Starting phenix.real_space_refine on Thu Mar 6 06:08:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xm6_38465/03_2025/8xm6_38465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xm6_38465/03_2025/8xm6_38465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xm6_38465/03_2025/8xm6_38465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xm6_38465/03_2025/8xm6_38465.map" model { file = "/net/cci-nas-00/data/ceres_data/8xm6_38465/03_2025/8xm6_38465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xm6_38465/03_2025/8xm6_38465.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.102 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 6 6.06 5 S 52 5.16 5 C 3422 2.51 5 N 827 2.21 5 O 898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5205 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2442 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain breaks: 3 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2444 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 3 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 177 Unusual residues: {' ZN': 3, 'AV0': 1, 'Y01': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 142 Unusual residues: {' ZN': 3, 'AV0': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2338 SG CYS B 433 39.864 24.143 26.658 1.00 72.85 S ATOM 4810 SG CYS A 437 39.094 30.166 53.026 1.00 69.64 S ATOM 2436 SG CYS B 446 37.845 32.662 27.780 1.00 49.37 S ATOM 2442 SG CYS B 447 41.991 33.675 26.705 1.00 50.90 S ATOM 4782 SG CYS A 433 30.984 24.325 45.844 1.00 71.84 S ATOM 2366 SG CYS B 437 31.037 26.848 20.080 1.00 74.96 S ATOM 4880 SG CYS A 446 31.054 33.460 43.352 1.00 57.72 S ATOM 4886 SG CYS A 447 27.237 34.038 44.096 1.00 57.24 S Time building chain proxies: 4.06, per 1000 atoms: 0.78 Number of scatterers: 5205 At special positions: 0 Unit cell: (65.728, 119.808, 68.224, 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 6 29.99 S 52 16.00 O 898 8.00 N 827 7.00 C 3422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.4 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=" SG CYS B 437 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 413 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 408 " 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 B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 370 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 387 " 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=" SG CYS A 437 " pdb="ZN ZN B 602 " - pdb=" ND1 HIS B 408 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 373 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 447 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 446 " 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 65.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.515A pdb=" N ARG B 10 " --> pdb=" O ARG B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.858A pdb=" N PHE B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 63 removed outlier: 4.137A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) 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 289 through 293 Processing helix chain 'B' and resid 315 through 344 Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 352 through 362 Processing helix chain 'B' and resid 395 through 410 removed outlier: 3.807A pdb=" N VAL B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.691A pdb=" N LEU A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 62 removed outlier: 3.809A pdb=" N ARG A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 106 Processing helix chain 'A' and resid 112 through 136 removed outlier: 3.637A pdb=" N VAL A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N HIS A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 272 removed outlier: 3.551A pdb=" N ASP A 255 " --> pdb=" O HIS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.559A pdb=" N VAL A 313 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 344 removed outlier: 4.029A 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 361 Processing helix chain 'A' and resid 396 through 409 removed outlier: 3.645A pdb=" N THR A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 369 through 376 removed outlier: 7.152A pdb=" N VAL B 369 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LYS B 389 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS B 387 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 376 removed outlier: 6.872A pdb=" N VAL A 369 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LYS A 389 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 382 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N THR A 416 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA