Starting phenix.real_space_refine on Sat Jul 20 20:33:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/07_2024/8uvt_42628.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/07_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_42628/07_2024/8uvt_42628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/07_2024/8uvt_42628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/07_2024/8uvt_42628.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/07_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.85, per 1000 atoms: 0.65 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: 5.11 Conformation dependent library (CDL) restraints added in 2.1 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: 1.00 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: 3.88 Time building geometry restraints manager: 5.58 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 2.440 nonbonded pdb=" OG SER C 84 " pdb=" O MET C 87 " model vdw 2.233 2.440 nonbonded pdb=" OG SER D 84 " pdb=" O MET D 87 " model vdw 2.233 2.440 nonbonded pdb=" OG SER B 84 " pdb=" O MET B 87 " model vdw 2.233 2.440 nonbonded pdb=" OD2 ASP D 165 " pdb=" OH TYR D 190 " model vdw 2.253 2.440 ... (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 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 36.590 Find NCS groups from input model: 0.470 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.190 ------------------------------------------------------------------------------- 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 : 1.347 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: 1.1357 time to fit residues: 300.0644 Evaluate side-chains 183 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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: 0.7980 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 392 HIS A 443 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 392 HIS B 443 GLN C 202 GLN C 392 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN D 392 HIS D 443 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12340 Z= 0.233 Angle : 0.524 5.937 16736 Z= 0.271 Chirality : 0.037 0.160 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.811 14.256 1688 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.59 % Allowed : 9.76 % Favored : 87.65 % 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: 3.15 (0.21), residues: 1520 helix: 2.90 (0.13), residues: 1228 sheet: 0.10 (0.55), residues: 40 loop : -2.08 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.005 0.001 HIS C 392 PHE 0.018 0.002 PHE A 205 TYR 0.030 0.002 TYR B 124 ARG 0.004 0.000 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 232 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 1.287 Fit side-chains REVERT: A 171 MET cc_start: 0.7757 (mmp) cc_final: 0.7495 (mmm) REVERT: A 296 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7841 (mtt90) REVERT: A 310 ASP cc_start: 0.8349 (m-30) cc_final: 0.8115 (m-30) REVERT: A 385 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7773 (ttp-110) REVERT: B 310 ASP cc_start: 0.8354 (m-30) cc_final: 0.8105 (m-30) REVERT: C 143 THR cc_start: 0.8625 (m) cc_final: 0.8268 (m) REVERT: C 310 ASP cc_start: 0.8366 (m-30) cc_final: 0.8141 (m-30) REVERT: C 385 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7721 (ttp80) REVERT: C 427 MET cc_start: 0.8442 (ptt) cc_final: 0.8192 (ptt) REVERT: D 143 THR cc_start: 0.8627 (m) cc_final: 0.8268 (m) REVERT: D 310 ASP cc_start: 0.8359 (m-30) cc_final: 0.8132 (m-30) REVERT: D 385 ARG cc_start: 0.8039 (ttm110) cc_final: 0.7787 (ttp-110) REVERT: D 427 MET cc_start: 0.8467 (ptt) cc_final: 0.8207 (ptt) outliers start: 35 outliers final: 18 residues processed: 213 average time/residue: 1.2607 time to fit residues: 290.9594 Evaluate side-chains 202 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 348 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 16 CYS 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 69 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 69 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: 0.9980 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8089 moved from start: 0.1906 