Starting phenix.real_space_refine on Mon Aug 5 01:39:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/08_2024/8uvt_42628.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/08_2024/8uvt_42628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/08_2024/8uvt_42628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/08_2024/8uvt_42628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/08_2024/8uvt_42628.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/08_2024/8uvt_42628.cif" } resolution = 2.9 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= 0.003 sd= 0.114 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: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 7892 2.51 5 N 2024 2.21 5 O 2056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12104 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3026 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 13, 'TRANS': 372} Chain breaks: 2 Chain: "B" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3026 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 13, 'TRANS': 372} Chain breaks: 2 Chain: "C" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3026 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 13, 'TRANS': 372} Chain breaks: 2 Chain: "D" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3026 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 13, 'TRANS': 372} Chain breaks: 2 Time building chain proxies: 7.17, per 1000 atoms: 0.59 Number of scatterers: 12104 At special positions: 0 Unit cell: (110.004, 110.004, 91.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 2056 8.00 N 2024 7.00 C 7892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 83.2% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.874A pdb=" N PHE A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 79 Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'A' and resid 113 through 136 removed outlier: 4.379A pdb=" N ASN A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 175 removed outlier: 3.802A pdb=" N LYS A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 227 removed outlier: 5.030A pdb=" N GLY A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 340 removed outlier: 3.719A pdb=" N GLY A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Proline residue: A 331 - end of helix removed outlier: 3.704A pdb=" N VAL A 340 " --> pdb=" O MET A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 389 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.752A pdb=" N SER A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 423 through 445 removed outlier: 3.529A pdb=" N MET A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.875A pdb=" N PHE B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 79 Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'B' and resid 113 through 136 removed outlier: 4.379A pdb=" N ASN B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 175 removed outlier: 3.802A pdb=" N LYS B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 227 removed outlier: 5.030A pdb=" N GLY B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 340 removed outlier: 3.718A pdb=" N GLY B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix Proline residue: B 331 - end of helix removed outlier: 3.704A pdb=" N VAL B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 389 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.753A pdb=" N SER B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 423 through 445 removed outlier: 3.528A pdb=" N MET B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.875A pdb=" N PHE C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 79 Processing helix chain 'C' and resid 89 through 113 Processing helix chain 'C' and resid 113 through 136 removed outlier: 4.379A pdb=" N ASN C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 175 removed outlier: 3.802A pdb=" N LYS C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 227 removed outlier: 5.030A pdb=" N GLY C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 340 removed outlier: 3.718A pdb=" N GLY