Starting phenix.real_space_refine on Tue Mar 19 16:03:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/03_2024/8jm9_36410_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/03_2024/8jm9_36410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/03_2024/8jm9_36410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/03_2024/8jm9_36410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/03_2024/8jm9_36410_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jm9_36410/03_2024/8jm9_36410_neut.pdb" } resolution = 2.6 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 7824 2.51 5 N 2056 2.21 5 O 2096 1.98 5 H 12472 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24520 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Time building chain proxies: 10.74, per 1000 atoms: 0.44 Number of scatterers: 24520 At special positions: 0 Unit cell: (110.67, 110.67, 104.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2096 8.00 N 2056 7.00 C 7824 6.00 H 12472 1.00 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: 18.89 Conformation dependent library (CDL) restraints added in 2.9 seconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 85.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 65 Processing helix chain 'A' and resid 73 through 100 Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 161 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 369 Proline residue: A 347 - end of helix removed outlier: 3.753A pdb=" N THR A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE B 11 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 73 through 100 Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 161 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 369 Proline residue: B 347 - end of helix removed outlier: 3.753A pdb=" N THR B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE C 11 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 65 Processing helix chain 'C' and resid 73 through 100 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 124 through 161 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 369 Proline residue: C 347 - end of helix removed outlier: 3.753A pdb=" N THR C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 65 Processing helix chain 'D' and resid 73 through 100 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 Processing helix chain 'D' and resid 124 through 161 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 369 Proline residue: D 347 - end of helix removed outlier: 3.753A pdb=" N THR D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3228 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: 8.79 Time building geometry restraints manager: 19.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12440 1.03 - 1.22: 32 1.22 - 1.42: 5112 1.42 - 1.61: 7056 1.61 - 1.81: 112 Bond restraints: 24752 Sorted by residual: bond pdb=" CB LYS C 379 " pdb=" CG LYS C 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS D 379 " pdb=" CG LYS D 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS B 379 " pdb=" CG LYS B 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS A 379 " pdb=" CG LYS A 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" C LYS B 357 " pdb=" O LYS B 357 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.31e-02 5.83e+03 6.00e-01 ... (remaining 24747 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.23: 672 107.23 - 113.94: 29228 113.94 - 120.64: 9132 120.64 - 127.35: 5584 127.35 - 134.06: 104 Bond angle restraints: 44720 Sorted by residual: angle pdb=" N VAL D 69 " pdb=" CA VAL D 69 " pdb=" C VAL D 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL B 69 " pdb=" CA VAL B 69 " pdb=" C VAL B 