A 384 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLN A 418 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA A 386 " --> pdb=" O GLN A 418 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 969 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: 1.53 Time building geometry restraints manager: 2.03 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: 862 1.32 - 1.45: 1277 1.45 - 1.57: 3108 1.57 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 5319 Sorted by residual: bond pdb=" CAX Y01 B 606 " pdb=" OAF Y01 B 606 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.40e+00 bond pdb=" CAX Y01 B 607 " pdb=" OAF Y01 B 607 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" CAX Y01 A 605 " pdb=" OAH Y01 A 605 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" CAX Y01 B 605 " pdb=" OAH Y01 B 605 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.05e+00 bond pdb=" CAX Y01 A 606 " pdb=" OAF Y01 A 606 " ideal model delta sigma weight residual 1.247 1.307 -0.060 2.00e-02 2.50e+03 8.98e+00 ... (remaining 5314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 6994 1.55 - 3.10: 222 3.10 - 4.65: 37 4.65 - 6.20: 12 6.20 - 7.75: 7 Bond angle restraints: 7272 Sorted by residual: angle pdb=" C HIS A 408 " pdb=" CA HIS A 408 " pdb=" CB HIS A 408 " ideal model delta sigma weight residual 110.67 103.96 6.71 1.92e+00 2.71e-01 1.22e+01 angle pdb=" N ILE B 412 " pdb=" CA ILE B 412 " pdb=" C ILE B 412 " ideal model delta sigma weight residual 109.55 113.39 -3.84 1.38e+00 5.25e-01 7.75e+00 angle pdb=" C HIS B 413 " pdb=" CA HIS B 413 " pdb=" CB HIS B 413 " ideal model delta sigma weight residual 110.42 115.83 -5.41 1.99e+00 2.53e-01 7.38e+00 angle pdb=" C ILE B 412 " pdb=" CA ILE B 412 " pdb=" CB ILE B 412 " ideal model delta sigma weight residual 111.63 107.99 3.64 1.38e+00 5.25e-01 6.96e+00 angle pdb=" CA ILE B 412 " pdb=" C ILE B 412 " pdb=" N HIS B 413 " ideal model delta sigma weight residual 115.82 119.77 -3.95 1.52e+00 4.33e-01 6.74e+00 ... (remaining 7267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.10: 3287 28.10 - 56.20: 164 56.20 - 84.30: 44 84.30 - 112.39: 41 112.39 - 140.49: 18 Dihedral angle restraints: 3554 sinusoidal: 1687 harmonic: 1867 Sorted by residual: dihedral pdb=" CB CYS B 276 " pdb=" SG CYS B 276 " pdb=" SG CYS B 282 " pdb=" CB CYS B 282 " ideal model delta sinusoidal sigma weight residual -86.00 -176.33 90.33 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" OAJ AV0 A 604 " pdb=" CBN AV0 A 604 " pdb=" CCD AV0 A 604 " pdb=" OBZ AV0 A 604 " ideal model delta sinusoidal sigma weight residual 64.90 -75.59 140.49 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CCO AV0 A 604 " pdb=" CBN AV0 A 604 " pdb=" CCD AV0 A 604 " pdb=" OAJ AV0 A 604 " ideal model delta sinusoidal sigma weight residual 174.12 -46.66 -139.22 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 3551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 655 0.042 - 0.083: 205 0.083 - 0.125: 45 0.125 - 0.166: 5 0.166 - 0.208: 6 Chirality restraints: 916 Sorted by residual: chirality pdb=" CCV AV0 A 604 " pdb=" CCR AV0 A 604 " pdb=" CCT AV0 A 604 " pdb=" OAU AV0 A 604 " both_signs ideal model delta sigma weight residual False -2.30 -2.50 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CCV AV0 B 604 " pdb=" CCR AV0 B 604 " pdb=" CCT AV0 B 604 " pdb=" OAU AV0 B 604 " both_signs ideal model delta sigma weight residual False -2.30 -2.50 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CCW AV0 A 604 " pdb=" CCS AV0 A 604 " pdb=" CCU AV0 A 604 " pdb=" OAV AV0 A 604 " both_signs ideal model delta sigma weight residual False -2.29 -2.49 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 913 not shown) Planarity restraints: 853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 408 " 0.031 2.00e-02 2.50e+03 2.99e-02 1.34e+01 pdb=" CG HIS A 408 " -0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS A 408 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 408 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A 408 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS A 408 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 112 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO B 113 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 407 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C PHE B 407 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE B 407 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS B 408 " 0.010 2.00e-02 2.50e+03 ... (remaining 850 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 38 2.58 - 3.16: 4337 3.16 - 3.74: 8099 3.74 - 4.32: 10241 4.32 - 4.90: 17424 Nonbonded interactions: 40139 