Starting phenix.real_space_refine on Thu Mar 6 05:00:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmf_38475/03_2025/8xmf_38475.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmf_38475/03_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_38475/03_2025/8xmf_38475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmf_38475/03_2025/8xmf_38475.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmf_38475/03_2025/8xmf_38475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmf_38475/03_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-5624/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: 3.87, 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: 1.39 Conformation dependent library (CDL) restraints added in 994.5 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: 0.49 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: 1.38 Time building geometry restraints manager: 1.64 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.540 Find NCS groups from input model: 0.240 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- 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 : 0.535 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: 0.1539 time to fit residues: 38.5182 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 : 0.492 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4299 r_free = 0.4299 target = 0.177284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127858 restraints weight = 7232.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.133065 restraints weight = 4029.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.136392 restraints weight = 2890.967| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5026 Z= 0.263 Angle : 0.674 8.211 6873 Z= 0.326 Chirality : 0.044 0.376 877 Planarity : 0.004 0.046 814 Dihedral : 13.435 102.814 1019 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.63 % Allowed : 19.72 % Favored : 75.65 % 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: 2.07 (0.26), residues: 378 sheet: 0.00 (0.89), residues: 42 loop : -1.02 (0.45), 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 43 PHE 0.016 0.001 PHE A 19 TYR 0.014 0.001 TYR A 270 ARG 0.003 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 210 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.571 Fit side-chains REVERT: B 246 ARG cc_start: 0.6729 (mmm160) cc_final: 0.6403 (mmm160) REVERT: B 320 LEU cc_start: 0.9172 (tp) cc_final: 0.8896 (tp) REVERT: B 355 ASN cc_start: 0.8179 (t0) cc_final: 0.7925 (t0) REVERT: A 59 ARG cc_start: 0.8507 (ttm170) cc_final: 0.7945 (tpm170) REVERT: A 99 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8242 (tp30) REVERT: A 294 PHE cc_start: 0.8106 (t80) cc_final: 0.7625 (t80) REVERT: A 380 SER cc_start: 0.9292 (t) cc_final: 0.9002 (t) outliers start: 23 outliers final: 20 residues processed: 191 average time/residue: 0.1646 time to fit residues: 39.9300 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 : 0.533 ------------------------------------------------------------------------------- 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 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 332 THR 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: 0.5980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 127 ASN ** 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 = 0.180192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.131080 restraints weight = 7305.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136346 restraints weight = 4082.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.139874 restraints weight = 2935.892| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2126 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= 0.187 Angle : 0.611 8.639 6873 Z= 0.299 Chirality : 0.040 0.244 877 Planarity : 0.004 0.032 814 Dihedral : 10.349 94.218 1019 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.82 % Allowed : 25.55 % Favored : 70.62 % 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: 1.48 (0.35), residues: 620 helix: 2.12 (0.26), residues: 378 sheet: -0.20 (0.90), residues: 42 loop : -1.01 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 273 HIS 0.008 0.001 HIS B 413 PHE 0.018 0.001 PHE A 287 TYR 0.007 0.001 TYR B 396 ARG 0.002 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 205 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.553 Fit side-chains REVERT: B 246 ARG cc_start: 0.6738 (mmm160) cc_final: 0.6447 (mmm160) REVERT: B 320 LEU cc_start: 0.9058 (tp) cc_final: 0.8783 (tp) REVERT: B 355 ASN cc_start: 0.8156 (t0) cc_final: 0.7829 (t0) REVERT: A 59 ARG cc_start: 0.8489 (ttm170) cc_final: 0.7977 (tpm170) REVERT: A 99 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8213 (tp30) REVERT: A 103 ARG cc_start: 0.8993 (ttm170) cc_final: 0.8764 (ttm-80) REVERT: A 294 PHE cc_start: 0.8029 (t80) cc_final: 0.7290 (t80) outliers start: 19 outliers final: 17 residues processed: 188 average time/residue: 0.1698 time to fit residues: 40.7821 Evaluate side-chains 189 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 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 415 THR Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 37 MET 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: 1.9990 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.179300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129107 restraints weight = 7394.