Starting phenix.real_space_refine on Tue Jan 14 01:32:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmf_38475/01_2025/8xmf_38475.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmf_38475/01_2025/8xmf_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/cci-nas-00/data/ceres_data/8xmf_38475/01_2025/8xmf_38475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmf_38475/01_2025/8xmf_38475.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmf_38475/01_2025/8xmf_38475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmf_38475/01_2025/8xmf_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-5571/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: 3.90, per 1000 atoms: 0.79 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: 1.28 Conformation dependent library (CDL) restraints added in 762.9 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: 0.42 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: 1.32 Time building geometry restraints manager: 1.46 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: 0.000 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 1.330 Process input model: 15.480 Find NCS groups from input model: 0.220 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- 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 : 0.585 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: 0.1696 time to fit residues: 42.7883 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 : 0.532 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.127676 restraints weight = 7246.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.132889 restraints weight = 4022.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.136239 restraints weight = 2884.896| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.523 Fit side-chains REVERT: B 246 ARG cc_start: 0.6752 (mmm160) cc_final: 0.6432 (mmm160) REVERT: B 320 LEU cc_start: 0.9161 (tp) cc_final: 0.8896 (tp) REVERT: B 355 ASN cc_start: 0.8207 (t0) cc_final: 0.7935 (t0) REVERT: A 59 ARG cc_start: 0.8513 (ttm170) cc_final: 0.7936 (tpm170) REVERT: A 99 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8213 (tp30) REVERT: A 294 PHE cc_start: 0.8133 (t80) cc_final: 0.7640 (t80) REVERT: A 380 SER cc_start: 0.9285 (t) cc_final: 0.8994 (t) outliers start: 24 outliers final: 20 residues processed: 194 average time/residue: 0.1619 time to fit residues: 39.9243 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 : 0.558 ------------------------------------------------------------------------------- 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 53 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.0020 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.179920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130422 restraints weight = 7216.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.135728 restraints weight = 4050.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.139185 restraints weight = 2928.764| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5026 Z= 0.193 Angle : 0.609 7.014 6873 Z= 0.299 Chirality : 0.040 0.221 877 Planarity : 0.004 0.033 814 Dihedral : 9.824 93.164 1019 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.23 % Allowed : 25.55 % Favored : 70.22 % 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: 1.44 (0.35), residues: 620 helix: 2.11 (0.26), residues: 378 sheet: -0.38 (0.88), residues: 42 loop : -1.03 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 273 HIS 0.009 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 209 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.534 Fit side-chains REVERT: B 246 ARG cc_start: 0.6758 (mmm160) cc_final: 0.6468 (mmm160) REVERT: B 320 LEU cc_start: 0.9055 (tp) cc_final: 0.8779 (tp) REVERT: B 355 ASN cc_start: 0.8182 (t0) cc_final: 0.7847 (t0) REVERT: A 59 ARG cc_start: 0.8489 (ttm170) cc_final: 0.7985 (tpm170) REVERT: A 99 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8193 (tp30) REVERT: A 103 ARG cc_start: 0.8977 (ttm170) cc_final: 0.8743 (ttm-80) REVERT: A 294 PHE cc_start: 0.8036 (t80) cc_final: 0.7298 (t80) outliers start: 21 outliers final: 20 residues processed: 190 average time/residue: 0.1681 time to fit residues: 40.5735 Evaluate side-chains 195 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER 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 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 37 MET 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 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 284 ASN ** A 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 = 0.4312 r_free = 0.4312 target = 0.179343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129129 restraints weight = 7427.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.134333 restraints weight = 4228.