Sorted by model distance: nonbonded pdb=" OE1 GLU B 420 " pdb="ZN ZN B 601 " model vdw 2.004 2.230 nonbonded pdb=" OE2 GLU A 371 " pdb="ZN ZN A 603 " model vdw 2.004 2.230 nonbonded pdb=" OE1 GLU B 371 " pdb="ZN ZN B 603 " model vdw 2.051 2.230 nonbonded pdb=" OE2 GLU A 420 " pdb="ZN ZN A 601 " model vdw 2.110 2.230 nonbonded pdb=" O LEU B 341 " pdb=" OG1 THR B 346 " model vdw 2.329 3.040 ... (remaining 40134 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 242 and (name N or nam \ e CA or name C or name O or name CB )) or resid 243 through 357 or (resid 358 an \ d (name N or name CA or name C or name O or name CB )) or resid 359 through 390 \ or (resid 391 through 392 and (name N or name CA or name C or name O or name CB \ )) or resid 393 through 397 or (resid 398 and (name N or name CA or name C or na \ me O or name CB )) or resid 399 through 447 or resid 601 through 606)) selection = (chain 'B' and (resid 6 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 135 or (resid 136 and (name N or \ name CA or name C or name O or name CB )) or resid 240 through 353 or (resid 35 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 355 through \ 394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or re \ sid 396 through 400 or (resid 401 and (name N or name CA or name C or name O or \ name CB )) or resid 402 through 404 or (resid 405 and (name N or name CA or name \ C or name O or name CB )) or resid 406 through 429 or (resid 430 and (name N or \ name CA or name C or name O or name CB )) or resid 431 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: 1.210 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: 0.030 Set scattering table: 0.050 Process input model: 19.610 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:3.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 5319 Z= 0.295 Angle : 0.681 7.753 7272 Z= 0.319 Chirality : 0.043 0.208 916 Planarity : 0.004 0.048 853 Dihedral : 23.935 140.492 2330 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.35), residues: 629 helix: 3.21 (0.25), residues: 381 sheet: -0.27 (0.92), residues: 43 loop : -0.62 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 273 HIS 0.029 0.002 HIS A 408 PHE 0.011 0.001 PHE B 19 TYR 0.006 0.001 TYR A 270 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: B 245 MET cc_start: 0.6134 (ttm) cc_final: 0.5895 (tpp) REVERT: B 359 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7189 (mp0) REVERT: A 245 MET cc_start: 0.6235 (tmm) cc_final: 0.6017 (tmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1937 time to fit residues: 30.7386 Evaluate side-chains 110 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 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 108 HIS B 111 GLN ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS A 108 HIS A 127 ASN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.192645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157410 restraints weight = 5265.895| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.15 r_work: 0.3573 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5319 Z= 0.191 Angle : 0.633 8.215 7272 Z= 0.279 Chirality : 0.045 0.370 916 Planarity : 0.004 0.034 853 Dihedral : 14.316 122.269 1282 Min Nonbonded Distance : 1.553 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.54 % Allowed : 13.51 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.36), residues: 629 helix: 3.03 (0.25), residues: 392 sheet: -0.46 (0.91), residues: 45 loop : -0.13 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 273 HIS 0.008 0.001 HIS B 135 PHE 0.011 0.001 PHE B 407 TYR 0.006 0.001 TYR B 396 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.557 Fit side-chains REVERT: B 44 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7495 (ttm) REVERT: B 135 HIS cc_start: 0.7123 (p90) cc_final: 0.6915 (p90) REVERT: B 245 MET cc_start: 0.7066 (ttm) cc_final: 0.6521 (tpp) REVERT: B 359 GLU cc_start: 0.7813 (mt-10) cc_final: 0.6980 (mp0) REVERT: B 397 MET cc_start: 0.6965 (mmm) cc_final: 0.6754 (tpp) REVERT: A 125 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8241 (mm) REVERT: A 245 MET cc_start: 0.6101 (tmm) cc_final: 0.5828 (tmm) REVERT: A 409 ASN cc_start: 0.8031 (m-40) cc_final: 0.7724 (m-40) outliers start: 8 outliers final: 2 residues processed: 117 average time/residue: 0.1967 time to fit residues: 30.6924 Evaluate side-chains 114 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 125 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.191333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.155522 restraints weight = 5328.304| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.12 r_work: 0.3592 