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.134270 restraints weight = 4185.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.137607 restraints weight = 3038.927| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2431 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= 0.215 Angle : 0.618 8.962 6873 Z= 0.308 Chirality : 0.039 0.159 877 Planarity : 0.003 0.033 814 Dihedral : 9.307 90.187 1019 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.23 % Allowed : 26.76 % 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: 1.48 (0.35), residues: 620 helix: 2.14 (0.27), residues: 378 sheet: -0.30 (0.90), residues: 42 loop : -1.04 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 197 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.521 Fit side-chains REVERT: B 246 ARG cc_start: 0.6767 (mmm160) cc_final: 0.6501 (mmm160) REVERT: B 320 LEU cc_start: 0.9062 (tp) cc_final: 0.8789 (tp) REVERT: B 355 ASN cc_start: 0.8112 (t0) cc_final: 0.7773 (t0) REVERT: A 59 ARG cc_start: 0.8507 (ttm170) cc_final: 0.7966 (tpm170) REVERT: A 99 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8258 (tp30) REVERT: A 277 SER cc_start: 0.8878 (p) cc_final: 0.8617 (t) REVERT: A 294 PHE cc_start: 0.8048 (t80) cc_final: 0.7275 (t80) outliers start: 26 outliers final: 23 residues processed: 180 average time/residue: 0.1551 time to fit residues: 35.7483 Evaluate side-chains 188 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 328 LEU 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 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: 0.8980 chunk 48 optimal weight: 0.0980 chunk 31 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 0.0000 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.180885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.131166 restraints weight = 7473.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.136654 restraints weight = 4140.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140132 restraints weight = 2958.848| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2680 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= 0.179 Angle : 0.583 5.687 6873 Z= 0.294 Chirality : 0.039 0.211 877 Planarity : 0.003 0.032 814 Dihedral : 8.626 86.195 1019 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.03 % Allowed : 28.57 % Favored : 66.40 % 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: 1.54 (0.35), residues: 620 helix: 2.14 (0.27), residues: 378 sheet: 0.09 (0.88), residues: 40 loop : -1.00 (0.44), residues: 202 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 0.018 0.001 PHE A 287 TYR 0.013 0.001 TYR A 396 ARG 0.001 0.000 ARG B 76 *********************** 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 200 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.504 Fit side-chains REVERT: B 30 ARG cc_start: 0.7716 (tpt170) cc_final: 0.7497 (tpt90) REVERT: B 246 ARG cc_start: 0.6757 (mmm160) cc_final: 0.6494 (mmm160) REVERT: B 320 LEU cc_start: 0.9018 (tp) cc_final: 0.8744 (tp) REVERT: B 355 ASN cc_start: 0.8039 (t0) cc_final: 0.7824 (t0) REVERT: B 362 ASN cc_start: 0.8096 (t0) cc_final: 0.7852 (t0) REVERT: A 59 ARG cc_start: 0.8500 (ttm170) cc_final: 0.7958 (tpm170) REVERT: A 99 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8254 (tp30) outliers start: 25 outliers final: 23 residues processed: 182 average time/residue: 0.1509 time to fit residues: 35.2763 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 : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 317 ASP Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 366 VAL 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: 0.6980 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 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 = 0.4291 r_free = 0.4291 target = 0.177788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127120 restraints weight = 7351.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.132232 restraints weight = 4208.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135510 restraints weight = 3071.739| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2846 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= 0.246 Angle : 0.607 5.810 6873 Z= 0.308 Chirality : 0.040 0.174 877 Planarity : 0.003 0.036 814 Dihedral : 8.585 86.551 1019 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.04 % Allowed : 29.18 % 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: 1.44 (0.34), residues: 620 helix: 2.04 (0.26), residues: 378 sheet: -0.16 (0.90), residues: 40 loop : -0.93 (0.44), 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 0.019 0.001 PHE A 19 TYR 0.012 0.001 TYR A 396 ARG 0.002 0.000 ARG A 30 *********************** 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 208 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.551 Fit