Starting phenix.real_space_refine on Thu Nov 14 07:53:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmf_38475/11_2024/8xmf_38475.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmf_38475/11_2024/8xmf_38475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmf_38475/11_2024/8xmf_38475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmf_38475/11_2024/8xmf_38475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmf_38475/11_2024/8xmf_38475.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmf_38475/11_2024/8xmf_38475.cif" } resolution = 3.64 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= -0.002 sd= 0.060 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 52 5.16 5 C 3245 2.51 5 N 780 2.21 5 O 844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4929 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2365 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2357 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 121 Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 86 Unusual residues: {' ZN': 4, 'AV0': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2274 SG CYS B 433 47.132 34.125 96.780 1.00159.45 S ATOM 2359 SG CYS B 446 45.358 32.849 87.669 1.00120.18 S ATOM 2365 SG CYS B 447 45.777 37.314 87.705 1.00125.67 S ATOM 4652 SG CYS A 437 23.534 28.522 91.663 1.00150.23 S ATOM 2298 SG CYS B 437 53.483 28.164 92.832 1.00147.75 S ATOM 4628 SG CYS A 433 29.856 22.059 96.573 1.00150.75 S ATOM 4716 SG CYS A 446 31.375 22.860 86.211 1.00121.94 S ATOM 4722 SG CYS A 447 30.698 18.796 88.022 1.00131.94 S Time building chain proxies: 4.07, per 1000 atoms: 0.83 Number of scatterers: 4929 At special positions: 0 Unit cell: (77.376, 56.576, 121.472, 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 52 16.00 O 844 8.00 N 780 7.00 C 3245 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 767.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 413 " pdb="ZN ZN A 601 " - pdb=" SG CYS B 437 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 387 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 370 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 433 " pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 447 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 446 " pdb=" ZN A 604 " pdb="ZN ZN A 604 " - pdb=" NE2 HIS A 43 " pdb="ZN ZN A 604 " - pdb=" NE2 HIS A 251 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 433 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 370 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 387 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 373 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 447 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 446 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 251 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 43 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" SG CYS A 437 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 408 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 413 " 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1208 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 3 sheets defined 63.7% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 11 through 33 removed outlier: 4.145A pdb=" N LEU B 17 " --> pdb=" O CYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 62 Processing helix chain 'B' and resid 76 through 106 Processing helix chain 'B' and resid 112 through 133 removed outlier: 3.507A pdb=" N VAL B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS B 132 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 273 Processing helix chain 'B' and resid 291 through 298 removed outlier: 4.161A pdb=" N VAL B 295 " --> pdb=" O CYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 344 removed outlier: 4.095A pdb=" N VAL B 323 " --> pdb=" O THR B 319 " (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 399 through 410 removed outlier: 3.658A pdb=" N HIS B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 33 removed outlier: 3.842A pdb=" N LEU A 17 " --> pdb=" O CYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 