C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Proline residue: C 315 - end of helix Proline residue: C 331 - end of helix removed outlier: 3.704A pdb=" N VAL C 340 " --> pdb=" O MET C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 389 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 394 through 410 removed outlier: 3.752A pdb=" N SER C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 423 through 445 removed outlier: 3.529A pdb=" N MET C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 444 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.875A pdb=" N PHE D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 79 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'D' and resid 113 through 136 removed outlier: 4.380A pdb=" N ASN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 175 removed outlier: 3.803A pdb=" N LYS D 175 " --> pdb=" O MET D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 227 removed outlier: 5.029A pdb=" N GLY D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 340 removed outlier: 3.718A pdb=" N GLY D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix Proline residue: D 331 - end of helix removed outlier: 3.704A pdb=" N VAL D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 389 Proline residue: D 368 - end of helix Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.752A pdb=" N SER D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 423 through 445 removed outlier: 3.528A pdb=" N MET D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 444 " --> pdb=" O ILE D 440 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AA3, first strand: chain 'C' and resid 37 through 41 Processing sheet with id=AA4, first strand: chain 'D' and resid 37 through 41 1040 hydrogen bonds defined for protein. 3096 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: 3.24 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3754 1.34 - 1.46: 2268 1.46 - 1.58: 6118 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 12340 Sorted by residual: bond pdb=" C GLU C 367 " pdb=" N PRO C 368 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.96e+00 bond pdb=" C GLU A 367 " pdb=" N PRO A 368 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.92e+00 bond pdb=" C GLU D 367 " pdb=" N PRO D 368 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.88e+00 bond pdb=" C GLU B 367 " pdb=" N PRO B 368 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.80e+00 bond pdb=" C LEU A 122 " pdb=" O LEU A 122 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.17e-02 7.31e+03 8.31e-01 ... (remaining 12335 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.64: 320 106.64 - 113.48: 7084 113.48 - 120.32: 4371 120.32 - 127.16: 4853 127.16 - 134.00: 108 Bond angle restraints: 16736 Sorted by residual: angle pdb=" N GLY B 313 " pdb=" CA GLY B 313 " pdb=" C GLY B 313 " ideal model delta sigma weight residual 112.50 116.40 -3.90 1.16e+00 7.43e-01 1.13e+01 angle pdb=" N GLY C 313 " pdb=" CA GLY C 313 " pdb=" C GLY C 313 " ideal model delta sigma weight residual 112.50 116.40 -3.90 1.16e+00 7.43e-01 1.13e+01 angle pdb=" N GLY D 313 " pdb=" CA GLY D 313 " pdb=" C GLY D 313 " ideal model delta sigma weight residual 112.50 116.40 -3.90 1.16e+00 7.43e-01 1.13e+01 angle pdb=" N GLY A 313 " pdb=" CA GLY A 313 " pdb=" C GLY A 313 " ideal model delta sigma weight residual 112.50 116.38 -3.88 1.16e+00 7.43e-01 1.12e+01 angle pdb=" C VAL D 366 " pdb=" N GLU D 367 " pdb=" CA GLU D 367 " ideal model delta sigma weight residual 120.26 124.59 -4.33 1.34e+00 5.57e-01 1.04e+01 ... (remaining 16731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 6562 17.80 - 35.60: 662 35.60 - 53.40: 108 53.40 - 71.20: 28 71.20 - 89.01: 20 Dihedral angle restraints: 7380 sinusoidal: 2876 harmonic: 4504 Sorted by residual: dihedral pdb=" CB GLU B 40 " pdb=" CG GLU B 40 " pdb=" CD GLU B 40 " pdb=" OE1 GLU B 40 " ideal model delta sinusoidal sigma weight residual 0.00 86.33 -86.33 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CB GLU D 40 " pdb=" CG GLU D 40 " pdb=" CD GLU D 40 " pdb=" OE1 GLU D 40 " ideal