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.137689 restraints weight = 3070.691| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2533 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= 0.208 Angle : 0.610 7.665 6873 Z= 0.306 Chirality : 0.039 0.136 877 Planarity : 0.003 0.033 814 Dihedral : 9.094 88.749 1019 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.03 % Allowed : 27.57 % Favored : 67.40 % 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: 1.42 (0.35), residues: 620 helix: 2.12 (0.27), residues: 378 sheet: -0.52 (0.88), residues: 42 loop : -1.07 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 273 HIS 0.005 0.001 HIS B 413 PHE 0.017 0.001 PHE A 19 TYR 0.013 0.001 TYR A 396 ARG 0.002 0.000 ARG A 103 *********************** 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 198 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.547 Fit side-chains REVERT: B 246 ARG cc_start: 0.6799 (mmm160) cc_final: 0.6517 (mmm160) REVERT: B 320 LEU cc_start: 0.9055 (tp) cc_final: 0.8783 (tp) REVERT: B 355 ASN cc_start: 0.8119 (t0) cc_final: 0.7776 (t0) REVERT: A 59 ARG cc_start: 0.8516 (ttm170) cc_final: 0.7981 (tpm170) REVERT: A 99 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8237 (tp30) REVERT: A 103 ARG cc_start: 0.9001 (ttm170) cc_final: 0.8731 (ttm110) REVERT: A 277 SER cc_start: 0.8904 (p) cc_final: 0.8691 (t) outliers start: 25 outliers final: 20 residues processed: 180 average time/residue: 0.1578 time to fit residues: 36.5353 Evaluate side-chains 188 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER 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 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 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 317 ASP Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 329 LEU 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 59 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS A 284 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 = 0.4321 r_free = 0.4321 target = 0.179519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129425 restraints weight = 7328.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134668 restraints weight = 4154.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.138054 restraints weight = 3014.410| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5026 Z= 0.197 Angle : 0.593 5.625 6873 Z= 0.300 Chirality : 0.040 0.199 877 Planarity : 0.003 0.033 814 Dihedral : 8.637 85.898 1019 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.23 % Allowed : 28.77 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.35), residues: 620 helix: 2.14 (0.26), residues: 378 sheet: -0.55 (0.88), residues: 42 loop : -1.04 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 273 HIS 0.004 0.001 HIS B 413 PHE 0.019 0.001 PHE A 287 TYR 0.013 0.001 TYR A 396 ARG 0.002 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 198 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.487 Fit side-chains REVERT: B 30 ARG cc_start: 0.7674 (tpt170) cc_final: 0.7447 (tpt90) REVERT: B 246 ARG cc_start: 0.6768 (mmm160) cc_final: 0.6503 (mmm160) REVERT: B 320 LEU cc_start: 0.9042 (tp) cc_final: 0.8765 (tp) REVERT: B 355 ASN cc_start: 0.8048 (t0) cc_final: 0.7773 (t0) REVERT: B 362 ASN cc_start: 0.8111 (t0) cc_final: 0.7871 (t0) REVERT: A 59 ARG cc_start: 0.8511 (ttm170) cc_final: 0.7951 (tpm170) REVERT: A 99 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8223 (tp30) REVERT: A 103 ARG cc_start: 0.8998 (ttm170) cc_final: 0.8769 (ttm110) outliers start: 26 outliers final: 23 residues processed: 178 average time/residue: 0.1574 time to fit residues: 36.0822 Evaluate side-chains 186 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER 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 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 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 272 SER 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 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.179153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.129032 restraints weight = 7344.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.134236 restraints weight = 4151.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.137589 restraints weight = 3014.116| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5026 Z= 0.205 Angle : 0.587 5.756 6873 Z= 0.297 Chirality : 0.040 0.172 877 Planarity : 0.003 0.034 814 Dihedral : 8.375 83.087 1019 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 6.24 % Allowed : 27.97 % Favored : 65.79 % 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: 1.38 (0.35), residues: 620 helix: 2.08 (0.26), residues: 378 sheet: -0.60 (0.88), residues: 42 loop : -1.04 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 273 HIS 0.003 0.001 HIS A 413 PHE 0.018 0.001 PHE A 19 TYR 0.012 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 198 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.525 Fit side-chains REVERT: B 246 ARG cc_start: 0.6780 (mmm160) cc_final: 0.6523 (mmm160) REVERT: B 320 LEU cc_start: 0.9043 (tp) cc_final: 0.8757 (tp) REVERT: B 355 ASN cc_start: 0.8066 (t0) cc_final: 0.7815 (t0) REVERT: A 59 ARG