Starting phenix.real_space_refine on Thu Jun 27 07:19:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/06_2024/8vv3_43548_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/06_2024/8vv3_43548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/06_2024/8vv3_43548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/06_2024/8vv3_43548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/06_2024/8vv3_43548_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/06_2024/8vv3_43548_updated.pdb" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.369 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 7928 2.51 5 N 2028 2.21 5 O 2084 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 "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 12172 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3031 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 2 Chain: "B" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3031 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 2 Chain: "C" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3031 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 2 Chain: "D" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3031 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.48, per 1000 atoms: 0.53 Number of scatterers: 12172 At special positions: 0 Unit cell: (111.072, 110.004, 93.984, 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 2084 8.00 N 2028 7.00 C 7928 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: 4.90 Conformation dependent library (CDL) restraints added in 1.8 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 4 sheets defined 77.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 removed outlier: 3.605A pdb=" N ILE A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 79 Processing helix chain 'A' and resid 91 through 112 Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 141 through 172 Processing helix chain 'A' and resid 179 through 226 removed outlier: 3.524A pdb=" N VAL A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 340 removed outlier: 5.157A 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 Processing helix chain 'A' and resid 345 through 388 Proline residue: A 368 - end of helix removed outlier: 3.882A pdb=" N GLU A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 409 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 424 through 444 removed outlier: 3.574A pdb=" N PHE A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 31 removed outlier: 3.605A pdb=" N ILE B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 26 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 79 Processing helix chain 'B' and resid 91 through 112 Processing helix chain 'B' and resid 114 through 135 Processing helix chain 'B' and resid 141 through 172 Processing helix chain 'B' and resid 179 through 226 removed outlier: 3.525A pdb=" N VAL B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 340 removed outlier: 5.156A 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 Processing helix chain 'B' and resid 345 through 388 Proline residue: B 368 - end of helix removed outlier: 3.883A pdb=" N GLU B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 409 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 424 through 444 removed outlier: 3.574A pdb=" N PHE B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 31 removed outlier: 3.604A pdb=" N ILE C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 26 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 79 Processing helix chain 'C' and resid 91 through 112 Processing helix chain 'C' and resid 114 through 135 Processing helix chain 'C' and resid 141 through 172 Processing helix chain 'C' and resid 179 through 226 removed outlier: 3.524A pdb=" N VAL C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 340 removed outlier: 5.156A 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 Processing helix chain 'C' and resid 345 through 388 Proline residue: C 368 - end of helix removed outlier: 3.882A pdb=" N GLU C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 409 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 424 through 444 removed outlier: 3.574A pdb=" N PHE C 444 " --> pdb=" O ILE C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 31 removed outlier: 3.604A pdb=" N ILE D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 26 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 79 Processing helix chain 'D' and resid 91 through 112 Processing helix chain 'D' and resid 114 through 135 Processing helix chain 'D' and resid 141 through 172 Processing helix chain 'D' and resid 179 through 226 removed outlier: 3.525A pdb=" N VAL D 183 " --> pdb=" O GLN D 179 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 340 removed outlier: 5.156A 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 Processing helix chain 'D' and resid 345 through 388 Proline residue: D 368 - end of helix removed outlier: 3.882A pdb=" N GLU D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 409 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 424 through 444 removed outlier: 3.574A pdb=" N PHE D 444 " --> pdb=" O ILE D 440 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 41 Processing sheet with id= B, first strand: chain 'B' and resid 37 through 41 Processing sheet with id= C, first strand: chain 'C' and resid 37 through 41 Processing sheet with id= D, first strand: chain 'D' and resid 37 through 41 968 hydrogen bonds defined for protein. 