model delta sinusoidal sigma weight residual 0.00 86.32 -86.32 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CB GLU A 40 " pdb=" CG GLU A 40 " pdb=" CD GLU A 40 " pdb=" OE1 GLU A 40 " ideal model delta sinusoidal sigma weight residual 0.00 86.32 -86.32 1 3.00e+01 1.11e-03 9.98e+00 ... (remaining 7377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1330 0.027 - 0.054: 448 0.054 - 0.081: 186 0.081 - 0.108: 77 0.108 - 0.134: 15 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CG LEU B 386 " pdb=" CB LEU B 386 " pdb=" CD1 LEU B 386 " pdb=" CD2 LEU B 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CG LEU D 386 " pdb=" CB LEU D 386 " pdb=" CD1 LEU D 386 " pdb=" CD2 LEU D 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CG LEU C 386 " pdb=" CB LEU C 386 " pdb=" CD1 LEU C 386 " pdb=" CD2 LEU C 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2053 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 424 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO B 425 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 425 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 425 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 424 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 425 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 425 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 425 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 424 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 425 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.016 5.00e-02 4.00e+02 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2125 2.77 - 3.30: 12287 3.30 - 3.83: 21314 3.83 - 4.37: 23750 4.37 - 4.90: 42212 Nonbonded interactions: 101688 Sorted by model distance: nonbonded pdb=" OG SER A 84 " pdb=" O MET A 87 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 84 " pdb=" O MET C 87 " model vdw 2.233 3.040 nonbonded pdb=" OG SER D 84 " pdb=" O MET D 87 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 84 " pdb=" O MET B 87 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP D 165 " pdb=" OH TYR D 190 " model vdw 2.253 3.040 ... (remaining 101683 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.650 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:10.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.003 0.026 12340 Z= 0.185 Angle : 0.474 4.985 16736 Z= 0.260 Chirality : 0.036 0.134 2056 Planarity : 0.003 0.029 2020 Dihedral : 15.275 89.006 4468 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.21), residues: 1520 helix: 2.32 (0.14), residues: 1228 sheet: -0.45 (0.55), residues: 40 loop : -2.38 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 193 HIS 0.004 0.001 HIS C 392 PHE 0.014 0.001 PHE D 205 TYR 0.008 0.001 TYR C 124 ARG 0.003 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.428 Fit side-chains REVERT: A 296 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7900 (mtt90) REVERT: A 310 ASP cc_start: 0.8256 (m-30) cc_final: 0.7970 (m-30) REVERT: B 310 ASP cc_start: 0.8288 (m-30) cc_final: 0.7960 (m-30) REVERT: B 387 MET cc_start: 0.8775 (mtm) cc_final: 0.8573 (mtm) REVERT: C 427 MET cc_start: 0.8635 (ptt) cc_final: 0.8348 (ptt) REVERT: D 427 MET cc_start: 0.8631 (ptt) cc_final: 0.8352 (ptt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 1.0998 time to fit residues: 291.1584 Evaluate side-chains 183 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 392 HIS A 443 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 392 HIS C 358 HIS C 392 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS D 392 HIS D 443 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12340 Z= 0.247 Angle : 0.546 6.125 16736 Z= 0.283 Chirality : 0.038 0.155 2056 Planarity : 0.004 0.030 2020 Dihedral : 3.859 15.578 1688 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.29 % Allowed : 10.50 % Favored : 87.20 % 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: 3.08 (0.21), residues: 1520 helix: 2.85 (0.13), residues: 1228 sheet: 0.06 (0.54), residues: 40 loop : -2.09 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.005 0.001 