cc_start: 0.8528 (ttm170) cc_final: 0.7976 (tpm170) REVERT: A 103 ARG cc_start: 0.8980 (ttm170) cc_final: 0.8762 (ttm110) outliers start: 31 outliers final: 27 residues processed: 174 average time/residue: 0.1659 time to fit residues: 36.9871 Evaluate side-chains 189 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 264 VAL Chi-restraints excluded: chain B residue 265 ASN 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 37 MET Chi-restraints excluded: chain A residue 71 THR 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 317 ASP Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 THR 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 33 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 108 HIS ** 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 = 0.4305 r_free = 0.4305 target = 0.178591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129090 restraints weight = 7258.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134260 restraints weight = 4106.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.137546 restraints weight = 2972.400| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5026 Z= 0.207 Angle : 0.604 6.856 6873 Z= 0.306 Chirality : 0.040 0.167 877 Planarity : 0.003 0.033 814 Dihedral : 8.300 82.090 1019 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.24 % Allowed : 28.97 % 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: 1.43 (0.34), residues: 620 helix: 2.13 (0.26), residues: 378 sheet: -0.29 (0.89), residues: 40 loop : -1.13 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 273 HIS 0.003 0.001 HIS A 413 PHE 0.014 0.001 PHE A 287 TYR 0.012 0.001 TYR A 396 ARG 0.002 0.000 ARG A 76 *********************** 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 202 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.543 Fit side-chains REVERT: B 99 GLU cc_start: 0.8658 (tp30) cc_final: 0.8452 (tp30) REVERT: B 102 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 108 HIS cc_start: 0.7294 (m170) cc_final: 0.6992 (m170) REVERT: B 246 ARG cc_start: 0.6786 (mmm160) cc_final: 0.6527 (mmm160) REVERT: B 320 LEU cc_start: 0.9039 (tp) cc_final: 0.8748 (tp) REVERT: B 355 ASN cc_start: 0.8105 (t0) cc_final: 0.7823 (t0) REVERT: B 404 LYS cc_start: 0.8852 (tptp) cc_final: 0.8292 (tptt) REVERT: A 59 ARG cc_start: 0.8529 (ttm170) cc_final: 0.7968 (tpm170) REVERT: A 103 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8787 (ttm110) outliers start: 31 outliers final: 27 residues processed: 179 average time/residue: 0.1649 time to fit residues: 37.9088 Evaluate side-chains 188 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 39 SER 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 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 37 MET Chi-restraints excluded: chain A residue 71 THR 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 317 ASP Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 47 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 108 HIS ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.176884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126694 restraints weight = 7410.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.131690 restraints weight = 4280.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134866 restraints weight = 3121.203| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5026 Z= 0.271 Angle : 0.634 7.125 6873 Z= 0.323 Chirality : 0.041 0.204 877 Planarity : 0.003 0.035 814 Dihedral : 8.446 84.054 1019 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 7.24 % Allowed : 28.57 % 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: 1.29 (0.34), residues: 620 helix: 1.99 (0.26), residues: 378 sheet: -0.48 (0.89), residues: 40 loop : -1.08 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 273 HIS 0.003 0.001 HIS A 413 PHE 0.024 0.001 PHE B 287 TYR 0.015 0.001 TYR A 396 ARG 0.004 0.000 ARG B 30 *********************** 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 206 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.495 Fit side-chains REVERT: B 30 ARG cc_start: 0.8363 (tpt90) cc_final: 0.8110 (tpt90) REVERT: B 108 HIS cc_start: 0.7322 (m170) cc_final: 0.7087 (m170) REVERT: B 246 ARG cc_start: 0.6748 (mmm160) cc_final: 0.6507 (mmm160) REVERT: B 320 LEU cc_start: 0.9079 (tp) cc_final: 0.8780 (tp) REVERT: B 355 ASN cc_start: 0.8108 (t0) cc_final: 0.7826 (t0) REVERT: A 59 ARG cc_start: 0.8537 (ttm170) cc_final: 0.7939 (tpm170) outliers start: 36 outliers final: 34 residues processed: 178 average time/residue: 0.1605 time to fit residues: 36.5894 Evaluate side-chains 202 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 39 SER 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 A residue 25 GLU Chi-restraints excluded: chain A residue 37 MET 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 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 317 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN A 85 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 = 0.4301 r_free = 0.4301 target = 0.178187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.128557 restraints weight = 7257.