2904 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: 3.70 Time building geometry restraints manager: 5.27 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: 3767 1.34 - 1.46: 2167 1.46 - 1.58: 6274 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 12408 Sorted by residual: bond pdb=" C2 SOE D 501 " pdb=" O6 SOE D 501 " ideal model delta sigma weight residual 1.500 1.426 0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C2 SOE B 501 " pdb=" O6 SOE B 501 " ideal model delta sigma weight residual 1.500 1.427 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C2 SOE A 501 " pdb=" O6 SOE A 501 " ideal model delta sigma weight residual 1.500 1.427 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C2 SOE C 501 " pdb=" O6 SOE C 501 " ideal model delta sigma weight residual 1.500 1.427 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C2 SOE A 501 " pdb=" O2 SOE A 501 " ideal model delta sigma weight residual 1.358 1.427 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 12403 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.57: 324 106.57 - 113.42: 7128 113.42 - 120.27: 4261 120.27 - 127.13: 5007 127.13 - 133.98: 116 Bond angle restraints: 16836 Sorted by residual: angle pdb=" CA TYR A 124 " pdb=" CB TYR A 124 " pdb=" CG TYR A 124 " ideal model delta sigma weight residual 113.90 119.48 -5.58 1.80e+00 3.09e-01 9.61e+00 angle pdb=" CA TYR B 124 " pdb=" CB TYR B 124 " pdb=" CG TYR B 124 " ideal model delta sigma weight residual 113.90 119.48 -5.58 1.80e+00 3.09e-01 9.60e+00 angle pdb=" CA TYR C 124 " pdb=" CB TYR C 124 " pdb=" CG TYR C 124 " ideal model delta sigma weight residual 113.90 119.46 -5.56 1.80e+00 3.09e-01 9.53e+00 angle pdb=" CA TYR D 124 " pdb=" CB TYR D 124 " pdb=" CG TYR D 124 " ideal model delta sigma weight residual 113.90 119.44 -5.54 1.80e+00 3.09e-01 9.47e+00 angle pdb=" C SER C 123 " pdb=" N TYR C 124 " pdb=" CA TYR C 124 " ideal model delta sigma weight residual 120.72 115.72 5.00 1.67e+00 3.59e-01 8.98e+00 ... (remaining 16831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 6680 16.96 - 33.92: 644 33.92 - 50.88: 108 50.88 - 67.84: 32 67.84 - 84.80: 20 Dihedral angle restraints: 7484 sinusoidal: 2968 harmonic: 4516 Sorted by residual: dihedral pdb=" CG ARG B 361 " pdb=" CD ARG B 361 " pdb=" NE ARG B 361 " pdb=" CZ ARG B 361 " ideal model delta sinusoidal sigma weight residual -180.00 -135.34 -44.66 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG A 361 " pdb=" CD ARG A 361 " pdb=" NE ARG A 361 " pdb=" CZ ARG A 361 " ideal model delta sinusoidal sigma weight residual -180.00 -135.37 -44.63 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG C 361 " pdb=" CD ARG C 361 " pdb=" NE ARG C 361 " pdb=" CZ ARG C 361 " ideal model delta sinusoidal sigma weight residual -180.00 -135.39 -44.61 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 7481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1509 0.035 - 0.070: 426 0.070 - 0.104: 104 0.104 - 0.139: 29 0.139 - 0.174: 8 Chirality restraints: 2076 Sorted by residual: chirality pdb=" CA TYR D 124 " pdb=" N TYR D 124 " pdb=" C TYR D 124 " pdb=" CB TYR D 124 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA TYR C 124 " pdb=" N TYR C 124 " pdb=" C TYR C 124 " pdb=" CB TYR C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA TYR A 124 " pdb=" N TYR A 124 " pdb=" C TYR A 124 " pdb=" CB TYR A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 2073 not shown) Planarity restraints: 2024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 124 " -0.002 2.00e-02 2.50e+03 1.20e-02 2.87e+00 pdb=" CG TYR A 124 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 124 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 124 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 124 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 124 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 124 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 124 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 124 " -0.002 2.00e-02 2.50e+03 1.19e-02 2.83e+00 pdb=" CG TYR B 124 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 124 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 124 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 124 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 124 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 124 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 124 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 124 " 0.002 2.00e-02 2.50e+03 1.19e-02 2.82e+00 pdb=" CG TYR C 124 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 124 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 124 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 124 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 124 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR C 124 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 124 " 0.002 2.00e-02 2.50e+03 ... (remaining 2021 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2162 2.77 - 3.30: 12368 3.30 - 3.83: 21701 3.83 - 4.37: 24818 4.37 - 4.90: 42920 Nonbonded interactions: 103969 Sorted by model distance: nonbonded pdb=" OD1 ASN A 222 " pdb=" NH2 ARG A 385 " model vdw 2.233 2.520 nonbonded pdb=" OD1 ASN C 222 " pdb=" NH2 ARG C 385 " model vdw 2.233 2.520 nonbonded pdb=" OD1 ASN D 222 " pdb=" NH2 ARG D 385 " model vdw 2.233 2.520 nonbonded pdb=" OD1 ASN B 222 " pdb=" NH2 ARG B 385 " model vdw 2.234 2.520 nonbonded pdb=" OD1 ASP A 99 " pdb=" NE2 HIS A 326 " model vdw 2.249 2.520 ... (remaining 103964 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: 2.970 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: 15.210 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.640 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.004 0.074 12408 Z= 0.247 Angle : 0.523 6.136 16836 Z= 0.271 Chirality : 0.037 0.174 2076 Planarity : 0.004 0.025 2024 Dihedral : 14.374 84.801 4564 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 2.23 (0.21), residues: 1524 helix: 2.35 (0.14), residues: 1216 sheet: -0.35 (0.86), residues: 40 loop : -2.60 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.002 0.001 HIS A 22 PHE 0.014 0.001 PHE C 203 TYR 0.022 0.001 TYR A 124 ARG 0.002 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6924 (ttt180) cc_final: 0.6094 (ttm-80) REVERT: A 91 MET cc_start: 0.5187 (tpp) cc_final: 0.4524 (ttt) REVERT: A 118 MET cc_start: 0.8008 (mmp) cc_final: 0.7797 (mmp) REVERT: A 133 ARG cc_start: 0.6573 (ttm110) cc_final: 0.5926 (ttp-110) REVERT: A 171 MET cc_start: 0.6591 (mtm) cc_final: 0.6209 (mmt) REVERT: A 197 MET cc_start: 0.7804 (tpt) cc_final: 0.7594 (tpp) REVERT: A 215 LYS cc_start: 0.8154 (tttm) cc_final: 0.7769 (ttmt) REVERT: A 289 GLU cc_start: 0.7077 (tt0) cc_final: 0.6539 (mm-30) REVERT: A 303 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6923 (mt-10) REVERT: A 310 ASP cc_start: 0.7880 (m-30) cc_final: 0.7573 (m-30) REVERT: B 38 ARG cc_start: 0.6981 (ttt180) cc_final: 0.6170 (ttp-110) REVERT: B 46 TYR cc_start: 0.6974 (m-80) cc_final: 0.6355 (m-80) REVERT: B 52 LYS cc_start: 0.7290 (mttt) cc_final: 0.6998 (mmmt) REVERT: B 91 MET cc_start: 0.5277 (tpp) cc_final: 0.4652 (ttt) REVERT: B 133 ARG cc_start: 0.6975 (ttm110) cc_final: 0.6298 (ttp-110) REVERT: B 167 CYS cc_start: 0.7745 (m) cc_final: 0.7543 (m) REVERT: B 205 PHE cc_start: 0.7160 (m-80) cc_final: 0.6786 (m-80) REVERT: B 219 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7286 (mt-10) REVERT: B 303 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6798 (mt-10) REVERT: B 310 ASP cc_start: 0.7878 (m-30) cc_final: 0.7536 (m-30) REVERT: C 38 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6356 (ttp-110) REVERT: C 91 MET cc_start: 0.5131 (tpp) cc_final: 0.4731 (ttt) REVERT: C 118 MET cc_start: 0.8007 (mmp) cc_final: 0.7757 (mmp) REVERT: C 119 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6907 (mtm-85) REVERT: C 197 MET cc_start: 0.7816 (tpt) cc_final: 0.7522 (tpp) REVERT: C 215 LYS cc_start: 0.8143 (tttm) cc_final: 0.7653 (ttpt) REVERT: C 303 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6960 (mt-10) REVERT: D 38 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6296 (ttp-110) REVERT: D 46 TYR cc_start: 0.6785 (m-80) cc_final: 0.6304 (m-80) REVERT: D 60 ILE cc_start: 0.7859 (pt) cc_final: 0.7561 (mp) REVERT: D 91 MET cc_start: 0.5248 (tpp) cc_final: 0.4821 (ttt) REVERT: D 118 MET cc_start: 0.8186 (mmp) cc_final: 0.7947 (mmp) REVERT: D 119 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6733 (mtm-85) REVERT: D 133 ARG cc_start: 0.6714 (ttm110) cc_final: 0.5997 (ttp-110) REVERT: D 167 CYS cc_start: 0.7713 (m) cc_final: 0.7491 (m) REVERT: D 205 PHE cc_start: 0.7235 (m-80) cc_final: 0.6892 (m-80) REVERT: D 310 ASP cc_start: 0.7968 (m-30) cc_final: 0.7588 (m-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 1.2003 time to fit residues: 374.7140 Evaluate side-chains 217 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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: 0.5980 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7388 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12408 Z= 0.236 Angle : 0.543 6.735 16836 Z= 0.284 Chirality : 0.038 0.153 2076 Planarity : 0.004 0.040 2024 Dihedral : 3.699 14.104 1784 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.11 % Allowed : 9.02 % Favored : 87.87 % 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: 2.62 (0.21), residues: 1524 helix: 2.68 (0.14), residues: 1196 sheet: 0.51 (0.81), residues: 40 loop : -2.50 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.005 0.001 HIS D 22 PHE 0.017 0.002 PHE C 203 TYR 0.038 0.002 TYR C 124 ARG 0.004 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7207 (ttt180) cc_final: 0.6318 (ttm-80) REVERT: A 60 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7613 (mt) REVERT: A 91 MET cc_start: 0.5492 (tpp) cc_final: 0.4792 (ttt) REVERT: A 133 ARG cc_start: 0.6700 (ttm110) cc_final: 0.6366 (ttm110) REVERT: A 171 MET cc_start: 0.6675 (mtm) cc_final: 0.6197 (mmt) REVERT: A 179 GLN cc_start: 0.7009 (pm20) cc_final: 0.6525 (pm20) REVERT: A 215 LYS cc_start: 0.8166 (tttm) cc_final: 0.7831 (ttmt) REVERT: A 289 GLU cc_start: 0.7423 (tt0) cc_final: 0.6527 (mm-30) REVERT: A 310 ASP cc_start: 0.7941 (m-30) cc_final: 0.7620 (m-30) REVERT: A 387 MET cc_start: 0.7344 (mmm) cc_final: 0.7002 (mtp) REVERT: B 38 ARG cc_start: 0.7007 (ttt180) cc_final: 0.6140 (ttm-80) REVERT: B 46 TYR cc_start: 0.6837 (m-80) cc_final: 0.6218 (m-80) REVERT: B 52 LYS cc_start: 0.7319 (mttt) cc_final: 0.6974 (mmmt) REVERT: B 91 MET cc_start: 0.5442 (tpp) cc_final: 0.4852 (ttt) REVERT: B 128 ILE cc_start: 0.5896 (OUTLIER) cc_final: 0.5464 (mm) REVERT: B 133 ARG cc_start: 0.6961 (ttm110) cc_final: 0.6670 (ttm110) REVERT: B 164 ASP cc_start: 0.7786 (t70) cc_final: 0.7560 (t70) REVERT: B 172 GLN cc_start: 0.6764 (mm110) cc_final: 0.6389 (mt0) REVERT: B 215 LYS cc_start: 0.8530 (mtpm) cc_final: 0.8275 (mtpt) REVERT: B 303 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6891 (mt-10) REVERT: B 310 ASP cc_start: 0.7907 (m-30) cc_final: 0.7551 (m-30) REVERT: C 38 ARG cc_start: 0.7363 (ttt180) cc_final: 0.6405 (ttp-110) REVERT: C 52 LYS cc_start: 0.7231 (mttt) cc_final: 0.6893 (mmmt) REVERT: C 91 MET cc_start: 0.5300 (tpp) cc_final: 0.4865 (ttt) REVERT: C 119 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6884 (mtm-85) REVERT: C 133 ARG cc_start: 0.6224 (ttm110) cc_final: 0.5644 (ttp-110) REVERT: C 179 GLN cc_start: 0.6724 (pm20) cc_final: 0.6223 (pm20) REVERT: C 215 LYS cc_start: 0.8180 (tttm) cc_final: 0.7877 (ttpt) REVERT: C 289 GLU cc_start: 0.7423 (tt0) cc_final: 0.6446 (mm-30) REVERT: C 435 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7733 (m) REVERT: D 38 ARG cc_start: 0.7090 (ttt180) cc_final: 0.6182 (ttp-110) REVERT: D 46 TYR cc_start: 0.6803 (m-80) cc_final: 0.6284 (m-80) REVERT: D 52 LYS cc_start: 0.7410 (mttt) cc_final: 0.7048 (mmmt) REVERT: D 60 ILE cc_start: 0.7839 (pt) cc_final: 0.7615 (mp) REVERT: D 91 MET cc_start: 0.5521 (tpp) cc_final: 0.5035 (ttt) REVERT: D 119 ARG cc_start: 0.7103 (mtm-85) cc_final: 0.6703 (mtm-85) REVERT: D 133 ARG cc_start: 0.6699 (ttm110) cc_final: 0.6435 (ttm110) REVERT: D 179 GLN cc_start: 0.6771 (pm20) cc_final: 0.6304 (pm20) REVERT: D 219 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7181 (mt-10) REVERT: D 289 GLU cc_start: 0.7457 (tt0) cc_final: 0.6483 (mm-30) REVERT: D 310 ASP cc_start: 0.8021 (m-30) cc_final: 0.7634 (m-30) REVERT: D 387 MET cc_start: 0.7521 (mmm) cc_final: 0.7082 (mtt) REVERT: D 435 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7770 (p) outliers start: 42 outliers final: 22 residues processed: 242 average time/residue: 1.2805 time to fit residues: 334.9387 Evaluate side-chains 240 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 214 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 435 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: 