63 removed outlier: 4.131A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (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 133 Processing helix chain 'A' and resid 245 through 273 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 315 through 344 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 410 removed outlier: 3.666A pdb=" N VAL A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 Processing sheet with id=AA1, first strand: chain 'B' and resid 370 through 378 removed outlier: 5.483A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS B 387 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLN B 418 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 386 " --> pdb=" O GLN B 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 376 removed outlier: 6.518A pdb=" N VAL A 369 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LYS A 389 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 414 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 376 removed outlier: 6.518A pdb=" N VAL A 369 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LYS A 389 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLN A 418 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 386 " --> pdb=" O GLN A 418 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLU A 420 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 388 " --> pdb=" O GLU A 420 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 954 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: 1.22 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 833 1.33 - 1.45: 1184 1.45 - 1.57: 2937 1.57 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 5026 Sorted by residual: bond pdb=" CA GLU A 420 " pdb=" C GLU A 420 " ideal model delta sigma weight residual 1.525 1.475 0.050 1.29e-02 6.01e+03 1.52e+01 bond pdb=" CA GLU A 420 " pdb=" CB GLU A 420 " ideal model delta sigma weight residual 1.525 1.481 0.044 1.29e-02 6.01e+03 1.19e+01 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 9.39e+00 bond pdb=" CAX Y01 B 606 " pdb=" OAH Y01 B 606 " ideal model delta sigma weight residual 1.248 1.309 -0.061 2.00e-02 2.50e+03 9.18e+00 bond pdb=" CAX Y01 B 607 " pdb=" OAH Y01 B 607 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.10e+00 ... (remaining 5021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 6589 1.53 - 3.06: 219 3.06 - 4.58: 50 4.58 - 6.11: 11 6.11 - 7.64: 4 Bond angle restraints: 6873 Sorted by residual: angle pdb=" N LYS A 444 " pdb=" CA LYS A 444 " pdb=" C LYS A 444 " ideal model delta sigma weight residual 111.07 107.17 3.90 1.07e+00 8.73e-01 1.33e+01 angle pdb=" N GLU B 420 " pdb=" CA GLU B 420 " pdb=" C GLU B 420 " ideal model delta sigma weight residual 107.69 100.85 6.84 2.01e+00 2.48e-01 1.16e+01 angle pdb=" CA PRO A 290 " pdb=" C PRO A 290 " pdb=" O PRO A 290 " ideal model delta sigma weight residual 121.34 118.15 3.19 1.14e+00 7.69e-01 7.84e+00 angle pdb=" N GLN B 440 " pdb=" CA GLN B 440 " pdb=" C GLN B 440 " ideal model delta sigma weight residual 108.76 113.41 -4.65 1.69e+00 3.50e-01 7.56e+00 angle pdb=" C PHE A 287 " pdb=" CA PHE A 287 " pdb=" CB PHE A 287 " ideal model delta sigma weight residual 108.76 112.27 -3.51 1.37e+00 5.33e-01 6.55e+00 ... (remaining 6868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.86: 2995 26.86 - 53.71: 160 53.71 - 80.57: 15 80.57 - 107.43: 19 107.43 - 134.28: 15 Dihedral angle restraints: 3204 sinusoidal: 1357 harmonic: 1847 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 93.00 37.81 55.19 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CB CYS A 276 " pdb=" SG CYS A 276 " pdb=" SG CYS A 282 " pdb=" CB CYS A 282 " ideal model delta sinusoidal sigma weight residual 93.00 47.38 45.62 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" OAJ AV0 B 605 " pdb=" CBN AV0 B 605 " pdb=" CCD AV0 B 605 " pdb=" OBZ AV0 B 605 " ideal model delta sinusoidal sigma weight residual 64.90 -69.38 134.28 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 3201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 731 0.052 - 