side-chains REVERT: B 246 ARG cc_start: 0.6774 (mmm160) cc_final: 0.6519 (mmm160) REVERT: B 320 LEU cc_start: 0.9076 (tp) cc_final: 0.8789 (tp) REVERT: B 355 ASN cc_start: 0.8104 (t0) cc_final: 0.7826 (t0) REVERT: B 362 ASN cc_start: 0.8172 (t0) cc_final: 0.7933 (t0) REVERT: A 59 ARG cc_start: 0.8529 (ttm170) cc_final: 0.7963 (tpm170) outliers start: 30 outliers final: 24 residues processed: 185 average time/residue: 0.1832 time to fit residues: 43.6850 Evaluate side-chains 194 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 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 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 366 VAL 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: 0.1980 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** 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 = 0.178795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.129299 restraints weight = 7244.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.134403 restraints weight = 4084.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.137736 restraints weight = 2972.435| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5026 Z= 0.201 Angle : 0.609 6.730 6873 Z= 0.308 Chirality : 0.040 0.177 877 Planarity : 0.003 0.034 814 Dihedral : 8.325 82.602 1019 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.63 % Allowed : 30.38 % Favored : 63.98 % 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: 1.50 (0.34), residues: 620 helix: 2.13 (0.27), residues: 378 sheet: -0.09 (0.89), residues: 40 loop : -1.03 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 273 HIS 0.003 0.001 HIS B 413 PHE 0.012 0.001 PHE A 287 TYR 0.011 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 199 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.694 Fit side-chains REVERT: B 102 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8163 (tm-30) REVERT: B 108 HIS cc_start: 0.7304 (m170) cc_final: 0.7000 (m170) REVERT: B 246 ARG cc_start: 0.6755 (mmm160) cc_final: 0.6508 (mmm160) REVERT: B 320 LEU cc_start: 0.9029 (tp) cc_final: 0.8735 (tp) REVERT: B 355 ASN cc_start: 0.8110 (t0) cc_final: 0.7825 (t0) REVERT: B 404 LYS cc_start: 0.8871 (tptp) cc_final: 0.8314 (tptt) REVERT: A 59 ARG cc_start: 0.8522 (ttm170) cc_final: 0.7963 (tpm170) outliers start: 28 outliers final: 24 residues processed: 179 average time/residue: 0.1919 time to fit residues: 43.9923 Evaluate side-chains 191 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 117 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 415 THR 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 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 366 VAL 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: 0.9990 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 108 HIS 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 = 0.178965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129651 restraints weight = 7370.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134864 restraints weight = 4116.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.138274 restraints weight = 2968.743| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3119 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= 0.207 Angle : 0.617 6.814 6873 Z= 0.312 Chirality : 0.040 0.156 877 Planarity : 0.003 0.033 814 Dihedral : 8.240 81.163 1019 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.24 % Allowed : 30.38 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.34), residues: 620 helix: 2.06 (0.26), residues: 378 sheet: -0.17 (0.89), residues: 40 loop : -1.06 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 273 HIS 0.003 0.001 HIS A 413 PHE 0.025 0.001 PHE B 287 TYR 0.009 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 203 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.547 Fit side-chains REVERT: B 25 GLU cc_start: 0.8730 (tp30) cc_final: 0.8478 (tp30) REVERT: B 30 ARG cc_start: 0.8406 (tpt90) cc_final: 0.8119 (tpt90) REVERT: B 246 ARG cc_start: 0.6701 (mmm160) cc_final: 0.6467 (mmm160) REVERT: B 320 LEU cc_start: 0.9030 (tp) cc_final: 0.8730 (tp) REVERT: B 355 ASN cc_start: 0.8110 (t0) cc_final: 0.7826 (t0) REVERT: B 404 LYS cc_start: 0.8854 (tptp) cc_final: 0.8294 (tptt) REVERT: A 59 ARG cc_start: 0.8531 (ttm170) cc_final: 0.7965 (tpm170) REVERT: A 372 LEU cc_start: 0.9190 (tt) cc_final: 0.8883 (tp) outliers start: 31 outliers final: 28 residues processed: 179 average time/residue: 0.2126 time to fit residues: 50.3929 Evaluate side-chains 191 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 117 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 415 THR 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 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 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: 0.8980 chunk 61 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 13 optimal weight: 7.9990 chunk 28 optimal weight: 0.2980 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.180232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130739 restraints weight = 7162.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136028 restraints weight = 4049.