: 3.11 (0.25), residues: 393 sheet: 1.38 (0.88), residues: 45 loop : 0.52 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 103 TYR 0.016 0.002 TYR B 396 PHE 0.011 0.001 PHE B 21 TRP 0.014 0.002 TRP B 312 HIS 0.006 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 4955) covalent geometry : angle 0.59609 ( 6763) hydrogen bonds : bond 0.04086 ( 323) hydrogen bonds : angle 3.24841 ( 963) metal coordination : bond 0.01327 ( 20) *********************** 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 118 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.183 Fit side-chains REVERT: B 78 GLU cc_start: 0.8281 (pm20) cc_final: 0.8010 (pp20) REVERT: B 401 LYS cc_start: 0.7545 (mttm) cc_final: 0.7335 (mptm) REVERT: B 434 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: B 445 GLN cc_start: 0.6483 (OUTLIER) cc_final: 0.6265 (tm-30) REVERT: A 37 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7515 (ttm) REVERT: A 65 HIS cc_start: 0.7761 (m90) cc_final: 0.6761 (p-80) REVERT: A 78 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 108 HIS cc_start: 0.7018 (m90) cc_final: 0.6644 (m-70) REVERT: A 112 GLN cc_start: 0.7473 (mt0) cc_final: 0.7179 (pt0) REVERT: A 129 LEU cc_start: 0.7726 (tt) cc_final: 0.7463 (mp) REVERT: A 397 MET cc_start: 0.8028 (tpt) cc_final: 0.7816 (mmt) outliers start: 21 outliers final: 6 residues processed: 102 average time/residue: 0.6272 time to fit residues: 66.2911 Evaluate side-chains 94 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 434 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 32 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 10 optimal weight: 0.0070 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 8.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114715 restraints weight = 4442.559| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.23 r_work: 0.3228 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4975 Z= 0.111 Angle : 0.498 6.234 6763 Z= 0.239 Chirality : 0.038 0.258 857 Planarity : 0.003 0.044 790 Dihedral : 11.871 137.548 1113 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.05 % Allowed : 15.48 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.79 (0.35), residues: 585 helix: 3.30 (0.25), residues: 391 sheet: 1.33 (0.91), residues: 46 loop : 0.65 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 63 TYR 0.017 0.001 TYR B 396 PHE 0.007 0.001 PHE B 104 TRP 0.011 0.001 TRP B 312 HIS 0.006 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 4955) covalent geometry : angle 0.49772 ( 6763) hydrogen bonds : bond 0.03515 ( 323) hydrogen bonds : angle 3.10515 ( 963) metal coordination : bond 0.00413 ( 20) *********************** 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 102 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.209 Fit side-chains REVERT: B 78 GLU cc_start: 0.8135 (pm20) cc_final: 0.7887 (pp20) REVERT: B 368 GLU cc_start: 0.7959 (pp20) cc_final: 0.7614 (pp20) REVERT: B 434 GLU cc_start: 0.7788 (mp0) cc_final: 0.7577 (mm-30) REVERT: A 65 HIS cc_start: 0.7604 (m90) cc_final: 0.6660 (p-80) REVERT: A 78 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 108 HIS cc_start: 0.6971 (m90) cc_final: 0.6730 (m-70) REVERT: A 129 LEU cc_start: 0.7665 (tt) cc_final: 0.7426 (mp) outliers start: 15 outliers final: 7 residues processed: 90 average time/residue: 0.5832 time to fit residues: 54.7070 Evaluate side-chains 90 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0040 chunk 58 optimal weight: 0.0040 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.152563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112744 restraints weight = 4333.176| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.09 r_work: 0.3163 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4975 Z= 0.123 Angle : 0.477 4.960 6763 Z= 0.237 Chirality : 0.038 0.182 857 Planarity : 0.003 0.041 790 Dihedral : 11.469 139.506 1113 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.67 % Allowed : 16.50 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.72 (0.35), residues: 585 helix: 3.26 (0.24), residues: 392 sheet: 1.11 (0.90), residues: 48 loop : 0.63 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 63 TYR 0.016 0.002 TYR B 396 PHE 0.006 0.001 PHE B 21 TRP 0.012 0.001 TRP B 312 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4955) covalent geometry : angle 0.47735 ( 6763) hydrogen bonds : bond 0.03556 ( 323) hydrogen bonds : angle 3.08804 ( 963) metal coordination : bond 0.00368 ( 20) *********************** 