0.104: 126 0.104 - 0.156: 15 0.156 - 0.208: 2 0.208 - 0.260: 3 Chirality restraints: 877 Sorted by residual: chirality pdb=" CA GLU B 371 " pdb=" N GLU B 371 " pdb=" C GLU B 371 " pdb=" CB GLU B 371 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA CYS A 291 " pdb=" N CYS A 291 " pdb=" C CYS A 291 " pdb=" CB CYS A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CCV AV0 A 605 " pdb=" CCR AV0 A 605 " pdb=" CCT AV0 A 605 " pdb=" OAU AV0 A 605 " both_signs ideal model delta sigma weight residual False -2.30 -2.50 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 874 not shown) Planarity restraints: 814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 284 " -0.047 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO A 285 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 43 " -0.020 2.00e-02 2.50e+03 1.79e-02 4.81e+00 pdb=" CG HIS B 43 " 0.025 2.00e-02 2.50e+03 pdb=" ND1 HIS B 43 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS B 43 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS B 43 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 43 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 289 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 290 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.029 5.00e-02 4.00e+02 ... (remaining 811 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 47 2.57 - 3.15: 4237 3.15 - 3.73: 7826 3.73 - 4.32: 9483 4.32 - 4.90: 15716 Nonbonded interactions: 37309 Sorted by model distance: nonbonded pdb=" OD2 ASP B 47 " pdb="ZN ZN B 603 " model vdw 1.982 2.230 nonbonded pdb=" OD1 ASP B 255 " pdb="ZN ZN B 603 " model vdw 1.986 2.230 nonbonded pdb=" OD2 ASP A 47 " pdb="ZN ZN A 604 " model vdw 1.987 2.230 nonbonded pdb=" OE2 GLU A 371 " pdb="ZN ZN A 603 " model vdw 1.992 2.230 nonbonded pdb=" OD2 ASP A 255 " pdb="ZN ZN A 604 " model vdw 1.992 2.230 ... (remaining 37304 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 11 through 280 or (resid 281 and (name N or name CA or nam \ e C or name O or name CB )) or resid 282 through 442 or (resid 443 and (name N o \ r name CA or name C or name O or name CB )) or resid 444 through 447 or resid 60 \ 1 through 606)) selection = (chain 'B' and (resid 11 through 305 or (resid 306 and (name N or name CA or nam \ e C or name O or name CB )) or resid 307 through 349 or (resid 350 through 352 a \ nd (name N or name CA or name C or name O or name CB )) or resid 353 through 360 \ or (resid 361 and (name N or name CA or name C or name O or name CB )) or resid \ 362 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 group one per residue 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.810 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.005 0.061 5026 Z= 0.325 Angle : 0.692 7.640 6873 Z= 0.365 Chirality : 0.042 0.260 877 Planarity : 0.005 0.072 814 Dihedral : 19.980 134.282 1990 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.35), residues: 620 helix: 2.05 (0.26), residues: 378 sheet: 0.32 (0.89), residues: 42 loop : -1.29 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 312 HIS 0.015 0.001 HIS B 43 PHE 0.026 0.001 PHE B 294 TYR 0.009 0.001 TYR B 396 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.557 Fit side-chains REVERT: B 99 GLU cc_start: 0.8673 (tp30) cc_final: 0.8400 (tp30) REVERT: B 103 ARG cc_start: 0.9084 (ttm-80) cc_final: 0.8783 (ttm110) REVERT: B 355 ASN cc_start: 0.8121 (t0) cc_final: 0.7864 (t0) REVERT: B 360 LEU cc_start: 0.9467 (mm) cc_final: 0.9245 (mm) REVERT: B 408 HIS cc_start: 0.9138 (t70) cc_final: 0.8489 (t70) REVERT: A 41 SER cc_start: 0.9339 (p) cc_final: 0.8660 (p) REVERT: A 59 ARG cc_start: 0.8428 (ttm170) cc_final: 0.7961 (tpm170) REVERT: A 99 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7773 (mm-30) REVERT: A 294 PHE cc_start: 0.8003 (t80) cc_final: 0.7623 (t80) REVERT: A 380 SER cc_start: 0.9221 (t) cc_final: 0.8934 (t) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1560 time to fit residues: 39.0642 Evaluate side-chains 168 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 HIS A 108 HIS A 127 