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= 0.251 Angle : 0.522 5.072 16736 Z= 0.271 Chirality : 0.037 0.130 2056 Planarity : 0.004 0.032 2020 Dihedral : 3.839 13.754 1688 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.33 % Allowed : 12.94 % Favored : 83.73 % 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: 3.14 (0.21), residues: 1520 helix: 2.93 (0.13), residues: 1236 sheet: 0.31 (0.51), residues: 40 loop : -2.54 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.004 0.001 HIS B 392 PHE 0.019 0.002 PHE A 205 TYR 0.027 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 243 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 198 time to evaluate : 1.438 Fit side-chains REVERT: A 296 ARG cc_start: 0.8184 (mtt90) cc_final: 0.7819 (mtt90) REVERT: A 310 ASP cc_start: 0.8348 (m-30) cc_final: 0.8123 (m-30) REVERT: A 385 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7850 (ttp-110) REVERT: B 171 MET cc_start: 0.7483 (mmm) cc_final: 0.7282 (mmp) REVERT: B 310 ASP cc_start: 0.8361 (m-30) cc_final: 0.8127 (m-30) REVERT: B 401 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7760 (tm-30) REVERT: C 87 MET cc_start: 0.4842 (mtt) cc_final: 0.3962 (mtt) REVERT: C 143 THR cc_start: 0.8571 (m) cc_final: 0.8180 (m) REVERT: C 296 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7932 (mtt-85) REVERT: C 310 ASP cc_start: 0.8353 (m-30) cc_final: 0.8124 (m-30) REVERT: C 385 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7810 (ttp80) REVERT: C 427 MET cc_start: 0.8425 (ptt) cc_final: 0.8214 (ptt) REVERT: D 87 MET cc_start: 0.4858 (mtt) cc_final: 0.3973 (mtt) REVERT: D 143 THR cc_start: 0.8558 (m) cc_final: 0.8155 (m) REVERT: D 296 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7936 (mtt-85) REVERT: D 310 ASP cc_start: 0.8362 (m-30) cc_final: 0.8135 (m-30) REVERT: D 385 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7854 (ttp-110) REVERT: D 427 MET cc_start: 0.8405 (ptt) cc_final: 0.8201 (ptt) outliers start: 45 outliers final: 20 residues processed: 223 average time/residue: 1.3252 time to fit residues: 318.5051 Evaluate side-chains 206 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 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 224 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 69 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 69 THR 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: 0.7980 chunk 103 optimal weight: 0.0670 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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: 0.8061 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12340 Z= 0.195 Angle : 0.499 5.835 16736 Z= 0.258 Chirality : 0.036 0.177 2056 Planarity : 0.003 0.033 2020 Dihedral : 3.757 13.952 1688 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.81 % Allowed : 15.53 % Favored : 81.66 % 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: 3.37 (0.21), residues: 1520 helix: 3.10 (0.13), residues: 1236 sheet: 0.58 (0.52), residues: 40 loop : -2.55 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS A 392 PHE 0.016 0.001 PHE A 205 TYR 0.024 0.001 TYR C 124 ARG 0.004 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 234 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 1.413 Fit side-chains REVERT: A 296 ARG cc_start: 0.8146 (mtt90) cc_final: 0.7786 (mtt90) REVERT: A 310 ASP cc_start: 0.8329 (m-30) cc_final: 0.8056 (m-30) REVERT: A 385 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7776 (ttp-110) REVERT: B 310 ASP cc_start: 0.8326 (m-30) cc_final: 0.8049 (m-30) REVERT: B 401 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7779 (tm-30) REVERT: C 87 MET cc_start: 0.4607 (mtt) cc_final: 0.3763 (mtt) REVERT: C 143 THR cc_start: 0.8538 (m) cc_final: 0.8135 (m) REVERT: C 296 ARG cc_start: 0.8139 (mtt90) cc_final: 0.7773 (mtt90) REVERT: C 310 ASP cc_start: 0.8356 (m-30) cc_final: 0.8127 (m-30) REVERT: C 385 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7637 (ttp80) REVERT: C 427 MET cc_start: 0.8416 (ptt) cc_final: 0.8157 (ptt) REVERT: D 87 MET cc_start: 0.4607 (mtt) cc_final: 0.3766 (mtt) REVERT: D 143 THR cc_start: 0.8526 (m) cc_final: 0.8130 (m) REVERT: D 296 