HIS B 392 PHE 0.019 0.002 PHE A 205 TYR 0.030 0.002 TYR B 124 ARG 0.004 0.001 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 195 time to evaluate : 1.508 Fit side-chains REVERT: A 171 MET cc_start: 0.7764 (mmp) cc_final: 0.7513 (mmm) REVERT: A 296 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7853 (mtt90) REVERT: A 310 ASP cc_start: 0.8351 (m-30) cc_final: 0.8110 (m-30) REVERT: A 385 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7872 (ttp-110) REVERT: A 387 MET cc_start: 0.9204 (mtm) cc_final: 0.8974 (mtm) REVERT: B 306 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7680 (mtp180) REVERT: B 310 ASP cc_start: 0.8361 (m-30) cc_final: 0.8044 (m-30) REVERT: B 387 MET cc_start: 0.9173 (mtm) cc_final: 0.8924 (mtm) REVERT: C 143 THR cc_start: 0.8655 (m) cc_final: 0.8321 (m) REVERT: C 310 ASP cc_start: 0.8395 (m-30) cc_final: 0.8155 (m-30) REVERT: C 427 MET cc_start: 0.8458 (ptt) cc_final: 0.8215 (ptt) REVERT: D 143 THR cc_start: 0.8656 (m) cc_final: 0.8323 (m) REVERT: D 310 ASP cc_start: 0.8367 (m-30) cc_final: 0.8134 (m-30) REVERT: D 385 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7849 (ttp-110) REVERT: D 427 MET cc_start: 0.8496 (ptt) cc_final: 0.8243 (ptt) outliers start: 31 outliers final: 16 residues processed: 210 average time/residue: 1.2671 time to fit residues: 288.3877 Evaluate side-chains 197 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.0970 chunk 137 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12340 Z= 0.201 Angle : 0.505 6.203 16736 Z= 0.263 Chirality : 0.036 0.125 2056 Planarity : 0.004 0.032 2020 Dihedral : 3.756 13.659 1688 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.74 % Allowed : 13.31 % Favored : 83.95 % 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: 3.25 (0.21), residues: 1520 helix: 3.01 (0.13), residues: 1236 sheet: 0.47 (0.50), residues: 40 loop : -2.53 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS C 392 PHE 0.016 0.001 PHE A 205 TYR 0.026 0.001 TYR B 124 ARG 0.004 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.378 Fit side-chains REVERT: A 296 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7805 (mtt90) REVERT: A 310 ASP cc_start: 0.8329 (m-30) cc_final: 0.8067 (m-30) REVERT: A 385 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7881 (ttp-110) REVERT: A 387 MET cc_start: 0.9176 (mtm) cc_final: 0.8961 (mtm) REVERT: B 284 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: B 306 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7705 (mtp180) REVERT: B 310 ASP cc_start: 0.8325 (m-30) cc_final: 0.7912 (m-30) REVERT: B 387 MET cc_start: 0.9163 (mtm) cc_final: 0.8901 (mtm) REVERT: B 401 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7821 (tm-30) REVERT: C 87 MET cc_start: 0.4205 (mtt) cc_final: 0.3233 (mtt) REVERT: C 143 THR cc_start: 0.8606 (m) cc_final: 0.8252 (m) REVERT: C 310 ASP cc_start: 0.8362 (m-30) cc_final: 0.8130 (m-30) REVERT: C 427 MET cc_start: 0.8448 (ptt) cc_final: 0.8220 (ptt) REVERT: D 143 THR cc_start: 0.8610 (m) cc_final: 0.8255 (m) REVERT: D 310 ASP cc_start: 0.8366 (m-30) cc_final: 0.8132 (m-30) REVERT: D 385 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7765 (ttm110) REVERT: D 427 MET cc_start: 0.8446 (ptt) cc_final: 0.8209 (ptt) outliers start: 37 outliers final: 16 residues processed: 224 average time/residue: 1.2132 time to fit residues: 295.1981 Evaluate side-chains 205 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.0040 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 0.0010 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12340 Z= 0.172 Angle : 0.495 6.784 16736 Z= 0.256 Chirality : 0.036 0.174 2056 Planarity : 0.003 0.030 2020 Dihedral : 3.692 13.665 1688 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.48 % Allowed : 15.24 % Favored : 81.29 % 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: 3.49 (0.21), residues: 1520 helix: 3.21 (0.14), residues: 1224 sheet: 0.93 (0.53), residues: 40 loop : -2.45 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.003 0.001 HIS D 392 PHE 0.015 0.001 PHE A 205 TYR 0.023 0.001 