0.8980 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 47 optimal weight: 0.0980 chunk 110 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12408 Z= 0.239 Angle : 0.540 5.274 16836 Z= 0.283 Chirality : 0.037 0.127 2076 Planarity : 0.004 0.031 2024 Dihedral : 3.736 14.186 1784 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.99 % Allowed : 11.69 % Favored : 84.32 % 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: 2.62 (0.21), residues: 1524 helix: 2.68 (0.14), residues: 1200 sheet: 0.38 (0.78), residues: 40 loop : -2.54 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.004 0.001 HIS C 22 PHE 0.017 0.002 PHE A 203 TYR 0.032 0.002 TYR C 124 ARG 0.003 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 218 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7090 (ttt180) cc_final: 0.6246 (ttm-80) REVERT: A 60 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7663 (mt) REVERT: A 91 MET cc_start: 0.5378 (tpp) cc_final: 0.4757 (ttt) REVERT: A 133 ARG cc_start: 0.6755 (ttm110) cc_final: 0.6036 (ttp-110) REVERT: A 171 MET cc_start: 0.6654 (mtm) cc_final: 0.6177 (mmt) REVERT: A 179 GLN cc_start: 0.6925 (pm20) cc_final: 0.6393 (pm20) REVERT: A 215 LYS cc_start: 0.8173 (tttm) cc_final: 0.7869 (ttpt) REVERT: A 289 GLU cc_start: 0.7442 (tt0) cc_final: 0.6629 (mm-30) REVERT: A 310 ASP cc_start: 0.7934 (m-30) cc_final: 0.7603 (m-30) REVERT: A 387 MET cc_start: 0.7387 (mmm) cc_final: 0.7035 (OUTLIER) REVERT: B 38 ARG cc_start: 0.7076 (ttt180) cc_final: 0.6236 (ttp-110) REVERT: B 46 TYR cc_start: 0.6929 (m-80) cc_final: 0.6239 (m-80) REVERT: B 52 LYS cc_start: 0.7327 (mttt) cc_final: 0.6976 (mmmt) REVERT: B 91 MET cc_start: 0.5469 (tpp) cc_final: 0.4895 (ttt) REVERT: B 128 ILE cc_start: 0.5940 (OUTLIER) cc_final: 0.5522 (mm) REVERT: B 133 ARG cc_start: 0.6988 (ttm110) cc_final: 0.6676 (ttm110) REVERT: B 172 GLN cc_start: 0.6749 (mm110) cc_final: 0.6368 (mt0) REVERT: B 215 LYS cc_start: 0.8513 (mtpm) cc_final: 0.8287 (mtpt) REVERT: B 310 ASP cc_start: 0.7887 (m-30) cc_final: 0.7529 (m-30) REVERT: C 38 ARG cc_start: 0.7300 (ttt180) cc_final: 0.6352 (ttp-110) REVERT: C 52 LYS cc_start: 0.7374 (mttt) cc_final: 0.7021 (mmmt) REVERT: C 91 MET cc_start: 0.5406 (tpp) cc_final: 0.4988 (ttt) REVERT: C 119 ARG cc_start: 0.7134 (mtm-85) cc_final: 0.6777 (mtm-85) REVERT: C 133 ARG cc_start: 0.6387 (ttm110) cc_final: 0.5724 (ttp-110) REVERT: C 179 GLN cc_start: 0.6852 (pm20) cc_final: 0.6330 (pm20) REVERT: C 215 LYS cc_start: 0.8189 (tttm) cc_final: 0.7895 (ttmt) REVERT: C 310 ASP cc_start: 0.7760 (m-30) cc_final: 0.7473 (m-30) REVERT: C 435 THR cc_start: 0.8061 (p) cc_final: 0.7778 (p) REVERT: D 38 ARG cc_start: 0.7108 (ttt180) cc_final: 0.6217 (ttp-110) REVERT: D 46 TYR cc_start: 0.6854 (m-80) cc_final: 0.6319 (m-80) REVERT: D 52 LYS cc_start: 0.7412 (mttt) cc_final: 0.7037 (mmmt) REVERT: D 91 MET cc_start: 0.5565 (tpp) cc_final: 0.5100 (ttt) REVERT: D 119 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6684 (mtm-85) REVERT: D 133 ARG cc_start: 0.6737 (ttm110) cc_final: 0.6465 (ttm110) REVERT: D 179 GLN cc_start: 0.6718 (pm20) cc_final: 0.6302 (pm20) REVERT: D 219 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7150 (mt-10) REVERT: D 289 GLU cc_start: 0.7463 (tt0) cc_final: 0.6536 (mm-30) REVERT: D 310 ASP cc_start: 0.8005 (m-30) cc_final: 0.7628 (m-30) REVERT: D 387 MET cc_start: 0.7469 (mmm) cc_final: 0.7122 (mtt) REVERT: D 435 THR cc_start: 0.8141 (p) cc_final: 0.7855 (p) outliers start: 54 outliers final: 37 residues processed: 249 average time/residue: 1.2247 time to fit residues: 330.1967 Evaluate side-chains 250 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 212 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 443 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 71 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 92 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12408 Z= 0.200 Angle : 0.515 6.928 16836 Z= 0.269 Chirality : 0.036 0.130 2076 Planarity : 0.004 0.030 2024 Dihedral : 3.639 14.142 1784 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.77 % Allowed : 14.13 % Favored : 82.10 % 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: 2.74 (0.21), residues: 1524 helix: 2.78 (0.14), residues: 1200 sheet: 0.33 (0.75), residues: 40 loop : -2.58 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.003 0.001 HIS D 22 PHE 0.017 0.002 PHE A 203 TYR 0.027 0.001 TYR C 124 ARG 0.002 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 216 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7152 (ttt180) cc_final: 0.6245 (ttm-80) REVERT: A 60 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7751 (mt) REVERT: A 91 MET cc_start: 0.5337 (tpp) cc_final: 0.4758 (ttt) REVERT: A 133 ARG cc_start: 0.6672 (ttm110) cc_final: 0.6359 (ttm110) REVERT: A 171 MET cc_start: 0.6687 (mtm) cc_final: 0.6177 (mmt) REVERT: A 179 GLN cc_start: 0.6984 (pm20) cc_final: 0.6605 (pm20) REVERT: A 215 LYS cc_start: 0.8158 (tttm) cc_final: 0.7872 (ttmt) REVERT: A 289 GLU cc_start: 0.7415 (tt0) cc_final: 0.6593 (mm-30) REVERT: A 310 ASP cc_start: 0.7933 (m-30) cc_final: 0.7603 (m-30) REVERT: A 387 MET cc_start: 0.7299 (mmm) cc_final: 0.6862 (OUTLIER) REVERT: B 38 ARG cc_start: 0.7104 (ttt180) cc_final: 0.6267 (ttp-110) REVERT: B 52 LYS cc_start: 0.7346 (mttt) cc_final: 0.7022 (mmmt) REVERT: B 60 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7716 (mt) REVERT: B 91 MET cc_start: 0.5464 (tpp) cc_final: 0.4892 (ttt) REVERT: B 128 ILE cc_start: 0.5923 (OUTLIER) cc_final: 0.5530 (mm) REVERT: B 133 ARG cc_start: 0.6889 (ttm110) cc_final: 0.6601 (ttm110) REVERT: B 215 LYS cc_start: 0.8496 (mtpm) cc_final: 0.8268 (mtpt) REVERT: B 310 ASP cc_start: 0.7881 (m-30) cc_final: 0.7519 (m-30) REVERT: C 38 ARG cc_start: 0.7247 (ttt180) cc_final: 0.6308 (ttp-110) REVERT: C 46 TYR cc_start: 0.7015 (m-80) cc_final: 0.6544 (m-80) REVERT: C 52 LYS cc_start: 0.7377 (mttt) cc_final: 0.7038 (mmmt) REVERT: C 91 MET cc_start: 0.5410 (tpp) cc_final: 0.4977 (ttt) REVERT: C 119 ARG cc_start: 0.7013 (mtm-85) cc_final: 0.6637 (mtm-85) REVERT: C 133 ARG cc_start: 0.6425 (ttm110) cc_final: 0.5736 (ttp-110) REVERT: C 179 GLN cc_start: 0.6862 (pm20) cc_final: 0.6324 (pm20) REVERT: C 215 LYS cc_start: 0.8141 (tttm) cc_final: 0.7853 (ttmt) REVERT: C 310 ASP cc_start: 0.7756 (m-30) cc_final: 0.7454 (m-30) REVERT: C 435 THR cc_start: 0.8040 (p) cc_final: 0.7752 (p) REVERT: D 38 ARG cc_start: 0.7127 (ttt180) cc_final: 0.6223 (ttp-110) REVERT: D 46 TYR cc_start: 0.6968 (m-80) cc_final: 0.6425 (m-80) REVERT: D 52 LYS cc_start: 0.7375 (mttt) cc_final: 0.7014 (mmmt) REVERT: D 91 MET cc_start: 0.5563 (tpp) cc_final: 0.5101 (ttt) REVERT: D 119 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6581 (mtm-85) REVERT: D 133 ARG cc_start: 0.6702 (ttm110) cc_final: 0.6404 (ttm110) REVERT: D 179 GLN cc_start: 0.6776 (pm20) cc_final: 0.6332 (pm20) REVERT: D 289 GLU cc_start: 0.7439 (tt0) cc_final: 0.6530 (mm-30) REVERT: D 310 ASP cc_start: 0.7886 (m-30) cc_final: 0.7515 (m-30) REVERT: D 435 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7807 (p) outliers start: 51 outliers final: 37 residues processed: 249 average time/residue: 1.1892 time to fit residues: 321.8203 Evaluate side-chains 252 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 212 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 435 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN D 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12408 Z= 0.313 Angle : 0.615 8.319 16836 Z= 0.317 Chirality : 0.040 0.152 2076 Planarity : 0.005 0.034 2024 Dihedral : 3.962 15.469 1784 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.62 % Allowed : 14.28 % 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: 2.29 (0.21), residues: 1524 helix: 2.38 (0.14), residues: 1220 sheet: 0.44 (0.72), residues: 40 loop : -2.73 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.006 0.001 HIS C 22 PHE 0.018 0.002 PHE A 203 TYR 0.027 0.002 TYR C 124 ARG 0.004 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 215 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7224 (ttt180) cc_final: 0.6363 (ttm-80) REVERT: A 60 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7722 (mt) REVERT: A 91 MET cc_start: 0.5358 (tpp) cc_final: 0.4819 (ttt) REVERT: A 119 ARG cc_start: 0.6934 (mtm-85) cc_final: 0.6482 (mtm-85) REVERT: A 133 ARG cc_start: 0.6959 (ttm110) cc_final: 0.6282 (ttp-110) REVERT: A 171 MET cc_start: 0.6846 (mtm) cc_final: 0.6293 (mmt) REVERT: A 179 GLN cc_start: 0.7225 (pm20) cc_final: 0.6921 (pm20) REVERT: A 215 LYS cc_start: 0.8275 (tttm) cc_final: 0.7988 (ttpt) REVERT: A 310 ASP cc_start: 0.7912 (m-30) cc_final: 0.7576 (m-30) REVERT: B 38 ARG cc_start: 0.7219 (ttt180) cc_final: 0.6301 (ttm-80) REVERT: B 46 TYR cc_start: 0.6780 (m-80) cc_final: 0.6171 (m-80) REVERT: B 52 LYS cc_start: 0.7359 (mttt) cc_final: 0.7018 (mmmt) REVERT: B 60 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7753 (mt) REVERT: B 91 MET cc_start: 0.5504 (tpp) cc_final: 0.4969 (ttt) REVERT: B 119 ARG cc_start: 0.6989 (mtm-85) cc_final: 0.6540 (mtm-85) REVERT: B 133 ARG cc_start: 0.6936 (ttm110) cc_final: 0.6254 (ttp-110) REVERT: B 215 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8295 (mtpt) REVERT: B 310 ASP cc_start: 0.7900 (m-30) cc_final: 0.7549 (m-30) REVERT: C 38 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6316 (ttp-110) REVERT: C 46 TYR cc_start: 0.7120 (m-80) cc_final: 0.6656 (m-80) REVERT: C 52 LYS cc_start: 0.7360 (mttt) cc_final: 0.7022 (mmmt) REVERT: C 91 MET cc_start: 0.5445 (tpp) cc_final: 0.5028 (ttt) REVERT: C 119 ARG cc_start: 0.7166 (mtm-85) cc_final: 0.6669 (mtm-85) REVERT: C 126 GLU cc_start: 0.4841 (pt0) cc_final: 0.4271 (mm-30) REVERT: C 133 ARG cc_start: 0.6732 (ttm110) cc_final: 0.6038 (ttp-110) REVERT: C 179 GLN cc_start: 0.6941 (pm20) cc_final: 0.6627 (pm20) REVERT: C 215 LYS cc_start: 0.8303 (tttm) cc_final: 0.8002 (ttpt) REVERT: C 310 ASP cc_start: 0.7902 (m-30) cc_final: 0.7575 (m-30) REVERT: C 435 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7772 (p) REVERT: D 38 ARG cc_start: 0.7179 (ttt180) cc_final: 0.6267 (ttm-80) REVERT: D 46 TYR cc_start: 0.6941 (m-80) cc_final: 0.6473 (m-80) REVERT: D 52 LYS cc_start: 0.7396 (mttt) cc_final: 0.7059 (mmmt) REVERT: D 91 MET cc_start: 0.5571 (tpp) cc_final: 0.5141 (ttt) REVERT: D 119 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6635 (mtm-85) REVERT: D 133 ARG cc_start: 0.6910 (ttm110) cc_final: 0.6602 (ttm110) REVERT: D 179 GLN cc_start: 0.6816 (pm20) cc_final: 0.6447 (pm20) REVERT: D 310 ASP cc_start: 0.7900 (m-30) cc_final: 0.7556 (m-30) REVERT: D 435 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7799 (p) outliers start: 76 outliers final: 52 residues processed: 268 average time/residue: 1.1874 time to fit residues: 347.1683 Evaluate side-chains 271 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 214 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 435 THR 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: 0.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 36 optimal weight: 0.0970 chunk 147 optimal weight: 0.0470 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12408 Z= 0.201 Angle : 0.534 8.291 16836 Z= 0.276 Chirality : 0.036 0.168 2076 Planarity : 0.004 0.032 2024 Dihedral : 3.740 14.745 1784 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.36 % Allowed : 17.09 % Favored : 78.55 % 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: 2.59 (0.21), residues: 1524 helix: 2.65 (0.14), residues: 1212 sheet: 0.62 (0.68), residues: 40 loop : -2.79 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.003 0.001 HIS D 22 PHE 0.016 0.002 PHE A 203 TYR 0.023 0.001 TYR D 124 ARG 0.002 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 215 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7246 (ttt180) cc_final: 0.6362 (ttm-80) REVERT: A 60 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7751 (mt) REVERT: A 91 MET cc_start: 0.5342 (tpp) cc_final: 0.4808 (ttt) REVERT: A 133 ARG cc_start: 0.6705 (ttm110) cc_final: 0.6386 (ttm110) REVERT: A 171 MET cc_start: 0.6839 (mtm) cc_final: 0.6316 (mmt) REVERT: A 179 GLN cc_start: 0.7267 (pm20) cc_final: 0.6862 (pm20) REVERT: A 215 LYS cc_start: 0.8215 (tttm) cc_final: 0.7851 (ttmt) REVERT: A 273 