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7902 (mtt-85) REVERT: D 310 ASP cc_start: 0.8369 (m-30) cc_final: 0.8142 (m-30) REVERT: D 385 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7574 (ttm110) REVERT: D 427 MET cc_start: 0.8408 (ptt) cc_final: 0.8172 (ptt) outliers start: 38 outliers final: 25 residues processed: 219 average time/residue: 1.3922 time to fit residues: 327.7090 Evaluate side-chains 210 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 224 THR Chi-restraints excluded: chain B residue 324 LEU 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 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 17 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 0.0370 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2182 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= 0.243 Angle : 0.526 6.866 16736 Z= 0.271 Chirality : 0.037 0.143 2056 Planarity : 0.004 0.034 2020 Dihedral : 3.840 13.793 1688 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.03 % Allowed : 16.27 % Favored : 80.70 % 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: 3.22 (0.21), residues: 1520 helix: 2.99 (0.13), residues: 1236 sheet: 0.71 (0.52), residues: 40 loop : -2.63 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS A 392 PHE 0.018 0.002 PHE A 205 TYR 0.024 0.001 TYR B 124 ARG 0.004 0.000 ARG A 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 228 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 187 time to evaluate : 1.460 Fit side-chains REVERT: A 296 ARG cc_start: 0.8151 (mtt90) cc_final: 0.7911 (mtt-85) REVERT: A 310 ASP cc_start: 0.8347 (m-30) cc_final: 0.8122 (m-30) REVERT: A 385 ARG cc_start: 0.8070 (ttm110) cc_final: 0.7758 (ttp-110) REVERT: B 310 ASP cc_start: 0.8361 (m-30) cc_final: 0.8129 (m-30) REVERT: B 401 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7781 (tm-30) REVERT: C 87 MET cc_start: 0.4641 (mtt) cc_final: 0.3817 (mtt) REVERT: C 143 THR cc_start: 0.8553 (m) cc_final: 0.8140 (m) REVERT: C 151 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7937 (tt) REVERT: C 296 ARG cc_start: 0.8151 (mtt90) cc_final: 0.7916 (mtt-85) REVERT: C 310 ASP cc_start: 0.8346 (m-30) cc_final: 0.8118 (m-30) REVERT: C 385 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7687 (ttp80) REVERT: C 427 MET cc_start: 0.8406 (ptt) cc_final: 0.8175 (ptt) REVERT: D 87 MET cc_start: 0.4643 (mtt) cc_final: 0.3821 (mtt) REVERT: D 143 THR cc_start: 0.8552 (m) cc_final: 0.8148 (m) REVERT: D 296 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7926 (mtt-85) REVERT: D 310 ASP cc_start: 0.8360 (m-30) cc_final: 0.8128 (m-30) REVERT: D 385 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7769 (ttp-110) REVERT: D 427 MET cc_start: 0.8406 (ptt) cc_final: 0.8178 (ptt) outliers start: 41 outliers final: 28 residues processed: 210 average time/residue: 1.4272 time to fit residues: 321.6275 Evaluate side-chains 209 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 224 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP 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 69 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 77 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: ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2253 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= 0.241 Angle : 0.525 6.987 16736 Z= 0.270 Chirality : 0.037 0.129 2056 Planarity : 0.004 0.035 2020 Dihedral : 3.856 13.673 1688 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.25 % Allowed : 16.64 % Favored : 80.10 % 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: 3.19 (0.21), residues: 1520 helix: 2.97 (0.13), residues: 1236 sheet: 0.75 (0.52), residues: 40 loop : -2.64 (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 B 392 PHE 0.018 0.002 PHE A 205 TYR 0.024 0.001 TYR C 124 ARG 0.004 0.000 ARG A 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 230 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 186 time to evaluate : 1.138 Fit side-chains REVERT: A 296 ARG cc_start: 0.8151 (mtt90) cc_final: 0.7910 (mtt-85) REVERT: A 310 ASP cc_start: 0.8356 (m-30) cc_final: 0.8137 (m-30) REVERT: A 385 ARG cc_start: 0.8051 (ttm110) cc_final: 0.7592 (ttm110) REVERT: B 