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5319 Z= 0.186 Angle : 0.567 6.393 7272 Z= 0.260 Chirality : 0.040 0.200 916 Planarity : 0.004 0.035 853 Dihedral : 12.815 150.081 1282 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.47 % Allowed : 16.02 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.35), residues: 629 helix: 2.98 (0.25), residues: 392 sheet: -0.41 (0.89), residues: 45 loop : -0.17 (0.51), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.008 0.001 HIS B 135 PHE 0.009 0.001 PHE B 104 TYR 0.005 0.001 TYR B 396 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.545 Fit side-chains REVERT: B 44 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7591 (ttm) REVERT: B 359 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7070 (mp0) REVERT: B 409 ASN cc_start: 0.7947 (m-40) cc_final: 0.7643 (t0) REVERT: B 434 GLU cc_start: 0.7537 (pt0) cc_final: 0.7287 (pt0) REVERT: A 104 PHE cc_start: 0.7644 (m-10) cc_final: 0.7434 (m-80) REVERT: A 112 GLN cc_start: 0.7983 (pt0) cc_final: 0.7084 (tp40) REVERT: A 125 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8159 (mm) REVERT: A 245 MET cc_start: 0.6053 (tmm) cc_final: 0.5602 (tmm) REVERT: A 409 ASN cc_start: 0.8118 (m-40) cc_final: 0.7778 (m-40) outliers start: 18 outliers final: 12 residues processed: 128 average time/residue: 0.1636 time to fit residues: 28.0716 Evaluate side-chains 129 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 369 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 62 optimal weight: 0.0010 chunk 12 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.192489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.156389 restraints weight = 5444.232| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.17 r_work: 0.3592 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5319 Z= 0.169 Angle : 0.537 6.253 7272 Z= 0.247 Chirality : 0.039 0.195 916 Planarity : 0.003 0.035 853 Dihedral : 11.710 130.911 1282 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.09 % Allowed : 18.53 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.36), residues: 629 helix: 2.96 (0.25), residues: 394 sheet: -0.37 (0.89), residues: 45 loop : -0.20 (0.52), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.007 0.001 HIS B 135 PHE 0.010 0.001 PHE B 21 TYR 0.004 0.001 TYR A 333 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.691 Fit side-chains REVERT: B 19 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8115 (t80) REVERT: B 44 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7599 (ttm) REVERT: B 359 GLU cc_start: 0.7740 (mt-10) cc_final: 0.6968 (mp0) REVERT: B 409 ASN cc_start: 0.7994 (m-40) cc_final: 0.7728 (t0) REVERT: A 58 GLU cc_start: 0.8294 (tp30) cc_final: 0.8026 (tp30) REVERT: A 125 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8140 (mm) REVERT: A 245 MET cc_start: 0.6066 (tmm) cc_final: 0.5607 (tmm) REVERT: A 409 ASN cc_start: 0.8188 (m-40) cc_final: 0.7850 (m-40) outliers start: 16 outliers final: 8 residues processed: 125 average time/residue: 0.1859 time to fit residues: 30.5252 Evaluate side-chains 123 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 369 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.0970 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 40.0000 chunk 53 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.192911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156790 restraints weight = 5397.532| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.18 r_work: 0.3603 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5319 Z= 0.168 Angle : 0.531 6.998 7272 Z= 0.246 Chirality : 0.039 0.190 916 Planarity : 0.003 0.036 853 Dihedral : 11.385 123.154 1282 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.90 % Allowed : 21.04 % Favored : 76.06 % 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: 2.69 (0.35), residues: 629 helix: 3.00 (0.25), residues: 390 sheet: -0.21 (0.91), residues: 44 loop : -0.32 (0.50), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 375 HIS 0.007 0.001 HIS B 135 PHE 0.011 0.001 PHE B 21 TYR 0.004 0.001 TYR A 333 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.451 Fit side-chains REVERT: B 44 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7488 (ttm) REVERT: B 106 GLU cc_start: 0.7150 (mp0) cc_final: 0.6547 (pt0) REVERT: B 245 MET cc_start: 0.7001 (ttm) cc_final: 0.6692 (tpp) REVERT: B 359 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7077 (mp0) REVERT: B 409 ASN cc_start: 0.8077 (m-40) cc_final: 0.7781 (t0) REVERT: A 112 GLN cc_start: 0.7693 (pt0) cc_final: 0.6834 (tp40) REVERT: A 125 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8127 (mm) REVERT: A 245 MET