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 108 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.206 Fit side-chains REVERT: B 78 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8012 (pp20) REVERT: B 368 GLU cc_start: 0.8166 (pp20) cc_final: 0.7690 (pp20) REVERT: B 401 LYS cc_start: 0.7539 (mptm) cc_final: 0.7229 (mptp) REVERT: B 434 GLU cc_start: 0.8019 (mp0) cc_final: 0.7687 (mm-30) REVERT: B 445 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.6383 (tm-30) REVERT: A 65 HIS cc_start: 0.7726 (m90) cc_final: 0.6913 (p-80) REVERT: A 108 HIS cc_start: 0.7378 (m90) cc_final: 0.7063 (m-70) REVERT: A 129 LEU cc_start: 0.7796 (tt) cc_final: 0.7573 (mp) outliers start: 18 outliers final: 7 residues processed: 96 average time/residue: 0.6145 time to fit residues: 61.2246 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 : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 78 GLU 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 125 LEU 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 23 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.153542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113343 restraints weight = 4373.967| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.10 r_work: 0.3174 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4975 Z= 0.105 Angle : 0.449 4.904 6763 Z= 0.223 Chirality : 0.037 0.135 857 Planarity : 0.003 0.036 790 Dihedral : 11.277 141.084 1113 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.85 % Allowed : 18.33 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.35), residues: 585 helix: 3.36 (0.24), residues: 392 sheet: 1.05 (0.89), residues: 48 loop : 0.59 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 63 TYR 0.015 0.001 TYR B 396 PHE 0.006 0.001 PHE B 104 TRP 0.009 0.001 TRP B 312 HIS 0.004 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4955) covalent geometry : angle 0.44884 ( 6763) hydrogen bonds : bond 0.03377 ( 323) hydrogen bonds : angle 3.06920 ( 963) metal coordination : bond 0.00265 ( 20) *********************** 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 94 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.195 Fit side-chains REVERT: B 78 GLU cc_start: 0.8226 (pm20) cc_final: 0.7949 (pp20) REVERT: B 368 GLU cc_start: 0.8141 (pp20) cc_final: 0.7632 (pp20) REVERT: B 401 LYS cc_start: 0.7535 (mptm) cc_final: 0.7041 (mmmt) REVERT: B 434 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: A 65 HIS cc_start: 0.7688 (m90) cc_final: 0.6819 (p-80) REVERT: A 108 HIS cc_start: 0.7318 (m90) cc_final: 0.6981 (m-70) REVERT: A 129 LEU cc_start: 0.7857 (tt) cc_final: 0.7634 (mp) REVERT: A 246 ARG cc_start: 0.7713 (tpt170) cc_final: 0.6366 (ttp80) outliers start: 14 outliers final: 5 residues processed: 85 average time/residue: 0.6652 time to fit residues: 58.5922 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 : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 LEU 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 1 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.151961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111673 restraints weight = 4353.847| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.09 r_work: 0.3147 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4975 Z= 0.126 Angle : 0.467 4.966 6763 Z= 0.233 Chirality : 0.038 0.136 857 Planarity : 0.003 0.037 790 Dihedral : 11.154 141.309 1113 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.67 % Allowed : 18.13 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.75 (0.35), residues: 585 helix: 3.32 (0.24), residues: 392 sheet: 0.73 (0.89), residues: 49 loop : 0.71 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 63 TYR 0.017 0.002 TYR B 396 PHE 0.006 0.001 PHE B 21 TRP 0.008 0.001 TRP B 312 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4955) covalent geometry : angle 0.46673 ( 6763) hydrogen bonds : bond 0.03587 ( 323) hydrogen bonds : angle 3.10654 ( 963) metal coordination : bond 0.00348 ( 20) *********************** 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 100 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.193 Fit side-chains REVERT: B 78 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7975 (pp20) REVERT: B 368 GLU cc_start: 0.8123 (pp20) cc_final: 0.7817 (pp20) REVERT: B 401 LYS cc_start: 0.7460 (mptm) cc_final: 0.6986 (mmmt) REVERT: B 434 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: A 65 HIS cc_start: 0.7750 (m90) cc_final: 0.6848 (p-80) REVERT: A 