TYR D 124 ARG 0.003 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 198 time to evaluate : 1.370 Fit side-chains REVERT: A 296 ARG cc_start: 0.8156 (mtt90) cc_final: 0.7783 (mtt90) REVERT: A 310 ASP cc_start: 0.8300 (m-30) cc_final: 0.8028 (m-30) REVERT: A 387 MET cc_start: 0.9144 (mtm) cc_final: 0.8940 (mtm) REVERT: B 284 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7147 (mp10) REVERT: B 310 ASP cc_start: 0.8277 (m-30) cc_final: 0.7997 (m-30) REVERT: B 387 MET cc_start: 0.9144 (mtm) cc_final: 0.8848 (mtm) REVERT: B 401 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 87 MET cc_start: 0.4238 (mtt) cc_final: 0.3187 (mtt) REVERT: C 143 THR cc_start: 0.8560 (m) cc_final: 0.8203 (m) REVERT: C 310 ASP cc_start: 0.8311 (m-30) cc_final: 0.8037 (m-30) REVERT: C 427 MET cc_start: 0.8455 (ptt) cc_final: 0.8200 (ptt) REVERT: D 87 MET cc_start: 0.4072 (mtt) cc_final: 0.3307 (mtt) REVERT: D 143 THR cc_start: 0.8564 (m) cc_final: 0.8202 (m) REVERT: D 310 ASP cc_start: 0.8313 (m-30) cc_final: 0.8036 (m-30) REVERT: D 385 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7715 (ttm110) REVERT: D 427 MET cc_start: 0.8436 (ptt) cc_final: 0.8188 (ptt) outliers start: 47 outliers final: 23 residues processed: 222 average time/residue: 1.2165 time to fit residues: 292.9825 Evaluate side-chains 210 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.0470 chunk 125 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 185 ASN B 202 GLN C 202 GLN D 185 ASN D 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12340 Z= 0.241 Angle : 0.537 6.958 16736 Z= 0.276 Chirality : 0.037 0.140 2056 Planarity : 0.004 0.032 2020 Dihedral : 3.810 13.788 1688 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.48 % Allowed : 15.90 % Favored : 80.62 % 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: 3.28 (0.21), residues: 1520 helix: 3.03 (0.13), residues: 1236 sheet: 1.21 (0.56), residues: 40 loop : -2.71 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 193 HIS 0.003 0.001 HIS D 392 PHE 0.018 0.002 PHE A 205 TYR 0.024 0.002 TYR C 124 ARG 0.004 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 205 time to evaluate : 1.301 Fit side-chains REVERT: A 296 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7929 (mtt-85) REVERT: A 310 ASP cc_start: 0.8352 (m-30) cc_final: 0.8124 (m-30) REVERT: A 387 MET cc_start: 0.9218 (mtm) cc_final: 0.8941 (mtm) REVERT: B 310 ASP cc_start: 0.8342 (m-30) cc_final: 0.8052 (m-30) REVERT: B 387 MET cc_start: 0.9200 (mtm) cc_final: 0.8911 (mtm) REVERT: B 401 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7883 (tm-30) REVERT: C 52 LYS cc_start: 0.7710 (mmtm) cc_final: 0.7351 (pttp) REVERT: C 87 MET cc_start: 0.4261 (mtt) cc_final: 0.3242 (mtt) REVERT: C 143 THR cc_start: 0.8567 (m) cc_final: 0.8206 (m) REVERT: C 151 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7947 (tt) REVERT: C 310 ASP cc_start: 0.8356 (m-30) cc_final: 0.8114 (m-30) REVERT: C 427 MET cc_start: 0.8442 (ptt) cc_final: 0.8202 (ptt) REVERT: D 52 LYS cc_start: 0.7709 (mmtm) cc_final: 0.7354 (pttp) REVERT: D 143 THR cc_start: 0.8570 (m) cc_final: 0.8206 (m) REVERT: D 151 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7974 (tt) REVERT: D 310 ASP cc_start: 0.8361 (m-30) cc_final: 0.8135 (m-30) REVERT: D 385 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7860 (ttp-110) REVERT: D 427 MET cc_start: 0.8446 (ptt) cc_final: 0.8208 (ptt) outliers start: 47 outliers final: 27 residues processed: 230 average time/residue: 1.2313 time to fit residues: 306.6612 Evaluate side-chains 223 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12340 Z= 0.269 Angle : 0.554 8.206 16736 Z= 0.284 Chirality : 0.038 0.130 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.901 14.336 1688 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.88 % Allowed : 17.09 % Favored : 80.03 % 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: 3.12 (0.21), residues: 1520 helix: 2.92 (0.13), residues: 1236 sheet: 1.21 (0.55), residues: 40 loop : -2.73 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 193 HIS 