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5026 Z= 0.262 Angle : 0.679 8.056 6873 Z= 0.328 Chirality : 0.044 0.350 877 Planarity : 0.004 0.045 814 Dihedral : 12.574 102.357 1019 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.83 % Allowed : 20.12 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.35), residues: 620 helix: 2.04 (0.26), residues: 378 sheet: 0.00 (0.88), residues: 42 loop : -1.04 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 273 HIS 0.005 0.001 HIS B 43 PHE 0.016 0.002 PHE B 19 TYR 0.013 0.001 TYR A 270 ARG 0.002 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.556 Fit side-chains REVERT: B 246 ARG cc_start: 0.6735 (mmm160) cc_final: 0.6403 (mmm160) REVERT: B 320 LEU cc_start: 0.9167 (tp) cc_final: 0.8899 (tp) REVERT: B 355 ASN cc_start: 0.8208 (t0) cc_final: 0.7933 (t0) REVERT: A 59 ARG cc_start: 0.8480 (ttm170) cc_final: 0.7930 (tpm170) REVERT: A 99 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8212 (tp30) REVERT: A 294 PHE cc_start: 0.8140 (t80) cc_final: 0.7646 (t80) REVERT: A 380 SER cc_start: 0.9249 (t) cc_final: 0.8957 (t) outliers start: 24 outliers final: 20 residues processed: 194 average time/residue: 0.1712 time to fit residues: 42.3288 Evaluate side-chains 196 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 19 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 362 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5026 Z= 0.255 Angle : 0.639 7.824 6873 Z= 0.316 Chirality : 0.041 0.221 877 Planarity : 0.004 0.033 814 Dihedral : 10.183 95.468 1019 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.23 % Allowed : 24.95 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.35), residues: 620 helix: 2.04 (0.26), residues: 378 sheet: -0.52 (0.90), residues: 42 loop : -0.98 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 273 HIS 0.008 0.001 HIS B 413 PHE 0.017 0.001 PHE A 287 TYR 0.007 0.001 TYR B 396 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.567 Fit side-chains REVERT: B 37 MET cc_start: 0.8584 (ttt) cc_final: 0.8377 (tpt) REVERT: B 246 ARG cc_start: 0.6806 (mmm160) cc_final: 0.6468 (mmm160) REVERT: B 320 LEU cc_start: 0.9148 (tp) cc_final: 0.8872 (tp) REVERT: B 355 ASN cc_start: 0.8198 (t0) cc_final: 0.7862 (t0) REVERT: A 59 ARG cc_start: 0.8498 (ttm170) cc_final: 0.7955 (tpm170) REVERT: A 99 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8171 (tp30) REVERT: A 294 PHE cc_start: 0.8065 (t80) cc_final: 0.7312 (t80) REVERT: A 380 SER cc_start: 0.9220 (t) cc_final: 0.8961 (t) outliers start: 26 outliers final: 23 residues processed: 191 average time/residue: 0.1687 time to fit residues: 41.0528 Evaluate side-chains 199 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5026 Z= 0.282 Angle : 0.632 5.709 6873 Z= 0.317 Chirality : 0.040 0.127 877 Planarity : 0.004 0.035 814 Dihedral : 9.462 91.759 1019 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 7.04 % Allowed : 24.95 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.35), residues: 620 helix: 2.00 (0.26), residues: 378 sheet: -0.72 (0.92), residues: 42 loop : -0.96 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 273 HIS 0.005 0.001 HIS B 413 PHE 0.016 0.001 PHE A 19 TYR 0.016 0.001 TYR A 396 ARG 0.001 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.511 Fit side-chains REVERT: B 25 GLU cc_start: 0.9199 (tp30) cc_final: 0.8807 (tp30) REVERT: B 320 LEU cc_start: 0.9155 (tp) cc_final: 0.8850 (tp) REVERT: B 355 ASN cc_start: 0.8143 (t0) cc_final: 0.7827 (t0) REVERT: A 59 ARG cc_start: 0.8519 (ttm170) cc_final: 0.7960 (tpm170) REVERT: A 380 SER cc_start: 0.9207 (t) cc_final: 0.8958 (t) outliers start: 35 outliers final: 30 residues processed: 196 average time/residue: 0.1484 time to fit residues: 37.8226 Evaluate side-chains 202 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 41 optimal weight: 0.0870 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 0.0370 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN A 108 HIS ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5026 Z= 0.187 Angle : 0.590 5.789 6873 Z= 0.297 Chirality : 0.039 0.170 877 Planarity : 0.003 0.032 814 Dihedral : 8.654 85.805 1019 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.63 % Allowed : 29.58 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.35), residues: 620 helix: 2.12 (0.26), residues: 378 sheet: -0.69 (0.90), residues: 42 loop : -0.94 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 273 HIS 0.004 0.001 HIS B 413 PHE 0.019 0.001 PHE A 287 TYR 0.014 0.001 TYR A 396 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.557 Fit side-chains REVERT: B 25 GLU cc_start: 0.9123 (tp30) cc_final: 0.8815 (tp30) REVERT: B 355 ASN cc_start: 0.8096 (t0) cc_final: 0.7880 (t0) REVERT: A 59 ARG cc_start: 0.8507 (ttm170) cc_final: 0.7960 (tpm170) outliers start: 28 outliers final: 23 residues processed: 186 average time/residue: 0.1699 time to fit residues: 40.5254 Evaluate side-chains 190 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN A 345 GLN A 362 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5026 Z= 0.225 Angle : 0.599 5.639 6873 Z= 0.305 Chirality : 0.039 0.139 877 Planarity : 0.003 0.033 814 Dihedral : 8.521 83.422 1019 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.24 % Allowed : 29.58 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.35), residues: 620 helix: 2.14 (0.27), residues: 378 sheet: -0.76 (0.89), residues: 42 loop : -0.93 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 273 HIS 0.003 0.001 HIS A 108 PHE 0.019 0.001 PHE A 19 TYR 0.010 0.001 TYR A 396 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.678 Fit side-chains REVERT: B 25 GLU cc_start: 0.9106 (tp30) cc_final: 0.8862 (tp30) REVERT: B 320 LEU cc_start: 0.9057 (tp) cc_final: 0.8754 (tp) REVERT: B 355 ASN cc_start: 0.8152 (t0) cc_final: 0.7872 (t0) REVERT: B 362 ASN cc_start: 0.8111 (t0) cc_final: 0.7869 (t0) REVERT: A 59 ARG cc_start: 0.8522 (ttm170) cc_final: 0.7953 (tpm170) REVERT: A 103 ARG cc_start: 0.8948 (ttm-80) cc_final: 0.8708 (tpp80) outliers start: 31 outliers final: 27 residues processed: 185 average time/residue: 0.1680 time to fit residues: 40.0652 Evaluate side-chains 200 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 362 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5026 Z= 0.222 Angle : 0.602 6.598 6873 Z= 0.305 Chirality : 0.039 0.133 877 Planarity : 0.003 0.032 814 Dihedral : 8.422 82.494 1019 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.64 % Allowed : 30.18 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.35), residues: 620 helix: 2.13 (0.26), residues: 378 sheet: -0.46 (0.90), residues: 40 loop : -1.03 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 273 HIS 0.006 0.001 HIS A 108 PHE 0.014 0.001 PHE B 287 TYR 0.009 0.001 TYR A 396 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.550 Fit side-chains REVERT: B 25 GLU cc_start: 0.9114 (tp30) cc_final: 0.8907 (tp30) REVERT: B 355 ASN cc_start: 0.8151 (t0) cc_final: 0.7873 (t0) REVERT: B 362 ASN cc_start: 0.8149 (t0) cc_final: 0.7885 (t0) REVERT: A 59 ARG cc_start: 0.8518 (ttm170) cc_final: 0.7954 (tpm170) outliers start: 33 outliers final: 29 residues processed: 186 average time/residue: 0.1570 time to fit residues: 37.8415 Evaluate side-chains 200 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 0.0030 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 0.0170 overall best weight: 0.4830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN A 362 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5026 Z= 0.199 Angle : 0.588 6.454 6873 Z= 0.298 Chirality : 0.039 0.138 877 Planarity : 0.003 0.031 814 Dihedral : 8.219 80.600 1019 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.04 % Allowed : 31.59 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.34), residues: 620 helix: 2.15 (0.26), residues: 378 sheet: -0.46 (0.89), residues: 40 loop : -1.08 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 273 HIS 0.005 0.001 HIS A 108 PHE 0.007 0.001 PHE A 42 TYR 0.008 0.001 TYR A 396 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.562 Fit side-chains REVERT: B 25 GLU cc_start: 0.9101 (tp30) cc_final: 