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL C 69 " pdb=" CA VAL C 69 " pdb=" C VAL C 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" CA LYS A 379 " pdb=" CB LYS A 379 " pdb=" CG LYS A 379 " ideal model delta sigma weight residual 114.10 118.99 -4.89 2.00e+00 2.50e-01 5.97e+00 ... (remaining 44715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 9532 11.72 - 23.45: 1192 23.45 - 35.17: 400 35.17 - 46.89: 220 46.89 - 58.62: 164 Dihedral angle restraints: 11508 sinusoidal: 6176 harmonic: 5332 Sorted by residual: dihedral pdb=" N GLN C 5 " pdb=" CA GLN C 5 " pdb=" CB GLN C 5 " pdb=" CG GLN C 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN B 5 " pdb=" CA GLN B 5 " pdb=" CB GLN B 5 " pdb=" CG GLN B 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN D 5 " pdb=" CA GLN D 5 " pdb=" CB GLN D 5 " pdb=" CG GLN D 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 11505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1516 0.036 - 0.071: 384 0.071 - 0.107: 80 0.107 - 0.142: 12 0.142 - 0.178: 4 Chirality restraints: 1996 Sorted by residual: chirality pdb=" CB THR B 46 " pdb=" CA THR B 46 " pdb=" OG1 THR B 46 " pdb=" CG2 THR B 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR C 46 " pdb=" CA THR C 46 " pdb=" OG1 THR C 46 " pdb=" CG2 THR C 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR A 46 " pdb=" CA THR A 46 " pdb=" OG1 THR A 46 " pdb=" CG2 THR A 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 1993 not shown) Planarity restraints: 3532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 83 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP C 83 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP C 83 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP C 83 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 83 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP D 83 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP D 83 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP D 83 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 83 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP B 83 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP B 83 " -0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP B 83 " -0.006 2.00e-02 2.50e+03 ... (remaining 3529 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1060 2.18 - 2.78: 49068 2.78 - 3.39: 73844 3.39 - 3.99: 91204 3.99 - 4.60: 146036 Nonbonded interactions: 361212 Sorted by model distance: nonbonded pdb=" OD1 ASN C 207 " pdb=" HG1 THR C 358 " model vdw 1.569 1.850 nonbonded pdb=" OD1 ASN D 207 " pdb=" HG1 THR D 358 " model vdw 1.569 1.850 nonbonded pdb=" OD1 ASN A 207 " pdb=" HG1 THR A 358 " model vdw 1.569 1.850 nonbonded pdb=" OD1 ASN B 207 " pdb=" HG1 THR B 358 " model vdw 1.569 1.850 nonbonded pdb=" OE2 GLU C 346 " pdb=" HE ARG C 402 " model vdw 1.622 1.850 ... (remaining 361207 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: 0.810 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: 0.350 Extract box with map and model: 4.390 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 77.770 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12280 Z= 0.193 Angle : 0.466 5.206 16656 Z= 0.263 Chirality : 0.034 0.178 1996 Planarity : 0.002 0.017 2040 Dihedral : 15.463 58.615 4376 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.61 % Allowed : 19.76 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.21), residues: 1508 helix: 2.97 (0.14), residues: 1256 sheet: 0.61 (0.68), residues: 48 loop : -1.37 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 38 HIS 0.001 0.000 HIS B 306 PHE 0.013 0.001 PHE C 125 TYR 0.008 0.001 TYR D 56 ARG 0.003 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6196 (tpt170) cc_final: 0.5099 (tpp-160) REVERT: A 78 VAL cc_start: 0.7240 (t) cc_final: 0.6845 (p) REVERT: A 328 TRP cc_start: 0.5594 (m100) cc_final: 0.5281 (m-90) REVERT: A 399 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6965 (ttp80) REVERT: A 403 THR cc_start: 0.7874 (m) cc_final: 0.7644 (p) REVERT: B 57 ARG cc_start: 0.6197 (tpt170) cc_final: 0.5100 (tpp-160) REVERT: B 78 VAL cc_start: 0.7241 (t) cc_final: 0.6846 (p) REVERT: B 328 TRP cc_start: 0.5592 (m100) cc_final: 0.5280 (m-90) REVERT: B 399 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6964 (ttp80) REVERT: B 403 THR cc_start: 0.7873 (m) cc_final: 0.7642 (p) REVERT: C 57 ARG cc_start: 0.6196 (tpt170) cc_final: 0.5098 (tpp-160) REVERT: C 78 VAL cc_start: 0.7240 (t) cc_final: 0.6846 (p) REVERT: C 328 TRP cc_start: 0.5593 (m100) cc_final: 0.5280 (m-90) REVERT: C 399 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.6964 (ttp80) REVERT: C 403 THR cc_start: 0.7874 (m) cc_final: 0.7643 (p) REVERT: D 57 ARG cc_start: 0.6197 (tpt170) cc_final: 0.5098 (tpp-160) REVERT: D 78 VAL cc_start: 0.7240 (t) cc_final: 0.6846 (p) REVERT: D 328 TRP cc_start: 0.5592 (m100) cc_final: 0.5280 (m-90) REVERT: D 399 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6963 (ttp80) REVERT: D 403 THR cc_start: 0.7875 (m) cc_final: 0.7645 (p) outliers start: 8 outliers final: 8 residues processed: 196 average time/residue: 2.7642 time to fit residues: 587.9532 Evaluate side-chains 180 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.6683 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12280 Z= 0.152 Angle : 0.425 4.673 16656 Z= 0.232 Chirality : 0.033 0.129 1996 Planarity : 0.002 0.019 2040 Dihedral : 4.482 52.245 1676 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 17.02 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.21), residues: 1508 helix: 3.07 (0.13), residues: 1256 sheet: 0.48 (0.69), residues: 48 loop : -1.42 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 38 HIS 0.001 0.000 HIS C 278 PHE 0.011 0.001 PHE B 422 TYR 0.008 0.001 TYR C 175 ARG 0.002 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6185 (tpt170) cc_final: 0.5092 (tpp-160) REVERT: A 67 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7279 (tt) REVERT: A 78 VAL cc_start: 0.7311 (t) cc_final: 0.6912 (p) REVERT: A 159 GLN cc_start: 0.5891 (OUTLIER) cc_final: 0.5476 (mt0) REVERT: A 328 TRP cc_start: 0.5580 (m100) cc_final: 0.5374 (m-90) REVERT: A 399 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6595 (mtt90) REVERT: B 57 ARG cc_start: 0.6186 (tpt170) cc_final: 0.5092 (tpp-160) REVERT: B 67 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7279 (tt) REVERT: B 78 VAL cc_start: 0.7313 (t) cc_final: 0.6914 (p) REVERT: B 159 GLN cc_start: 0.5890 (OUTLIER) cc_final: 0.5476 (mt0) REVERT: B 328 TRP cc_start: 0.5578 (m100) cc_final: 0.5375 (m-90) REVERT: B 399 ARG cc_start: 0.7236 (mtm-85) cc_final: 0.6597 (mtt90) REVERT: C 57 ARG cc_start: 0.6187 (tpt170) cc_final: 0.5093 (tpp-160) REVERT: C 67 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7278 (tt) REVERT: C 78 VAL cc_start: 0.7314 (t) cc_final: 0.6915 (p) REVERT: C 159 GLN cc_start: 0.5891 (OUTLIER) cc_final: 0.5476 (mt0) REVERT: C 328 TRP cc_start: 0.5578 (m100) cc_final: 0.5376 (m-90) REVERT: C 399 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6595 (mtt90) REVERT: D 57 ARG cc_start: 0.6186 (tpt170) cc_final: 0.5092 (tpp-160) REVERT: D 67 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7278 (tt) REVERT: D 78 VAL cc_start: 0.7313 (t) cc_final: 0.6914 (p) REVERT: D 159 GLN cc_start: 0.5892 (OUTLIER) cc_final: 0.5476 (mt0) REVERT: D 328 TRP cc_start: 0.5579 (m100) cc_final: 0.5375 (m-90) REVERT: D 