0.003 0.001 HIS B 370 PHE 0.019 0.002 PHE A 205 TYR 0.024 0.002 TYR D 124 ARG 0.005 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 1.323 Fit side-chains REVERT: A 296 ARG cc_start: 0.8173 (mtt90) cc_final: 0.7931 (mtt-85) REVERT: A 310 ASP cc_start: 0.8360 (m-30) cc_final: 0.8126 (m-30) REVERT: A 387 MET cc_start: 0.9233 (mtm) cc_final: 0.8966 (mtm) REVERT: B 310 ASP cc_start: 0.8363 (m-30) cc_final: 0.8133 (m-30) REVERT: B 387 MET cc_start: 0.9202 (mtm) cc_final: 0.8911 (mtm) REVERT: B 397 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8390 (p) REVERT: B 401 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 87 MET cc_start: 0.4293 (mtt) cc_final: 0.3312 (mtt) REVERT: C 143 THR cc_start: 0.8509 (m) cc_final: 0.8166 (m) REVERT: C 151 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7971 (tt) REVERT: C 224 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.7180 (p) REVERT: C 296 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7929 (mtt-85) REVERT: C 310 ASP cc_start: 0.8362 (m-30) cc_final: 0.8127 (m-30) REVERT: C 427 MET cc_start: 0.8441 (ptt) cc_final: 0.8206 (ptt) REVERT: D 87 MET cc_start: 0.4215 (mtt) cc_final: 0.3083 (mtt) REVERT: D 143 THR cc_start: 0.8552 (m) cc_final: 0.8174 (m) REVERT: D 151 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7973 (tt) REVERT: D 224 THR cc_start: 0.7420 (OUTLIER) cc_final: 0.7142 (p) REVERT: D 296 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7938 (mtt-85) REVERT: D 310 ASP cc_start: 0.8369 (m-30) cc_final: 0.8136 (m-30) REVERT: D 385 ARG cc_start: 0.8192 (ttm110) cc_final: 0.7882 (ttp-110) REVERT: D 427 MET cc_start: 0.8446 (ptt) cc_final: 0.8199 (ptt) outliers start: 39 outliers final: 23 residues processed: 216 average time/residue: 1.3473 time to fit residues: 313.7574 Evaluate side-chains 212 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 146 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12340 Z= 0.210 Angle : 0.527 7.865 16736 Z= 0.271 Chirality : 0.036 0.129 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.798 13.462 1688 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.03 % Allowed : 17.31 % Favored : 79.66 % 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: 3.25 (0.21), residues: 1520 helix: 3.01 (0.14), residues: 1236 sheet: 1.53 (0.59), residues: 40 loop : -2.73 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 193 HIS 0.002 0.001 HIS B 370 PHE 0.016 0.001 PHE A 205 TYR 0.022 0.001 TYR D 124 ARG 0.004 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 1.411 Fit side-chains REVERT: A 310 ASP cc_start: 0.8327 (m-30) cc_final: 0.8060 (m-30) REVERT: A 387 MET cc_start: 0.9180 (mtm) cc_final: 0.8906 (mtm) REVERT: B 310 ASP cc_start: 0.8329 (m-30) cc_final: 0.8044 (m-30) REVERT: B 387 MET cc_start: 0.9170 (mtm) cc_final: 0.8846 (mtm) REVERT: B 397 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 401 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 445 GLN cc_start: 0.6501 (mp-120) cc_final: 0.6300 (mp-120) REVERT: C 52 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7391 (pttp) REVERT: C 87 MET cc_start: 0.4084 (mtt) cc_final: 0.3052 (mtt) REVERT: C 143 THR cc_start: 0.8465 (m) cc_final: 0.8125 (m) REVERT: C 224 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.7074 (p) REVERT: C 296 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7911 (mtt-85) REVERT: C 310 ASP cc_start: 0.8327 (m-30) cc_final: 0.8064 (m-30) REVERT: C 427 MET cc_start: 0.8437 (ptt) cc_final: 0.8193 (ptt) REVERT: D 52 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7396 (pttp) REVERT: D 87 MET cc_start: 0.3912 (mtt) cc_final: 0.2726 (mtt) REVERT: D 143 THR cc_start: 0.8467 (m) cc_final: 0.8126 (m) REVERT: D 224 THR cc_start: 0.7266 (OUTLIER) cc_final: 0.7005 (p) REVERT: D 310 ASP cc_start: 0.8336 (m-30) cc_final: 0.8066 (m-30) REVERT: D 385 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7662 (ttm110) REVERT: D 427 MET cc_start: 0.8441 (ptt) cc_final: 0.8204 (ptt) outliers start: 41 outliers final: 26 residues processed: 220 average time/residue: 1.3055 time to fit residues: 