310 ASP cc_start: 0.8361 (m-30) cc_final: 0.8123 (m-30) REVERT: B 401 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 87 MET cc_start: 0.4635 (mtt) cc_final: 0.3812 (mtt) REVERT: C 143 THR cc_start: 0.8574 (m) cc_final: 0.8181 (m) REVERT: C 151 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7960 (tt) REVERT: C 296 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7911 (mtt-85) REVERT: C 310 ASP cc_start: 0.8355 (m-30) cc_final: 0.8124 (m-30) REVERT: C 385 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7756 (ttp80) REVERT: C 427 MET cc_start: 0.8405 (ptt) cc_final: 0.8168 (ptt) REVERT: D 87 MET cc_start: 0.4642 (mtt) cc_final: 0.3813 (mtt) REVERT: D 143 THR cc_start: 0.8573 (m) cc_final: 0.8189 (m) REVERT: D 296 ARG cc_start: 0.8148 (mtt90) cc_final: 0.7923 (mtt-85) REVERT: D 310 ASP cc_start: 0.8367 (m-30) cc_final: 0.8131 (m-30) REVERT: D 385 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7764 (ttp-110) REVERT: D 427 MET cc_start: 0.8405 (ptt) cc_final: 0.8169 (ptt) outliers start: 44 outliers final: 28 residues processed: 211 average time/residue: 1.4263 time to fit residues: 323.2486 Evaluate side-chains 209 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 224 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 69 THR 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 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 69 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 0.0980 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN C 44 GLN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12340 Z= 0.194 Angle : 0.509 8.747 16736 Z= 0.262 Chirality : 0.036 0.126 2056 Planarity : 0.003 0.036 2020 Dihedral : 3.772 13.594 1688 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.18 % Allowed : 17.60 % 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: 3.36 (0.21), residues: 1520 helix: 3.10 (0.13), residues: 1236 sheet: 0.95 (0.53), residues: 40 loop : -2.68 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 193 HIS 0.002 0.001 HIS A 392 PHE 0.019 0.001 PHE A 444 TYR 0.022 0.001 TYR C 124 ARG 0.004 0.000 ARG A 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 239 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 196 time to evaluate : 1.388 Fit side-chains REVERT: A 310 ASP cc_start: 0.8322 (m-30) cc_final: 0.8052 (m-30) REVERT: A 385 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7734 (ttp-110) REVERT: B 310 ASP cc_start: 0.8326 (m-30) cc_final: 0.8051 (m-30) REVERT: B 401 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7815 (tm-30) REVERT: C 87 MET cc_start: 0.4573 (mtt) cc_final: 0.3727 (mtt) REVERT: C 143 THR cc_start: 0.8586 (m) cc_final: 0.8193 (m) REVERT: C 151 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7884 (tt) REVERT: C 296 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7910 (mtt-85) REVERT: C 310 ASP cc_start: 0.8321 (m-30) cc_final: 0.8047 (m-30) REVERT: C 385 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7616 (ttp80) REVERT: C 427 MET cc_start: 0.8404 (ptt) cc_final: 0.8160 (ptt) REVERT: D 87 MET cc_start: 0.4581 (mtt) cc_final: 0.3740 (mtt) REVERT: D 143 THR cc_start: 0.8584 (m) cc_final: 0.8198 (m) REVERT: D 296 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7923 (mtt-85) REVERT: D 310 ASP cc_start: 0.8331 (m-30) cc_final: 0.8054 (m-30) REVERT: D 385 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7660 (ttp-110) REVERT: D 427 MET cc_start: 0.8407 (ptt) cc_final: 0.8164 (ptt) outliers start: 43 outliers final: 25 residues processed: 219 average time/residue: 1.3904 time to fit residues: 327.3872 Evaluate side-chains 212 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 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 224 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP 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 69 THR Chi-restraints excluded: chain D residue 193 TRP 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: 0.6980 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 0.0020 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2300 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= 0.213 Angle : 0.523 8.704 16736 Z= 0.269 Chirality : 0.036 0.197 2056 Planarity : 0.003 0.036 2020 Dihedral : 3.804 13.780 1688 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.88 % Allowed : 18.34 % Favored : 78.77 % 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: 3.30 (0.21), residues: 1520 helix: 3.06 (0.13), residues: 1236 sheet: 1.01 (0.54), residues: 40 loop : -2.71 (0.38), 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 392 PHE 0.016 0.001 PHE A 205 TYR 0.021 0.001 TYR B 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 223 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 1.456 Fit side-chains REVERT: A 87 MET cc_start: 0.4480 (mtt) cc_final: 0.4149 (mtt) REVERT: A 310 ASP cc_start: 0.8324 (m-30) cc_final: 0.8058 (m-30) REVERT: B 87 MET cc_start: 0.4584 (mtt) cc_final: 0.3785 (mtt) REVERT: B 310 ASP cc_start: 0.8323 (m-30) cc_final: 0.8054 (m-30) REVERT: B 401 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7816 (tm-30) REVERT: C 87 MET cc_start: 0.4525 (mtt) cc_final: 0.3687 (mtt) REVERT: C 143 THR cc_start: 0.8647 (m) cc_final: 0.8255 (m) REVERT: C 151 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7935 (tt) REVERT: C 296 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7914 (mtt-85) REVERT: C 310 ASP cc_start: 0.8350 (m-30) cc_final: 0.8126 (m-30) REVERT: C 385 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7680 (ttp80) REVERT: C 427 MET cc_start: 0.8398 (ptt) cc_final: 0.8153 (ptt) REVERT: D 87 MET cc_start: 0.4511 (mtt) cc_final: 0.3674 (mtt) REVERT: D 143 THR cc_start: 0.8650 (m) cc_final: 0.8268 (m) REVERT: D 296 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7926 (mtt-85) REVERT: D 310 ASP cc_start: 0.8362 (m-30) cc_final: 0.8135 (m-30) REVERT: D 385 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7730 (ttp-110) REVERT: D 427 MET cc_start: 0.8398 (ptt) cc_final: 0.8157 (ptt) outliers start: 39 outliers final: 30 residues processed: 207 average time/residue: 1.4412 time to fit residues: 320.0757 Evaluate side-chains 209 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 224 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 69 THR 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 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 69 THR 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: 1.9990 chunk 136 optimal weight: 0.0980 chunk 140 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.0370 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2307 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= 0.188 Angle : 0.509 9.155 16736 Z= 0.262 Chirality : 0.036 0.189 2056 Planarity : 0.003 0.036 2020 Dihedral : 3.751 13.650 1688 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.44 % Allowed : 18.79 % Favored : 78.77 % 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: 3.39 (0.21), residues: 1520 helix: 3.13 (0.13), residues: 1236 sheet: 1.22 (0.57), residues: 40 loop : -2.77 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.002 0.001 HIS C 370 PHE 0.019 0.001 PHE A 444 TYR 0.021 0.001 TYR A 124 ARG 0.003 0.000 ARG A 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 222 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 1.278 Fit side-chains REVERT: A 310 ASP cc_start: 0.8316 (m-30) cc_final: 0.8038 (m-30) REVERT: B 87 MET cc_start: 0.4550 (mtt) cc_final: 0.3693 (mtt) REVERT: B 310 ASP cc_start: 0.8316 (m-30) cc_final: 0.8043 (m-30) REVERT: B 401 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7838 (tm-30) REVERT: C 87 MET cc_start: 0.4477 (mtt) cc_final: 0.3652 (mtt) REVERT: C 143 THR cc_start: 0.8641 (m) cc_final: 0.8253 (m) REVERT: C 151 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7881 (tt) REVERT: C 296 ARG cc_start: 0.8133 (mtt90) cc_final: 0.7897 (mtt-85) REVERT: C 310 ASP cc_start: 0.8316 (m-30) cc_final: 0.8039 (m-30) REVERT: C 427 MET cc_start: 0.8400 (ptt) cc_final: 0.8173 (ptt) REVERT: D 87 MET cc_start: 0.4425 (mtt) cc_final: 0.3593 (mtt) REVERT: D 143 THR cc_start: 0.8643 (m) cc_final: 0.8259 (m) REVERT: D 296 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7867 (mtt-85) REVERT: D 310 ASP cc_start: 0.8324 (m-30) cc_final: 0.8042 (m-30) REVERT: D 427 MET cc_start: 0.8398 (ptt) cc_final: 0.8170 (ptt) outliers start: 33 outliers final: 27 residues processed: 209 average time/residue: 1.3562 time to fit residues: 306.1114 Evaluate side-chains 210 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 224 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 69 THR 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 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 69 THR 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 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: 2.9990 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12340 Z= 0.241 Angle : 0.542 8.268 16736 Z= 0.278 Chirality : 0.037 0.185 2056 Planarity : 0.004 0.036 2020 Dihedral : 3.854 13.860 1688 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.22 % Allowed : 19.08 % Favored : 78.70 % 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: 3.19 (0.21), residues: 1520 helix: 2.98 (0.13), residues: 1236 sheet: 1.16 (0.58), residues: 40 loop : -2.79 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS D 370 PHE 0.024 0.002 PHE B 444 TYR 0.022 0.001 TYR B 124 ARG 0.004 0.000 ARG A 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 213 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.472 Fit side-chains REVERT: A 87 MET cc_start: 0.4565 (mtt) cc_final: 0.4201 (mtt) REVERT: A 310 ASP cc_start: 0.8359 (m-30) cc_final: 0.8123 (m-30) REVERT: B 87 MET cc_start: 0.4543 (mtt) cc_final: 0.3732 (mtt) REVERT: B 310 ASP cc_start: 0.8332 (m-30) cc_final: 0.8056 (m-30) REVERT: B 401 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7832 (tm-30) REVERT: C 87 MET cc_start: 0.4528 (mtt) cc_final: 0.3710 (mtt) REVERT: C 143 THR cc_start: 0.8677 (m) cc_final: 0.8298 (m) REVERT: C 151 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7947 (tt) REVERT: C 296 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7912 (mtt-85) REVERT: C 310 ASP cc_start: 0.8359 (m-30) cc_final: 0.8133 (m-30) REVERT: C 385 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7705 (ttp80) REVERT: C 427 MET cc_start: 0.8406 (ptt) cc_final: 0.8165 (ptt) REVERT: D 87 MET cc_start: 0.4531 (mtt) cc_final: 0.3699 (mtt) REVERT: D 143 THR cc_start: 0.8681 (m) cc_final: 0.8306 (m) REVERT: D 296 ARG cc_start: 0.8108 (mtt90) cc_final: 0.7875 (mtt-85) REVERT: D 310 ASP cc_start: 0.8367 (m-30) cc_final: 0.8136 (m-30) REVERT: D 427 MET cc_start: 0.8405 (ptt) cc_final: 0.8170 (ptt) outliers start: 30 outliers final: 26 residues processed: 200 average time/residue: 1.4711 time to fit residues: 315.9695 Evaluate side-chains 205 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 178 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 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 211 ARG Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 69 THR 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 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 69 THR 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 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: 0.5980 chunk 111 optimal weight: 0.0000 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 chunk 6 optimal weight: 0.0170 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 284 GLN ** 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 = 0.3773 r_free = 0.3773 target = 0.155172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126665 restraints weight = 12585.219| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.36 r_work: 0.3238 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12340 Z= 0.165 Angle : 0.499 7.883 16736 Z= 0.257 Chirality : 0.036 0.184 2056 Planarity : 0.003 0.037 2020 Dihedral : 3.699 13.763 1688 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.07 % Allowed : 19.53 % Favored : 78.40 % 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: 3.47 (0.21), residues: 1520 helix: 3.19 (0.14), residues: 1236 sheet: 1.32 (0.57), residues: 40 loop : -2.80 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 193 HIS 0.002 0.000 HIS D 392 PHE 0.015 0.001 PHE A 444 TYR 0.020 0.001 TYR B 124 ARG 0.003 0.000 ARG A 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5181.56 seconds wall clock time: 91 minutes 19.52 seconds (5479.52 seconds total)