MET cc_start: 0.5518 (mmm) cc_final: 0.5262 (tpt) REVERT: A 310 ASP cc_start: 0.7890 (m-30) cc_final: 0.7547 (m-30) REVERT: B 38 ARG cc_start: 0.7235 (ttt180) cc_final: 0.6331 (ttm-80) REVERT: B 52 LYS cc_start: 0.7418 (mttt) cc_final: 0.7122 (mmmt) REVERT: B 60 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7812 (mt) REVERT: B 91 MET cc_start: 0.5495 (tpp) cc_final: 0.4961 (ttt) REVERT: B 133 ARG cc_start: 0.6901 (ttm110) cc_final: 0.6590 (ttm110) REVERT: B 215 LYS cc_start: 0.8507 (mtpm) cc_final: 0.8237 (mtpt) REVERT: B 219 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7213 (mt-10) REVERT: B 310 ASP cc_start: 0.7880 (m-30) cc_final: 0.7525 (m-30) REVERT: C 38 ARG cc_start: 0.7263 (ttt180) cc_final: 0.6327 (ttp-110) REVERT: C 46 TYR cc_start: 0.7106 (m-80) cc_final: 0.6629 (m-80) REVERT: C 52 LYS cc_start: 0.7341 (mttt) cc_final: 0.7030 (mmmt) REVERT: C 91 MET cc_start: 0.5508 (tpp) cc_final: 0.5054 (ttt) REVERT: C 119 ARG cc_start: 0.6943 (mtm-85) cc_final: 0.6548 (mtm-85) REVERT: C 133 ARG cc_start: 0.6581 (ttm110) cc_final: 0.5824 (ttp-110) REVERT: C 179 GLN cc_start: 0.6976 (pm20) cc_final: 0.6633 (pm20) REVERT: C 215 LYS cc_start: 0.8244 (tttm) cc_final: 0.7882 (ttmt) REVERT: C 310 ASP cc_start: 0.7747 (m-30) cc_final: 0.7443 (m-30) REVERT: C 435 THR cc_start: 0.8018 (p) cc_final: 0.7739 (m) REVERT: D 38 ARG cc_start: 0.7165 (ttt180) cc_final: 0.6263 (ttp-110) REVERT: D 46 TYR cc_start: 0.6970 (m-80) cc_final: 0.6467 (m-80) REVERT: D 52 LYS cc_start: 0.7365 (mttt) cc_final: 0.7023 (mmmt) REVERT: D 91 MET cc_start: 0.5597 (tpp) cc_final: 0.5101 (ttt) REVERT: D 133 ARG cc_start: 0.6758 (ttm110) cc_final: 0.6475 (ttm110) REVERT: D 179 GLN cc_start: 0.6933 (pm20) cc_final: 0.6489 (pm20) REVERT: D 310 ASP cc_start: 0.7875 (m-30) cc_final: 0.7522 (m-30) REVERT: D 435 THR cc_start: 0.8028 (p) cc_final: 0.7761 (m) outliers start: 59 outliers final: 46 residues processed: 260 average time/residue: 1.1856 time to fit residues: 334.8292 Evaluate side-chains 258 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 210 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 356 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7435 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12408 Z= 0.273 Angle : 0.590 9.852 16836 Z= 0.302 Chirality : 0.038 0.165 2076 Planarity : 0.004 0.033 2024 Dihedral : 3.878 15.201 1784 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.40 % Allowed : 16.27 % Favored : 78.33 % 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: 2.41 (0.21), residues: 1524 helix: 2.50 (0.14), residues: 1216 sheet: 0.63 (0.67), residues: 40 loop : -2.86 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 354 HIS 0.004 0.001 HIS C 22 PHE 0.018 0.002 PHE A 203 TYR 0.024 0.002 TYR A 124 ARG 0.004 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 209 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7294 (ttt180) cc_final: 0.6400 (ttm-80) REVERT: A 60 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7747 (mt) REVERT: A 91 MET cc_start: 0.5419 (tpp) cc_final: 0.4873 (ttt) REVERT: A 133 ARG cc_start: 0.6760 (ttm110) cc_final: 0.6442 (ttm110) REVERT: A 171 MET cc_start: 0.6952 (mtm) cc_final: 0.6399 (mmt) REVERT: A 179 GLN cc_start: 0.7275 (pm20) cc_final: 0.7050 (pm20) REVERT: A 215 LYS cc_start: 0.8262 (tttm) cc_final: 0.7902 (ttpp) REVERT: A 289 GLU cc_start: 0.7704 (tt0) cc_final: 0.7187 (tt0) REVERT: A 310 ASP cc_start: 0.7881 (m-30) cc_final: 0.7548 (m-30) REVERT: B 38 ARG cc_start: 0.7219 (ttt180) cc_final: 0.6327 (ttm-80) REVERT: B 52 LYS cc_start: 0.7446 (mttt) cc_final: 0.7132 (mmmt) REVERT: B 60 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7809 (mt) REVERT: B 91 MET cc_start: 0.5623 (tpp) cc_final: 0.5067 (ttt) REVERT: B 133 ARG cc_start: 0.6936 (ttm110) cc_final: 0.6323 (ttp-110) REVERT: B 215 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8259 (mtpt) REVERT: B 310 ASP cc_start: 0.7884 (m-30) cc_final: 0.7523 (m-30) REVERT: C 38 ARG cc_start: 0.7244 (ttt180) cc_final: 0.6329 (ttp-110) REVERT: C 46 TYR cc_start: 0.7026 (m-80) cc_final: 0.6570 (m-80) REVERT: C 52 LYS cc_start: 0.7289 (mttt) cc_final: 0.7039 (mmmt) REVERT: C 91 MET cc_start: 0.5505 (tpp) cc_final: 0.5072 (ttt) REVERT: C 119 ARG cc_start: 0.6945 (mtm-85) cc_final: 0.6570 (mtm-85) REVERT: C 133 ARG cc_start: 0.6656 (ttm110) cc_final: 0.6353 (ttm110) REVERT: C 179 GLN cc_start: 0.6968 (pm20) cc_final: 0.6545 (pm20) REVERT: C 215 LYS cc_start: 0.8261 (tttm) cc_final: 0.7937 (ttpp) REVERT: C 310 ASP cc_start: 0.7866 (m-30) cc_final: 0.7546 (m-30) REVERT: C 435 THR cc_start: 0.8037 (p) cc_final: 0.7757 (m) REVERT: D 38 ARG cc_start: 0.7188 (ttt180) cc_final: 0.6270 (ttm-80) REVERT: D 46 TYR cc_start: 0.6930 (m-80) cc_final: 0.6414 (m-80) REVERT: D 52 LYS cc_start: 0.7417 (mttt) cc_final: 0.7069 (mmmt) REVERT: D 60 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7793 (mt) REVERT: D 91 MET cc_start: 0.5631 (tpp) cc_final: 0.5160 (ttt) REVERT: D 119 ARG cc_start: 0.6989 (mtm-85) cc_final: 0.6569 (mtm-85) REVERT: D 133 ARG cc_start: 0.6813 (ttm110) cc_final: 0.6527 (ttm110) REVERT: D 179 GLN cc_start: 0.6953 (pm20) cc_final: 0.6600 (pm20) REVERT: D 289 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6911 (tt0) REVERT: D 310 ASP cc_start: 0.7872 (m-30) cc_final: 0.7525 (m-30) REVERT: D 435 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7817 (m) outliers start: 73 outliers final: 55 residues processed: 262 average time/residue: 1.1748 time to fit residues: 335.0558 Evaluate side-chains 269 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 208 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 435 THR 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: 0.9980 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7430 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 12408 Z= 0.263 Angle : 0.593 9.931 16836 Z= 0.302 Chirality : 0.038 0.144 2076 Planarity : 0.004 0.034 2024 Dihedral : 3.890 15.335 1784 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.03 % Allowed : 16.94 % Favored : 78.03 % 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: 2.40 (0.21), residues: 