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.139442 restraints weight = 2932.510| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5026 Z= 0.200 Angle : 0.612 7.102 6873 Z= 0.312 Chirality : 0.040 0.178 877 Planarity : 0.003 0.033 814 Dihedral : 8.161 80.639 1019 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.43 % Allowed : 31.59 % Favored : 62.98 % 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 (0.34), residues: 620 helix: 2.13 (0.26), residues: 376 sheet: -0.21 (0.88), residues: 40 loop : -1.13 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 273 HIS 0.004 0.001 HIS B 108 PHE 0.023 0.001 PHE B 287 TYR 0.014 0.001 TYR A 396 ARG 0.004 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 193 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.488 Fit side-chains REVERT: B 25 GLU cc_start: 0.8735 (tp30) cc_final: 0.8476 (tp30) REVERT: B 37 MET cc_start: 0.8353 (tpt) cc_final: 0.7632 (tpt) REVERT: B 246 ARG cc_start: 0.6690 (mmm160) cc_final: 0.6460 (mmm160) REVERT: B 320 LEU cc_start: 0.9013 (tp) cc_final: 0.8720 (tp) REVERT: B 355 ASN cc_start: 0.8089 (t0) cc_final: 0.7813 (t0) REVERT: B 404 LYS cc_start: 0.8837 (tptp) cc_final: 0.8284 (tptt) REVERT: A 59 ARG cc_start: 0.8532 (ttm170) cc_final: 0.7978 (tpm170) REVERT: A 324 MET cc_start: 0.8933 (tpp) cc_final: 0.8664 (ttt) outliers start: 27 outliers final: 24 residues processed: 174 average time/residue: 0.1582 time to fit residues: 35.4772 Evaluate side-chains 188 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 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 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 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: 5.9990 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 49 optimal weight: 0.0470 chunk 33 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.180885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.132111 restraints weight = 7317.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.137260 restraints weight = 4174.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.140694 restraints weight = 3024.107| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3310 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= 0.192 Angle : 0.612 7.232 6873 Z= 0.311 Chirality : 0.040 0.175 877 Planarity : 0.003 0.033 814 Dihedral : 8.055 79.627 1019 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: 1.40 (0.34), residues: 620 helix: 2.14 (0.26), residues: 374 sheet: -0.30 (0.87), residues: 40 loop : -1.14 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 312 HIS 0.009 0.001 HIS A 108 PHE 0.022 0.001 PHE B 287 TYR 0.015 0.001 TYR A 396 ARG 0.006 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 199 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: B 30 ARG cc_start: 0.8337 (tpt90) cc_final: 0.8044 (tpt90) REVERT: B 68 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8608 (tp40) REVERT: B 246 ARG cc_start: 0.6712 (mmm160) cc_final: 0.6503 (mmm160) REVERT: B 355 ASN cc_start: 0.8083 (t0) cc_final: 0.7813 (t0) REVERT: B 404 LYS cc_start: 0.8806 (tptp) cc_final: 0.8262 (tptt) REVERT: A 59 ARG cc_start: 0.8505 (ttm170) cc_final: 0.7957 (tpm170) REVERT: A 324 MET cc_start: 0.8882 (tpp) cc_final: 0.8626 (ttt) REVERT: A 372 LEU cc_start: 0.9114 (tt) cc_final: 0.8831 (tp) outliers start: 27 outliers final: 23 residues processed: 181 average time/residue: 0.1878 time to fit residues: 43.7281 Evaluate side-chains 191 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 117 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 415 THR 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 329 LEU 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 0 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.0070 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 0.0050 chunk 45 optimal weight: 0.5980 overall best weight: 0.3190 ------------------------------------------------------------------------------- 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 108 HIS A 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.176260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130347 restraints weight = 7009.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135258 restraints weight = 4001.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138433 restraints weight = 2868.932| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5026 Z= 0.182 Angle : 0.610 7.265 6873 Z= 0.308 Chirality : 0.039 0.142 877 Planarity : 0.003 0.033 814 Dihedral : 7.974 78.920 1019 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.03 % Allowed : 34.00 % Favored : 60.97 % 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 (0.34), residues: 620 helix: 2.16 (0.26), residues: 374 sheet: -0.22 (0.87), residues: 40 loop : -1.17 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 273 HIS 0.006 0.001 HIS A 108 PHE 0.021 0.001 PHE B 287 TYR 0.013 0.001 TYR A 396 ARG 0.006 0.000 ARG B 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2321.86 seconds wall clock time: 42 minutes 23.12 seconds (2543.12 seconds total)