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.133723 restraints weight = 4121.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136938 restraints weight = 2985.733| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5026 Z= 0.213 Angle : 0.620 7.113 6873 Z= 0.318 Chirality : 0.040 0.144 877 Planarity : 0.003 0.032 814 Dihedral : 8.288 81.814 1019 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.44 % Allowed : 30.38 % 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: 1.35 (0.34), residues: 620 helix: 2.10 (0.26), residues: 376 sheet: -0.38 (0.89), residues: 40 loop : -1.20 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 273 HIS 0.003 0.001 HIS B 413 PHE 0.022 0.001 PHE B 287 TYR 0.016 0.001 TYR A 396 ARG 0.003 0.000 ARG B 30 *********************** 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 200 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.656 Fit side-chains REVERT: B 25 GLU cc_start: 0.8729 (tp30) cc_final: 0.8461 (tp30) REVERT: B 102 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 108 HIS cc_start: 0.7273 (m170) cc_final: 0.7040 (m170) REVERT: B 246 ARG cc_start: 0.6718 (mmm160) cc_final: 0.6486 (mmm160) REVERT: B 355 ASN cc_start: 0.8072 (t0) cc_final: 0.7786 (t0) REVERT: B 404 LYS cc_start: 0.8860 (tptp) cc_final: 0.8294 (tptt) REVERT: A 59 ARG cc_start: 0.8532 (ttm170) cc_final: 0.7957 (tpm170) REVERT: A 324 MET cc_start: 0.8942 (tpp) cc_final: 0.8666 (ttt) outliers start: 32 outliers final: 29 residues processed: 177 average time/residue: 0.1674 time to fit residues: 37.8767 Evaluate side-chains 193 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 44 MET 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 A residue 25 GLU Chi-restraints excluded: chain A residue 37 MET 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 366 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.0470 chunk 53 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 108 HIS A 345 GLN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.180595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.131668 restraints weight = 7339.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.136880 restraints weight = 4174.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.140256 restraints weight = 3017.847| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5026 Z= 0.190 Angle : 0.603 7.203 6873 Z= 0.311 Chirality : 0.039 0.134 877 Planarity : 0.003 0.032 814 Dihedral : 8.059 79.185 1019 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % 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: 1.37 (0.34), residues: 620 helix: 2.16 (0.26), residues: 376 sheet: -0.46 (0.88), residues: 40 loop : -1.25 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 273 HIS 0.003 0.001 HIS B 108 PHE 0.022 0.001 PHE B 287 TYR 0.013 0.001 TYR A 396 ARG 0.004 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 200 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: B 30 ARG cc_start: 0.8330 (tpt90) cc_final: 0.8048 (tpt90) REVERT: B 246 ARG cc_start: 0.6669 (mmm160) cc_final: 0.6450 (mmm160) REVERT: B 355 ASN cc_start: 0.8079 (t0) cc_final: 0.7812 (t0) REVERT: B 404 LYS cc_start: 0.8782 (tptp) cc_final: 0.8248 (tptt) REVERT: A 59 ARG cc_start: 0.8509 (ttm170) cc_final: 0.7966 (tpm170) REVERT: A 324 MET cc_start: 0.8876 (tpp) cc_final: 0.8629 (ttt) outliers start: 30 outliers final: 26 residues processed: 181 average time/residue: 0.1692 time to fit residues: 39.4816 Evaluate side-chains 195 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 39 SER 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 389 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 37 MET 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 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.0060 chunk 37 optimal weight: 0.0470 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.181156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131735 restraints weight = 7455.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.137067 restraints weight = 4174.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.140587 restraints weight = 2998.692| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5026 Z= 0.203 Angle : 0.621 6.855 6873 Z= 0.317 Chirality : 0.040 0.136 877 Planarity : 0.003 0.033 814 Dihedral : 8.069 79.643 1019 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.43 % Allowed : 33.00 % Favored : 61.57 % 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: 2.14 (0.26), residues: 374 sheet: -0.57 (0.87), residues: 40 loop : -1.26 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 273 HIS 0.004 0.001 HIS B 108 PHE 0.021 0.001 PHE B 287 TYR 0.018 0.001 TYR A 396 ARG 0.004 0.000 ARG B 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1981.23 seconds wall clock time: 36 minutes 43.42 seconds (2203.42 seconds total)