108 HIS cc_start: 0.7352 (m90) cc_final: 0.7041 (m-70) REVERT: A 129 LEU cc_start: 0.7878 (tt) cc_final: 0.7646 (mp) outliers start: 18 outliers final: 8 residues processed: 90 average time/residue: 0.5426 time to fit residues: 51.0447 Evaluate side-chains 90 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 78 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 434 GLU 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 Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113539 restraints weight = 4284.423| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.08 r_work: 0.3173 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4975 Z= 0.102 Angle : 0.435 4.907 6763 Z= 0.219 Chirality : 0.037 0.144 857 Planarity : 0.003 0.035 790 Dihedral : 11.037 142.155 1113 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.05 % Allowed : 19.76 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.85 (0.35), residues: 585 helix: 3.42 (0.24), residues: 392 sheet: 0.66 (0.88), residues: 50 loop : 0.69 (0.56), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 63 TYR 0.015 0.001 TYR B 396 PHE 0.013 0.001 PHE B 88 TRP 0.015 0.001 TRP B 312 HIS 0.003 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 4955) covalent geometry : angle 0.43524 ( 6763) hydrogen bonds : bond 0.03323 ( 323) hydrogen bonds : angle 3.05434 ( 963) metal coordination : bond 0.00230 ( 20) *********************** 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 95 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.114 Fit side-chains REVERT: B 78 GLU cc_start: 0.8190 (pm20) cc_final: 0.7938 (pp20) REVERT: B 368 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7757 (pp20) REVERT: B 401 LYS cc_start: 0.7406 (mptm) cc_final: 0.6972 (mmmt) REVERT: B 405 ASP cc_start: 0.8180 (m-30) cc_final: 0.7709 (p0) REVERT: B 434 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: A 65 HIS cc_start: 0.7818 (m90) cc_final: 0.6736 (p-80) REVERT: A 78 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 108 HIS cc_start: 0.7384 (m90) cc_final: 0.7009 (m-70) outliers start: 15 outliers final: 7 residues processed: 86 average time/residue: 0.6028 time to fit residues: 53.8105 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 : 0.196 ------------------------------------------------------------------------------- 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 368 GLU Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 0.0020 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112154 restraints weight = 4379.601| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.09 r_work: 0.3154 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4975 Z= 0.114 Angle : 0.454 5.035 6763 Z= 0.227 Chirality : 0.037 0.137 857 Planarity : 0.003 0.035 790 Dihedral : 10.981 141.640 1113 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.67 % Allowed : 18.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.81 (0.35), residues: 585 helix: 3.39 (0.24), residues: 392 sheet: 0.61 (0.88), residues: 50 loop : 0.68 (0.56), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 63 TYR 0.015 0.001 TYR B 396 PHE 0.009 0.001 PHE B 88 TRP 0.013 0.001 TRP B 312 HIS 0.004 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4955) covalent geometry : angle 0.45433 ( 6763) hydrogen bonds : bond 0.03458 ( 323) hydrogen bonds : angle 3.06055 ( 963) metal coordination : bond 0.00288 ( 20) *********************** 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 98 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.191 Fit side-chains REVERT: B 78 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8003 (pp20) REVERT: B 368 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7767 (pp20) REVERT: B 401 LYS cc_start: 0.7421 (mptm) cc_final: 0.6952 (mmmt) REVERT: B 434 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: A 65 HIS cc_start: 0.7880 (m90) cc_final: 0.6833 (p-80) outliers start: 18 outliers final: 8 residues processed: 90 average time/residue: 0.5581 time to fit residues: 52.3465 Evaluate side-chains 91 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 67 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.151447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111181 restraints weight = 4310.374| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.07 r_work: 0.3138 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4975 Z= 0.139 Angle : 0.481 6.111 6763 Z= 0.239 Chirality : 0.038 0.142 857 Planarity : 0.003 0.034 790 Dihedral : 11.047 140.647 1113 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.46 % Allowed : 18.