399 ARG cc_start: 0.7234 (mtm-85) cc_final: 0.6594 (mtt90) outliers start: 16 outliers final: 4 residues processed: 200 average time/residue: 2.4886 time to fit residues: 544.8916 Evaluate side-chains 194 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 0.0070 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12280 Z= 0.212 Angle : 0.437 4.104 16656 Z= 0.242 Chirality : 0.033 0.133 1996 Planarity : 0.003 0.020 2040 Dihedral : 3.204 10.808 1660 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 16.11 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.21), residues: 1508 helix: 2.90 (0.13), residues: 1256 sheet: 0.33 (0.67), residues: 48 loop : -1.51 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 154 HIS 0.002 0.001 HIS D 286 PHE 0.026 0.001 PHE C 422 TYR 0.010 0.001 TYR C 56 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.792 Fit side-chains REVERT: A 57 ARG cc_start: 0.6228 (tpt170) cc_final: 0.5092 (tpp-160) REVERT: A 78 VAL cc_start: 0.7348 (t) cc_final: 0.6951 (p) REVERT: A 110 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: A 120 ASN cc_start: 0.6904 (p0) cc_final: 0.6022 (t160) REVERT: A 159 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.5459 (mt0) REVERT: A 276 ASP cc_start: 0.7374 (t0) cc_final: 0.6974 (m-30) REVERT: A 328 TRP cc_start: 0.5621 (m100) cc_final: 0.5398 (m-90) REVERT: A 399 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.6814 (mtt90) REVERT: B 57 ARG cc_start: 0.6229 (tpt170) cc_final: 0.5093 (tpp-160) REVERT: B 78 VAL cc_start: 0.7348 (t) cc_final: 0.6953 (p) REVERT: B 110 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: B 120 ASN cc_start: 0.6901 (p0) cc_final: 0.6018 (t160) REVERT: B 159 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.5460 (mt0) REVERT: B 276 ASP cc_start: 0.7375 (t0) cc_final: 0.6976 (m-30) REVERT: B 328 TRP cc_start: 0.5619 (m100) cc_final: 0.5396 (m-90) REVERT: B 399 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.6813 (mtt90) REVERT: C 57 ARG cc_start: 0.6230 (tpt170) cc_final: 0.5094 (tpp-160) REVERT: C 78 VAL cc_start: 0.7350 (t) cc_final: 0.6954 (p) REVERT: C 110 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6557 (m-30) REVERT: C 120 ASN cc_start: 0.6903 (p0) cc_final: 0.6020 (t160) REVERT: C 159 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.5460 (mt0) REVERT: C 276 ASP cc_start: 0.7375 (t0) cc_final: 0.6976 (m-30) REVERT: C 328 TRP cc_start: 0.5619 (m100) cc_final: 0.5398 (m-90) REVERT: C 399 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.6813 (mtt90) REVERT: D 57 ARG cc_start: 0.6228 (tpt170) cc_final: 0.5092 (tpp-160) REVERT: D 78 VAL cc_start: 0.7348 (t) cc_final: 0.6952 (p) REVERT: D 110 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: D 120 ASN cc_start: 0.6904 (p0) cc_final: 0.6022 (t160) REVERT: D 159 GLN cc_start: 0.5849 (OUTLIER) cc_final: 0.5459 (mt0) REVERT: D 276 ASP cc_start: 0.7377 (t0) cc_final: 0.6976 (m-30) REVERT: D 328 TRP cc_start: 0.5620 (m100) cc_final: 0.5397 (m-90) REVERT: D 399 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.6812 (mtt90) outliers start: 16 outliers final: 0 residues processed: 184 average time/residue: 2.8399 time to fit residues: 566.8303 Evaluate side-chains 184 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12280 Z= 0.265 Angle : 0.464 5.245 16656 Z= 0.256 Chirality : 0.035 0.135 1996 Planarity : 0.004 0.051 2040 Dihedral : 3.364 11.980 1660 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.82 % Allowed : 15.43 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.21), residues: 1508 helix: 2.73 (0.13), residues: 1256 sheet: 0.32 (0.66), residues: 48 loop : -1.54 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 