cc_start: 0.6085 (tmm) cc_final: 0.5352 (tmm) REVERT: A 409 ASN cc_start: 0.8220 (m-40) cc_final: 0.7864 (m-40) outliers start: 15 outliers final: 9 residues processed: 122 average time/residue: 0.3289 time to fit residues: 54.5032 Evaluate side-chains 122 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 369 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.187525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150951 restraints weight = 5398.800| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.14 r_work: 0.3511 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5319 Z= 0.274 Angle : 0.608 6.526 7272 Z= 0.285 Chirality : 0.041 0.199 916 Planarity : 0.004 0.049 853 Dihedral : 11.391 111.276 1282 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.25 % Allowed : 20.85 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.35), residues: 629 helix: 2.64 (0.25), residues: 390 sheet: -0.67 (0.91), residues: 43 loop : -0.26 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 375 HIS 0.009 0.002 HIS B 135 PHE 0.013 0.001 PHE B 21 TYR 0.006 0.001 TYR B 396 ARG 0.004 0.001 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8147 (t80) REVERT: B 44 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7602 (ttm) REVERT: B 106 GLU cc_start: 0.7279 (mp0) cc_final: 0.6708 (tp30) REVERT: B 245 MET cc_start: 0.7067 (ttm) cc_final: 0.6802 (tpp) REVERT: B 359 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7042 (mp0) REVERT: B 409 ASN cc_start: 0.8236 (m-40) cc_final: 0.7841 (t0) REVERT: A 112 GLN cc_start: 0.7922 (pt0) cc_final: 0.6920 (tp40) REVERT: A 125 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8214 (mm) outliers start: 22 outliers final: 13 residues processed: 123 average time/residue: 0.1602 time to fit residues: 25.9786 Evaluate side-chains 127 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 369 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 0.0570 chunk 39 optimal weight: 0.0770 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 overall best weight: 0.8258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.190125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153723 restraints weight = 5385.742| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.16 r_work: 0.3571 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5319 Z= 0.196 Angle : 0.567 7.313 7272 Z= 0.264 Chirality : 0.040 0.194 916 Planarity : 0.004 0.035 853 Dihedral : 10.853 105.133 1282 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.44 % Allowed : 21.24 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.35), residues: 629 helix: 2.79 (0.25), residues: 388 sheet: -0.58 (0.92), residues: 43 loop : -0.11 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.008 0.001 HIS B 135 PHE 0.011 0.001 PHE B 21 TYR 0.005 0.001 TYR A 333 ARG 0.007 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8162 (t80) REVERT: B 44 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7488 (ttm) REVERT: B 106 GLU cc_start: 0.7136 (mp0) cc_final: 0.6660 (tp30) REVERT: B 245 MET cc_start: 0.7119 (ttm) cc_final: 0.6855 (tpp) REVERT: B 359 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7011 (mp0) REVERT: B 409 ASN cc_start: 0.8290 (m-40) cc_final: 0.7887 (t0) REVERT: A 125 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8177 (mm) outliers start: 23 outliers final: 14 residues processed: 122 average time/residue: 0.1593 time to fit residues: 26.0431 Evaluate side-chains 129 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 399 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.189800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.153895 restraints weight = 5389.868| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.13 r_work: 0.3564 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5319 Z= 0.203 Angle : 0.580 8.381 7272 Z= 0.268 Chirality : 0.040 0.195 916 Planarity : 0.004 0.034 853 Dihedral : 10.537 104.389 1282 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.63 % Allowed : 21.43 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.35), residues: 629 helix: 2.73 (0.25), residues: 388 sheet: -0.78 (0.91), residues: 44 loop : -0.09 (0.50), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.008 0.001 HIS B 135 PHE 0.012 0.001 PHE B 21 TYR 0.004 0.001 TYR A 333 ARG 0.007 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: B 44 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7444 (ttm) REVERT: B 106 GLU cc_start: 0.7063 (mp0) cc_final: 0.6589 (tp30) REVERT: B 245 MET cc_start: 0.7071 (ttm) cc_final: 0.6822 (tpp) REVERT: B 359 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7057 (mp0) REVERT: B 397 MET cc_start: 0.6546 (mmm) cc_final: 