311.5435 Evaluate side-chains 218 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN D 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12340 Z= 0.247 Angle : 0.554 10.162 16736 Z= 0.284 Chirality : 0.037 0.137 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.883 13.885 1688 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.96 % Allowed : 17.60 % Favored : 79.44 % 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: 3.10 (0.21), residues: 1520 helix: 2.90 (0.13), residues: 1236 sheet: 1.59 (0.61), residues: 40 loop : -2.78 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS B 392 PHE 0.018 0.002 PHE A 205 TYR 0.023 0.002 TYR D 124 ARG 0.004 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 190 time to evaluate : 1.727 Fit side-chains REVERT: A 52 LYS cc_start: 0.7521 (mmtm) cc_final: 0.7229 (pttp) REVERT: A 296 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7928 (mtt-85) REVERT: A 310 ASP cc_start: 0.8365 (m-30) cc_final: 0.8145 (m-30) REVERT: A 387 MET cc_start: 0.9216 (mtm) cc_final: 0.8958 (mtm) REVERT: B 87 MET cc_start: 0.3987 (mtt) cc_final: 0.3150 (mtt) REVERT: B 310 ASP cc_start: 0.8340 (m-30) cc_final: 0.8051 (m-30) REVERT: B 387 MET cc_start: 0.9198 (mtm) cc_final: 0.8903 (mtm) REVERT: B 397 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8378 (p) REVERT: B 401 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 87 MET cc_start: 0.3966 (mtt) cc_final: 0.2938 (mtt) REVERT: C 143 THR cc_start: 0.8550 (m) cc_final: 0.8199 (m) REVERT: C 224 THR cc_start: 0.7401 (OUTLIER) cc_final: 0.7139 (p) REVERT: C 296 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7930 (mtt-85) REVERT: C 310 ASP cc_start: 0.8365 (m-30) cc_final: 0.8131 (m-30) REVERT: C 427 MET cc_start: 0.8430 (ptt) cc_final: 0.8192 (ptt) REVERT: C 445 GLN cc_start: 0.6662 (mp-120) cc_final: 0.6347 (mp10) REVERT: D 87 MET cc_start: 0.3918 (mtt) cc_final: 0.2749 (mtt) REVERT: D 143 THR cc_start: 0.8556 (m) cc_final: 0.8205 (m) REVERT: D 224 THR cc_start: 0.7386 (OUTLIER) cc_final: 0.7111 (p) REVERT: D 296 ARG cc_start: 0.8181 (mtt90) cc_final: 0.7935 (mtt-85) REVERT: D 310 ASP cc_start: 0.8375 (m-30) cc_final: 0.8136 (m-30) REVERT: D 385 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7870 (ttp-110) REVERT: D 427 MET cc_start: 0.8432 (ptt) cc_final: 0.8199 (ptt) REVERT: D 445 GLN cc_start: 0.6773 (mp-120) cc_final: 0.6530 (mp10) outliers start: 40 outliers final: 25 residues processed: 215 average time/residue: 1.3487 time to fit residues: 312.4243 Evaluate side-chains 213 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.3980 chunk 136 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 82 optimal weight: 0.2980 chunk 59 optimal weight: 0.0470 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12340 Z= 0.185 Angle : 0.522 10.284 16736 Z= 0.268 Chirality : 0.036 0.135 2056 Planarity : 0.003 0.032 2020 Dihedral : 3.769 13.661 1688 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.44 % Allowed : 18.34 % Favored : 79.22 % 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: 3.33 (0.21), residues: 1520 helix: 3.07 (0.14), residues: 1236 sheet: 1.88 (0.64), residues: 40 loop : -2.79 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.002 0.001 HIS D 139 PHE 0.015 0.001 PHE A 205 TYR 0.020 0.001 TYR B 124 ARG 0.003 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 1.232 Fit side-chains REVERT: A 310 ASP cc_start: 0.8313 (m-30) cc_final: 0.8043 (m-30) REVERT: A 387 MET cc_start: 0.9172 (mtm) cc_final: 0.8913 (mtm) REVERT: B 52 LYS cc_start: 0.7630 (mmtm) cc_final: 0.7308 (pttp) REVERT: B 310 ASP cc_start: 0.8316 (m-30) cc_final: 0.8040 (m-30) REVERT: B 387 MET cc_start: 0.9162 (mtm) cc_final: 0.8893 (mtm) REVERT: B 397 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8327 (p) REVERT: B 401 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7925 (tm-30) REVERT: C 52 LYS cc_start: 0.7665 (mmtm) cc_final: 0.7339 (pttp) REVERT: C 87 MET cc_start: 0.3882 (mtt) cc_final: 0.2798 (mtt) REVERT: C 143 THR cc_start: 0.8499 (m) cc_final: 0.8155 (m) REVERT: C 296 