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.67 (0.35), residues: 585 helix: 3.27 (0.24), residues: 392 sheet: 0.51 (0.87), residues: 50 loop : 0.72 (0.56), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.017 0.002 TYR B 396 PHE 0.008 0.001 PHE B 88 TRP 0.015 0.001 TRP B 312 HIS 0.004 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4955) covalent geometry : angle 0.48141 ( 6763) hydrogen bonds : bond 0.03699 ( 323) hydrogen bonds : angle 3.14309 ( 963) metal coordination : bond 0.00378 ( 20) *********************** 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 103 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.224 Fit side-chains REVERT: B 10 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7600 (mtt180) REVERT: B 78 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7938 (pp20) REVERT: B 368 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7776 (pp20) REVERT: B 401 LYS cc_start: 0.7476 (mptm) cc_final: 0.7035 (mmmt) REVERT: B 434 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: A 65 HIS cc_start: 0.7936 (m90) cc_final: 0.6865 (p-80) REVERT: A 112 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: A 366 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7912 (p) outliers start: 17 outliers final: 6 residues processed: 94 average time/residue: 0.6172 time to fit residues: 60.2437 Evaluate side-chains 97 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 33 SER Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 58 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112459 restraints weight = 4323.411| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.09 r_work: 0.3158 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4975 Z= 0.111 Angle : 0.451 4.903 6763 Z= 0.227 Chirality : 0.037 0.143 857 Planarity : 0.003 0.034 790 Dihedral : 10.879 140.897 1113 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.77 (0.35), residues: 585 helix: 3.36 (0.24), residues: 392 sheet: 0.59 (0.87), residues: 50 loop : 0.70 (0.56), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 63 TYR 0.017 0.001 TYR B 396 PHE 0.009 0.001 PHE B 88 TRP 0.016 0.001 TRP B 312 HIS 0.003 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4955) covalent geometry : angle 0.45080 ( 6763) hydrogen bonds : bond 0.03478 ( 323) hydrogen bonds : angle 3.10902 ( 963) metal coordination : bond 0.00261 ( 20) ********************** 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 96 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.203 Fit side-chains REVERT: B 78 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7985 (pp20) REVERT: B 368 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7784 (pp20) REVERT: B 401 LYS cc_start: 0.7460 (mptm) cc_final: 0.7021 (mmmt) REVERT: B 405 ASP cc_start: 0.8119 (m-30) cc_final: 0.7655 (p0) REVERT: B 434 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: A 65 HIS cc_start: 0.7974 (m90) cc_final: 0.6926 (p-80) REVERT: A 380 SER cc_start: 0.8711 (t) cc_final: 0.8494 (t) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.6241 time to fit residues: 56.2941 Evaluate side-chains 89 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 78 GLU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 434 GLU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.0270 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.152163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112125 restraints weight = 4345.511| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.08 r_work: 0.3150 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4975 Z= 0.115 Angle : 0.460 5.285 6763 Z= 0.229 Chirality : 0.037 0.137 857 Planarity : 0.003 0.034 790 Dihedral : 10.795 140.150 1113 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.05 % Allowed : 19.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.78 (0.35), residues: 585 helix: 3.37 (0.24), residues: 392 sheet: 0.60 (0.87), residues: 50 loop : 0.68 (0.56), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.017 0.001 TYR B 396 PHE 0.008 0.001 PHE B 88 TRP 0.017 0.001 TRP B 312 HIS 0.003 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4955) covalent geometry : angle 0.45955 ( 6763) hydrogen bonds : bond 0.03505 ( 323) hydrogen bonds : angle 3.10954 ( 963) metal coordination : bond 0.00288 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.78 seconds wall clock time: 40 minutes 9.65 seconds (2409.65 seconds total)