0.8830 (tp30) REVERT: B 355 ASN cc_start: 0.8118 (t0) cc_final: 0.7840 (t0) REVERT: B 404 LYS cc_start: 0.8841 (tptp) cc_final: 0.8291 (tptt) REVERT: A 59 ARG cc_start: 0.8510 (ttm170) cc_final: 0.7958 (tpm170) outliers start: 30 outliers final: 27 residues processed: 186 average time/residue: 0.1718 time to fit residues: 40.6918 Evaluate side-chains 199 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 362 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5026 Z= 0.225 Angle : 0.611 6.706 6873 Z= 0.313 Chirality : 0.040 0.137 877 Planarity : 0.003 0.033 814 Dihedral : 8.242 80.550 1019 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.24 % Allowed : 32.39 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.35), residues: 620 helix: 2.11 (0.26), residues: 378 sheet: -0.61 (0.87), residues: 40 loop : -1.09 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 273 HIS 0.006 0.001 HIS A 108 PHE 0.015 0.001 PHE B 287 TYR 0.007 0.001 TYR A 396 ARG 0.001 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.787 Fit side-chains REVERT: B 37 MET cc_start: 0.8710 (tpt) cc_final: 0.8487 (tpt) REVERT: B 355 ASN cc_start: 0.8140 (t0) cc_final: 0.7859 (t0) REVERT: B 404 LYS cc_start: 0.8847 (tptp) cc_final: 0.8293 (tptt) REVERT: A 59 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8003 (tpm170) REVERT: A 324 MET cc_start: 0.8932 (tpp) cc_final: 0.8618 (ttt) outliers start: 31 outliers final: 30 residues processed: 189 average time/residue: 0.1778 time to fit residues: 42.6982 Evaluate side-chains 202 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.0470 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN A 362 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5026 Z= 0.224 Angle : 0.633 6.978 6873 Z= 0.324 Chirality : 0.040 0.147 877 Planarity : 0.003 0.035 814 Dihedral : 8.223 80.585 1019 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.24 % Allowed : 33.40 % Favored : 60.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.34), residues: 620 helix: 2.06 (0.26), residues: 378 sheet: -0.66 (0.87), residues: 40 loop : -1.12 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 273 HIS 0.005 0.001 HIS A 108 PHE 0.022 0.001 PHE A 19 TYR 0.006 0.001 TYR A 330 ARG 0.003 0.000 ARG B 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.612 Fit side-chains REVERT: B 30 ARG cc_start: 0.7982 (tpt90) cc_final: 0.7728 (tpt90) REVERT: B 37 MET cc_start: 0.8661 (tpt) cc_final: 0.8429 (tpt) REVERT: B 355 ASN cc_start: 0.8135 (t0) cc_final: 0.7857 (t0) REVERT: B 404 LYS cc_start: 0.8845 (tptp) cc_final: 0.8293 (tptt) REVERT: A 59 ARG cc_start: 0.8519 (ttm170) cc_final: 0.7977 (tpm170) REVERT: A 324 MET cc_start: 0.8916 (tpp) cc_final: 0.8612 (ttt) outliers start: 31 outliers final: 29 residues processed: 182 average time/residue: 0.1799 time to fit residues: 42.1854 Evaluate side-chains 197 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.0570 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN A 362 ASN ** A 408 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 = 0.4304 r_free = 0.4304 target = 0.179042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129987 restraints weight = 7262.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.135132 restraints weight = 4112.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.138380 restraints weight = 2985.012| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5026 Z= 0.216 Angle : 0.641 6.973 6873 Z= 0.326 Chirality : 0.040 0.209 877 Planarity : 0.003 0.034 814 Dihedral : 8.172 80.251 1019 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.44 % Allowed : 33.20 % Favored : 60.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.34), residues: 620 helix: 2.06 (0.26), residues: 378 sheet: -0.69 (0.87), residues: 40 loop : -1.12 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 273 HIS 0.005 0.001 HIS A 108 PHE 0.016 0.001 PHE B 287 TYR 0.008 0.001 TYR A 396 ARG 0.003 0.000 ARG B 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1599.81 seconds wall clock time: 29 minutes 56.44 seconds (1796.44 seconds total)