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7891 (mtt-85) REVERT: C 310 ASP cc_start: 0.8317 (m-30) cc_final: 0.8040 (m-30) REVERT: C 427 MET cc_start: 0.8431 (ptt) cc_final: 0.8179 (ptt) REVERT: C 445 GLN cc_start: 0.6698 (mp-120) cc_final: 0.6413 (mp10) REVERT: D 52 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7346 (pttp) REVERT: D 143 THR cc_start: 0.8502 (m) cc_final: 0.8157 (m) REVERT: D 310 ASP cc_start: 0.8323 (m-30) cc_final: 0.8039 (m-30) REVERT: D 385 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7620 (ttm110) REVERT: D 427 MET cc_start: 0.8433 (ptt) cc_final: 0.8184 (ptt) outliers start: 33 outliers final: 22 residues processed: 216 average time/residue: 1.2608 time to fit residues: 294.8696 Evaluate side-chains 208 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN C 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12340 Z= 0.261 Angle : 0.566 10.267 16736 Z= 0.290 Chirality : 0.038 0.148 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.905 13.872 1688 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.85 % Allowed : 18.93 % Favored : 79.22 % 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: 3.07 (0.21), residues: 1520 helix: 2.88 (0.14), residues: 1236 sheet: 1.72 (0.64), residues: 40 loop : -2.83 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 193 HIS 0.003 0.001 HIS D 392 PHE 0.025 0.002 PHE A 444 TYR 0.022 0.002 TYR B 124 ARG 0.004 0.000 ARG D 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 1.318 Fit side-chains REVERT: A 52 LYS cc_start: 0.7640 (mmtm) cc_final: 0.7318 (pttp) REVERT: A 129 VAL cc_start: 0.8335 (t) cc_final: 0.7859 (m) REVERT: A 296 ARG cc_start: 0.8143 (mtt90) cc_final: 0.7920 (mtt-85) REVERT: A 310 ASP cc_start: 0.8359 (m-30) cc_final: 0.8136 (m-30) REVERT: A 387 MET cc_start: 0.9230 (mtm) cc_final: 0.8962 (mtm) REVERT: B 310 ASP cc_start: 0.8370 (m-30) cc_final: 0.8127 (m-30) REVERT: B 387 MET cc_start: 0.9206 (mtm) cc_final: 0.8914 (mtm) REVERT: B 397 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8380 (p) REVERT: B 401 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 52 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7369 (pttp) REVERT: C 87 MET cc_start: 0.3919 (mtt) cc_final: 0.2894 (mtt) REVERT: C 143 THR cc_start: 0.8548 (m) cc_final: 0.8213 (m) REVERT: C 296 ARG cc_start: 0.8179 (mtt90) cc_final: 0.7931 (mtt-85) REVERT: C 310 ASP cc_start: 0.8370 (m-30) cc_final: 0.8138 (m-30) REVERT: C 427 MET cc_start: 0.8439 (ptt) cc_final: 0.8204 (ptt) REVERT: C 445 GLN cc_start: 0.6643 (mp10) cc_final: 0.6433 (mp10) REVERT: D 52 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7373 (pttp) REVERT: D 143 THR cc_start: 0.8552 (m) cc_final: 0.8218 (m) REVERT: D 296 ARG cc_start: 0.8179 (mtt90) cc_final: 0.7933 (mtt-85) REVERT: D 310 ASP cc_start: 0.8367 (m-30) cc_final: 0.8130 (m-30) REVERT: D 385 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7907 (ttp-110) REVERT: D 427 MET cc_start: 0.8432 (ptt) cc_final: 0.8201 (ptt) outliers start: 25 outliers final: 24 residues processed: 205 average time/residue: 1.4091 time to fit residues: 310.8019 Evaluate side-chains 206 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.0030 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124078 restraints weight = 12747.495| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.30 r_work: 0.3220 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12340 Z= 0.228 Angle : 0.549 9.886 16736 Z= 0.282 Chirality : 0.037 0.143 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.854 13.634 1688 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.85 % Allowed : 18.71 % Favored : 79.44 % 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: 3.11 (0.21), residues: 1520 helix: 2.90 (0.14), residues: 1236 sheet: 1.75 (0.63), residues: 40 loop : -2.83 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.003 0.001 HIS B 392 PHE 0.023 0.002 PHE A 444 TYR 0.022 0.001 TYR B 124 ARG 0.004 0.000 ARG D 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4858.46 seconds wall clock time: 85 minutes 29.43 seconds (5129.43 seconds total)