1524 helix: 2.50 (0.14), residues: 1216 sheet: 0.62 (0.67), residues: 40 loop : -2.87 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 354 HIS 0.004 0.001 HIS C 22 PHE 0.017 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.003 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 210 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7300 (ttt180) cc_final: 0.6413 (ttm-80) REVERT: A 60 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7744 (mt) REVERT: A 91 MET cc_start: 0.5513 (tpp) cc_final: 0.4988 (ttt) REVERT: A 133 ARG cc_start: 0.6759 (ttm110) cc_final: 0.6051 (ttp-110) REVERT: A 179 GLN cc_start: 0.7286 (pm20) cc_final: 0.7057 (pm20) REVERT: A 215 LYS cc_start: 0.8240 (tttm) cc_final: 0.7903 (ttpp) REVERT: A 310 ASP cc_start: 0.7915 (m-30) cc_final: 0.7586 (m-30) REVERT: B 38 ARG cc_start: 0.7227 (ttt180) cc_final: 0.6340 (ttm-80) REVERT: B 52 LYS cc_start: 0.7423 (mttt) cc_final: 0.7124 (mmmt) REVERT: B 60 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7827 (mt) REVERT: B 91 MET cc_start: 0.5633 (tpp) cc_final: 0.5090 (ttt) REVERT: B 133 ARG cc_start: 0.6926 (ttm110) cc_final: 0.6323 (ttp-110) REVERT: B 215 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8252 (mtpt) REVERT: B 219 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7191 (mt-10) REVERT: B 310 ASP cc_start: 0.7878 (m-30) cc_final: 0.7520 (m-30) REVERT: C 38 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6325 (ttp-110) REVERT: C 46 TYR cc_start: 0.7000 (m-80) cc_final: 0.6542 (m-80) REVERT: C 52 LYS cc_start: 0.7293 (mttt) cc_final: 0.7053 (mmmt) REVERT: C 60 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7744 (mt) REVERT: C 91 MET cc_start: 0.5540 (tpp) cc_final: 0.5134 (ttt) REVERT: C 119 ARG cc_start: 0.6936 (mtm-85) cc_final: 0.6541 (mtm-85) REVERT: C 133 ARG cc_start: 0.6670 (ttm110) cc_final: 0.6355 (ttm110) REVERT: C 179 GLN cc_start: 0.7029 (pm20) cc_final: 0.6710 (pm20) REVERT: C 310 ASP cc_start: 0.7855 (m-30) cc_final: 0.7530 (m-30) REVERT: C 387 MET cc_start: 0.7407 (mmm) cc_final: 0.7063 (mtt) REVERT: C 419 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.6552 (mmm) REVERT: C 435 THR cc_start: 0.8048 (p) cc_final: 0.7773 (m) REVERT: D 38 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6277 (ttm-80) REVERT: D 46 TYR cc_start: 0.6987 (m-80) cc_final: 0.6472 (m-80) REVERT: D 52 LYS cc_start: 0.7384 (mttt) cc_final: 0.7065 (mmmt) REVERT: D 60 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7760 (mt) REVERT: D 91 MET cc_start: 0.5629 (tpp) cc_final: 0.5167 (ttt) REVERT: D 119 ARG cc_start: 0.6982 (mtm-85) cc_final: 0.6481 (mtm-85) REVERT: D 133 ARG cc_start: 0.6801 (ttm110) cc_final: 0.6508 (ttm110) REVERT: D 179 GLN cc_start: 0.6920 (pm20) cc_final: 0.6523 (pm20) REVERT: D 289 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6917 (tt0) REVERT: D 310 ASP cc_start: 0.7869 (m-30) cc_final: 0.7522 (m-30) REVERT: D 387 MET cc_start: 0.7372 (mmm) cc_final: 0.7088 (mtt) REVERT: D 435 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7817 (m) outliers start: 68 outliers final: 55 residues processed: 261 average time/residue: 1.1357 time to fit residues: 322.8229 Evaluate side-chains 271 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 208 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 435 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 0.2980 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7417 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12408 Z= 0.227 Angle : 0.566 9.041 16836 Z= 0.290 Chirality : 0.037 0.134 2076 Planarity : 0.004 0.034 2024 Dihedral : 3.839 16.957 1784 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.88 % Allowed : 17.46 % Favored : 77.66 % 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: 2.48 (0.21), residues: 1524 helix: 2.53 (0.14), residues: 1220 sheet: 0.61 (0.66), residues: 40 loop : -2.77 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 354 HIS 0.003 0.001 HIS C 22 PHE 0.017 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.002 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 217 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7307 (ttt180) cc_final: 0.6414 (ttm-80) REVERT: A 60 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7748 (mt) REVERT: A 91 MET cc_start: 0.5519 (tpp) cc_final: 0.4990 (ttt) REVERT: A 133 ARG cc_start: 0.6698 (ttm110) cc_final: 0.6002 (ttp-110) REVERT: A 179 GLN cc_start: 0.7289 (pm20) cc_final: 0.7011 (pm20) REVERT: A 215 LYS cc_start: 0.8189 (tttm) cc_final: 0.7870 (ttpp) REVERT: A 274 MET cc_start: 0.3294 (tpp) cc_final: 0.2483 (mmt) REVERT: A 310 ASP cc_start: 0.7852 (m-30) cc_final: 0.7507 (m-30) REVERT: B 38 ARG cc_start: 0.7232 (ttt180) cc_final: 0.6335 (ttm-80) REVERT: B 52 LYS cc_start: 0.7428 (mttt) cc_final: 0.7129 (mmmt) REVERT: B 60 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7813 (mt) REVERT: B 91 MET cc_start: 0.5641 (tpp) cc_final: 0.5114 (ttt) REVERT: B 133 ARG cc_start: 0.6875 (ttm110) cc_final: 0.6186 (ttp-110) REVERT: B 215 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8271 (mtpt) REVERT: B 219 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7191 (mt-10) REVERT: B 310 ASP cc_start: 0.7896 (m-30) cc_final: 0.7530 (m-30) REVERT: C 38 ARG cc_start: 0.7226 (ttt180) cc_final: 0.6327 (ttp-110) REVERT: C 46 TYR cc_start: 0.7044 (m-80) cc_final: 0.6533 (m-80) REVERT: C 52 LYS cc_start: 0.7296 (mttt) cc_final: 0.7055 (mmmt) REVERT: C 60 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7775 (mt) REVERT: C 91 MET cc_start: 0.5491 (tpp) cc_final: 0.5044 (ttt) REVERT: C 119 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6515 (mtm-85) REVERT: C 133 ARG cc_start: 0.6616 (ttm110) cc_final: 0.6335 (ttm110) REVERT: C 179 GLN cc_start: 0.7010 (pm20) cc_final: 0.6637 (pm20) REVERT: C 297 MET cc_start: 0.7784 (mtm) cc_final: 0.7491 (ttp) REVERT: C 310 ASP cc_start: 0.7728 (m-30) cc_final: 0.7431 (m-30) REVERT: C 387 MET cc_start: 0.7327 (mmm) cc_final: 0.7035 (mtt) REVERT: C 435 THR cc_start: 0.8031 (p) cc_final: 0.7771 (m) REVERT: D 38 ARG cc_start: 0.7220 (ttt180) cc_final: 0.6300 (ttm-80) REVERT: D 46 TYR cc_start: 0.6968 (m-80) cc_final: 0.6395 (m-80) REVERT: D 52 LYS cc_start: 0.7370 (mttt) cc_final: 0.7038 (mmmt) REVERT: D 60 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7816 (mt) REVERT: D 91 MET cc_start: 0.5616 (tpp) cc_final: 0.5135 (ttt) REVERT: D 133 ARG cc_start: 0.6693 (ttm110) cc_final: 0.6415 (ttm110) REVERT: D 179 GLN cc_start: 0.6944 (pm20) cc_final: 0.6628 (pm20) REVERT: D 289 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6934 (tt0) REVERT: D 310 ASP cc_start: 0.7883 (m-30) cc_final: 0.7533 (m-30) REVERT: D 419 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.6859 (mmm) REVERT: D 435 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7813 (m) outliers start: 66 outliers final: 56 residues processed: 268 average time/residue: 1.1817 time to fit residues: 344.0820 Evaluate side-chains 274 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 210 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 435 THR 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: 1.9990 chunk 100 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 12 optimal weight: 0.0370 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12408 Z= 0.241 Angle : 0.579 9.380 16836 Z= 0.296 Chirality : 0.038 0.161 2076 Planarity : 0.004 0.034 2024 Dihedral : 3.857 17.156 1784 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.10 % Allowed : 17.53 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.21), residues: 1524 helix: 2.48 (0.14), residues: 1220 sheet: 0.61 (0.66), residues: 40 loop : -2.80 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 354 HIS 0.004 0.001 HIS C 22 PHE 0.018 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.002 0.000 ARG A 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 211 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7314 (ttt180) cc_final: 0.6427 (ttm-80) REVERT: A 60 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7744 (mt) REVERT: A 91 MET cc_start: 0.5517 (tpp) cc_final: 0.4977 (ttt) REVERT: A 133 ARG cc_start: 0.6713 (ttm110) cc_final: 0.6012 (ttp-110) REVERT: A 215 LYS cc_start: 0.8195 (tttm) cc_final: 0.7888 (ttpp) REVERT: A 274 MET cc_start: 0.3566 (tpp) cc_final: 0.2637 (mmt) REVERT: A 310 ASP cc_start: 0.7862 (m-30) cc_final: 0.7522 (m-30) REVERT: B 38 ARG cc_start: 0.7282 (ttt180) cc_final: 0.6378 (ttm-80) REVERT: B 52 LYS cc_start: 0.7434 (mttt) cc_final: 0.7133 (mmmt) REVERT: B 60 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7813 (mt) REVERT: B 91 MET cc_start: 0.5643 (tpp) cc_final: 0.5105 (ttt) REVERT: B 133 ARG cc_start: 0.6841 (ttm110) cc_final: 0.6154 (ttp-110) REVERT: B 215 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8272 (mtpt) REVERT: B 219 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7181 (mt-10) REVERT: B 310 ASP cc_start: 0.7897 (m-30) cc_final: 0.7533 (m-30) REVERT: C 38 ARG cc_start: 0.7235 (ttt180) cc_final: 0.6306 (ttm-80) REVERT: C 46 TYR cc_start: 0.7037 (m-80) cc_final: 0.6531 (m-80) REVERT: C 52 LYS cc_start: 0.7300 (mttt) cc_final: 0.7058 (mmmt) REVERT: C 60 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7768 (mt) REVERT: C 91 MET cc_start: 0.5520 (tpp) cc_final: 0.5094 (ttt) REVERT: C 119 ARG cc_start: 0.6908 (mtm-85) cc_final: 0.6513 (mtm-85) REVERT: C 133 ARG cc_start: 0.6666 (ttm110) cc_final: 0.6408 (ttm110) REVERT: C 179 GLN cc_start: 0.7017 (pm20) cc_final: 0.6801 (pm20) REVERT: C 297 MET cc_start: 0.7798 (mtm) cc_final: 0.7507 (ttp) REVERT: C 310 ASP cc_start: 0.7858 (m-30) cc_final: 0.7538 (m-30) REVERT: C 419 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.6526 (mmm) REVERT: C 435 THR cc_start: 0.8032 (p) cc_final: 0.7772 (m) REVERT: D 38 ARG cc_start: 0.7257 (ttt180) cc_final: 0.6323 (ttm-80) REVERT: D 46 TYR cc_start: 0.6956 (m-80) cc_final: 0.6387 (m-80) REVERT: D 52 LYS cc_start: 0.7395 (mttt) cc_final: 0.7068 (mmmt) REVERT: D 60 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7826 (mt) REVERT: D 91 MET cc_start: 0.5671 (tpp) cc_final: 0.5202 (ttt) REVERT: D 133 ARG cc_start: 0.6712 (ttm110) cc_final: 0.6429 (ttm110) REVERT: D 179 GLN cc_start: 0.6931 (pm20) cc_final: 0.6545 (pm20) REVERT: D 289 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6946 (tt0) REVERT: D 310 ASP cc_start: 0.7879 (m-30) cc_final: 0.7542 (m-30) REVERT: D 387 MET cc_start: 0.7380 (mmm) cc_final: 0.7048 (mtt) REVERT: D 406 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8449 (mp) REVERT: D 419 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.6839 (mmm) REVERT: D 435 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7799 (m) outliers start: 69 outliers final: 56 residues processed: 263 average time/residue: 1.1516 time to fit residues: 329.3585 Evaluate side-chains 277 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 211 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 435 THR 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: 0.0570 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 120 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.0020 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.3306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN C 351 GLN D 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.255549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.225959 restraints weight = 10243.456| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 1.25 r_work: 0.4321 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4215 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12408 Z= 0.179 Angle : 0.533 9.110 16836 Z= 0.272 Chirality : 0.036 0.149 2076 Planarity : 0.004 0.034 2024 Dihedral : 3.677 17.170 1784 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.22 % Allowed : 18.57 % Favored : 77.22 % 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: 2.74 (0.21), residues: 1524 helix: 2.75 (0.14), residues: 1204 sheet: 0.80 (0.67), residues: 40 loop : -2.55 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 354 HIS 0.002 0.000 HIS C 22 PHE 0.015 0.002 PHE A 203 TYR 0.022 0.001 TYR A 124 ARG 0.002 0.000 ARG C 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5333.10 seconds wall clock time: 93 minutes 46.88 seconds (5626.88 seconds total)