0.5466 (mtp) REVERT: B 409 ASN cc_start: 0.8283 (m-40) cc_final: 0.7894 (t0) REVERT: A 29 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8830 (p) REVERT: A 125 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8170 (mm) outliers start: 24 outliers final: 14 residues processed: 123 average time/residue: 0.1526 time to fit residues: 25.7661 Evaluate side-chains 128 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 399 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.191738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156023 restraints weight = 5321.770| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.12 r_work: 0.3590 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5319 Z= 0.177 Angle : 0.557 7.991 7272 Z= 0.257 Chirality : 0.039 0.194 916 Planarity : 0.003 0.034 853 Dihedral : 9.665 104.502 1282 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.28 % Allowed : 22.59 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.35), residues: 629 helix: 2.84 (0.25), residues: 387 sheet: -0.75 (0.91), residues: 44 loop : -0.13 (0.49), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.008 0.001 HIS B 135 PHE 0.011 0.001 PHE B 21 TYR 0.004 0.001 TYR A 333 ARG 0.007 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 44 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7336 (ttm) REVERT: B 245 MET cc_start: 0.7061 (ttm) cc_final: 0.6834 (tpp) REVERT: B 359 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7101 (mp0) REVERT: B 397 MET cc_start: 0.6168 (mmm) cc_final: 0.5481 (mtp) REVERT: B 409 ASN cc_start: 0.8300 (m-40) cc_final: 0.7895 (t0) REVERT: A 29 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8844 (p) REVERT: A 112 GLN cc_start: 0.7071 (pt0) cc_final: 0.5863 (tt0) REVERT: A 125 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8154 (mm) outliers start: 17 outliers final: 11 residues processed: 121 average time/residue: 0.1312 time to fit residues: 21.7449 Evaluate side-chains 129 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.192020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.156080 restraints weight = 5371.485| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.12 r_work: 0.3595 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5319 Z= 0.180 Angle : 0.570 7.886 7272 Z= 0.263 Chirality : 0.040 0.195 916 Planarity : 0.004 0.034 853 Dihedral : 9.575 104.135 1282 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.90 % Allowed : 23.17 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.35), residues: 629 helix: 2.84 (0.25), residues: 387 sheet: -0.62 (0.92), residues: 44 loop : -0.08 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 375 HIS 0.008 0.001 HIS B 135 PHE 0.010 0.001 PHE B 104 TYR 0.006 0.001 TYR B 396 ARG 0.007 0.000 ARG B 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.593 Fit side-chains REVERT: B 44 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7289 (ttm) REVERT: B 102 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7810 (mm-30) REVERT: B 245 MET cc_start: 0.7051 (ttm) cc_final: 0.6835 (tpp) REVERT: B 359 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7076 (mp0) REVERT: B 397 MET cc_start: 0.6209 (mmm) cc_final: 0.5605 (mtp) REVERT: B 409 ASN cc_start: 0.8366 (m-40) cc_final: 0.7978 (m110) REVERT: A 29 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8839 (p) REVERT: A 112 GLN cc_start: 0.7004 (pt0) cc_final: 0.5887 (tt0) REVERT: A 125 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8165 (mm) outliers start: 15 outliers final: 11 residues processed: 113 average time/residue: 0.1598 time to fit residues: 25.9529 Evaluate side-chains 122 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 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 108 HIS ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.191304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155218 restraints weight = 5411.341| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.14 r_work: 0.3584 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5319 Z= 0.190 Angle : 0.573 7.731 7272 Z= 0.265 Chirality : 0.040 0.196 916 Planarity : 0.004 0.034 853 Dihedral : 9.509 103.702 1282 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.28 % Allowed : 22.39 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.35), residues: 629 helix: 2.84 (0.25), residues: 387 sheet: -0.65 (0.91), residues: 44 loop : -0.05 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.008 0.001 HIS B 135 PHE 0.010 0.001 PHE B 21 TYR 0.008 0.001 TYR B 396 ARG 0.007 0.000 ARG B 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3075.44 seconds wall clock time: 56 minutes 4.94 seconds (3364.94 seconds total)