154 HIS 0.002 0.001 HIS A 278 PHE 0.026 0.002 PHE B 422 TYR 0.009 0.001 TYR A 56 ARG 0.005 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6270 (tpt170) cc_final: 0.5094 (tpp-160) REVERT: A 78 VAL cc_start: 0.7181 (t) cc_final: 0.6800 (p) REVERT: A 120 ASN cc_start: 0.6888 (p0) cc_final: 0.6009 (t0) REVERT: A 159 GLN cc_start: 0.5849 (OUTLIER) cc_final: 0.5463 (mt0) REVERT: A 276 ASP cc_start: 0.7279 (t0) cc_final: 0.6887 (m-30) REVERT: A 328 TRP cc_start: 0.5581 (m100) cc_final: 0.5357 (m-90) REVERT: A 399 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.6813 (mtt90) REVERT: B 57 ARG cc_start: 0.6270 (tpt170) cc_final: 0.5094 (tpp-160) REVERT: B 78 VAL cc_start: 0.7183 (t) cc_final: 0.6803 (p) REVERT: B 120 ASN cc_start: 0.6887 (p0) cc_final: 0.6007 (t0) REVERT: B 159 GLN cc_start: 0.5850 (OUTLIER) cc_final: 0.5463 (mt0) REVERT: B 276 ASP cc_start: 0.7279 (t0) cc_final: 0.6887 (m-30) REVERT: B 328 TRP cc_start: 0.5581 (m100) cc_final: 0.5357 (m-90) REVERT: B 399 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.6813 (mtt90) REVERT: C 57 ARG cc_start: 0.6271 (tpt170) cc_final: 0.5094 (tpp-160) REVERT: C 78 VAL cc_start: 0.7185 (t) cc_final: 0.6804 (p) REVERT: C 120 ASN cc_start: 0.6888 (p0) cc_final: 0.6009 (t0) REVERT: C 159 GLN cc_start: 0.5849 (OUTLIER) cc_final: 0.5462 (mt0) REVERT: C 276 ASP cc_start: 0.7280 (t0) cc_final: 0.6887 (m-30) REVERT: C 328 TRP cc_start: 0.5581 (m100) cc_final: 0.5358 (m-90) REVERT: C 399 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.6812 (mtt90) REVERT: D 57 ARG cc_start: 0.6270 (tpt170) cc_final: 0.5094 (tpp-160) REVERT: D 78 VAL cc_start: 0.7183 (t) cc_final: 0.6802 (p) REVERT: D 120 ASN cc_start: 0.6890 (p0) cc_final: 0.6010 (t0) REVERT: D 159 GLN cc_start: 0.5850 (OUTLIER) cc_final: 0.5463 (mt0) REVERT: D 276 ASP cc_start: 0.7280 (t0) cc_final: 0.6888 (m-30) REVERT: D 328 TRP cc_start: 0.5583 (m100) cc_final: 0.5358 (m-90) REVERT: D 399 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.6811 (mtt90) outliers start: 24 outliers final: 16 residues processed: 192 average time/residue: 2.6597 time to fit residues: 556.3841 Evaluate side-chains 204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12280 Z= 0.307 Angle : 0.479 4.988 16656 Z= 0.265 Chirality : 0.036 0.132 1996 Planarity : 0.004 0.046 2040 Dihedral : 3.510 13.279 1660 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.82 % Allowed : 15.12 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.21), residues: 1508 helix: 2.51 (0.13), residues: 1256 sheet: 0.27 (0.66), residues: 48 loop : -1.61 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.003 0.001 HIS A 286 PHE 0.032 0.002 PHE B 422 TYR 0.010 0.001 TYR A 56 ARG 0.008 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6275 (tpt170) cc_final: 0.5139 (tpp-160) REVERT: A 78 VAL cc_start: 0.7184 (t) cc_final: 0.6805 (p) REVERT: A 110 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6554 (m-30) REVERT: A 120 ASN cc_start: 0.6829 (p0) cc_final: 0.5916 (t0) REVERT: A 276 ASP cc_start: 0.7258 (t0) cc_final: 0.6922 (m-30) REVERT: A 328 TRP cc_start: 0.5575 (m100) cc_final: 0.4918 (m-10) REVERT: A 399 ARG cc_start: 0.7511 (mtm-85) cc_final: 0.6828 (mtt90) REVERT: B 57 ARG cc_start: 0.6274 (tpt170) cc_final: 0.5138 (tpp-160) REVERT: B 78 VAL cc_start: 0.7185 (t) cc_final: 0.6806 (p) REVERT: B 110 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6553 (m-30) REVERT: B 120 ASN cc_start: 0.6827 (p0) cc_final: 0.5913 (t0) REVERT: B 276 ASP cc_start: 0.7257 (t0) cc_final: 0.6922 (m-30) REVERT: B 328 TRP cc_start: 0.5576 (m100) cc_final: 0.4920 (m-10) REVERT: B 399 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.6828 (mtt90) REVERT: C 57 ARG cc_start: 0.6277 (tpt170) cc_final: 0.5139 (tpp-160) REVERT: C 78 VAL cc_start: 0.7188 (t) cc_final: 0.6809 (p) REVERT: C 110 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6553 (m-30) REVERT: C 120 ASN cc_start: 0.6828 (p0) cc_final: 0.5911 (t0) REVERT: C 276 ASP cc_start: 0.7258 (t0) cc_final: 0.6922 (m-30) REVERT: C 328 TRP cc_start: 0.5576 (m100) cc_final: 0.4920 (m-10) REVERT: C 399 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.6828 (mtt90) REVERT: D 57 ARG cc_start: 0.6274 (tpt170) cc_final: 0.5138 (tpp-160) REVERT: D 78 VAL cc_start: 0.7184 (t) cc_final: 0.6806 (p) REVERT: D 110 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6554 (m-30) REVERT: D 120 ASN cc_start: 0.6829 (p0) cc_final: 0.5916 (t0) REVERT: D 276 ASP cc_start: 0.7259 (t0) cc_final: 0.6923 (m-30) REVERT: D 328 TRP cc_start: 0.5577 (m100) cc_final: 0.4919 (m-10) REVERT: D 399 ARG cc_start: 0.7512 (mtm-85) cc_final: 0.6827 (mtt90) outliers start: 24 outliers final: 12 residues processed: 204 average time/residue: 2.7376 time to fit residues: 607.0619 Evaluate side-chains 196 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12280 Z= 0.181 Angle : 0.440 5.758 16656 Z= 0.241 Chirality : 0.033 0.126 1996 Planarity : 0.003 0.054 2040 Dihedral : 3.369 11.990 1660 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 16.11 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.21), residues: 1508 helix: 2.78 (0.14), residues: 1256 sheet: 0.32 (0.68), residues: 48 loop : -1.46 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.001 0.000 HIS B 278 PHE 0.031 0.002 PHE B 422 TYR 0.007 0.001 TYR B 56 ARG 0.008 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6271 (tpt170) cc_final: 0.5081 (tpp-160) REVERT: A 67 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7327 (tt) REVERT: A 78 VAL cc_start: 0.7169 (t) cc_final: 0.6784 (p) REVERT: A 120 ASN cc_start: 0.6830 (p0) cc_final: 0.5911 (t160) REVERT: A 276 ASP cc_start: 0.7224 (t0) cc_final: 0.6878 (m-30) REVERT: A 328 TRP cc_start: 0.5560 (m100) cc_final: 0.4913 (m-10) REVERT: A 399 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.6824 (mtt90) REVERT: B 57 ARG cc_start: 0.6270 (tpt170) cc_final: 0.5082 (tpp-160) REVERT: B 67 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7327 (tt) REVERT: B 78 VAL cc_start: 0.7172 (t) cc_final: 0.6787 (p) REVERT: B 120 ASN cc_start: 0.6829 (p0) cc_final: 0.5908 (t160) REVERT: B 276 ASP cc_start: 0.7223 (t0) cc_final: 0.6878 (m-30) REVERT: B 328 TRP cc_start: 0.5560 (m100) cc_final: 0.4914 (m-10) REVERT: B 399 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.6824 (mtt90) REVERT: C 57 ARG cc_start: 0.6270 (tpt170) cc_final: 0.5082 (tpp-160) REVERT: C 67 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7329 (tt) REVERT: C 78 VAL cc_start: 0.7172 (t) cc_final: 0.6787 (p) REVERT: C 120 ASN cc_start: 0.6828 (p0) cc_final: 0.5907 (t160) REVERT: C 276 ASP cc_start: 0.7222 (t0) cc_final: 0.6878 (m-30) REVERT: C 328 TRP cc_start: 0.5560 (m100) cc_final: 0.4914 (m-10) REVERT: C 399 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.6822 (mtt90) REVERT: D 57 ARG cc_start: 0.6271 (tpt170) cc_final: 0.5081 (tpp-160) REVERT: D 67 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7327 (tt) REVERT: D 78 VAL cc_start: 0.7171 (t) cc_final: 0.6786 (p) REVERT: D 120 ASN cc_start: 0.6830 (p0) cc_final: 0.5909 (t160) REVERT: D 276 ASP cc_start: 0.7224 (t0) cc_final: 0.6880 (m-30) REVERT: D 328 TRP cc_start: 0.5561 (m100) cc_final: 0.4913 (m-10) REVERT: D 399 ARG cc_start: 0.7496 (mtm-85) cc_final: 0.6821 (mtt90) outliers start: 16 outliers final: 12 residues processed: 187 average time/residue: 2.5887 time to fit residues: 529.1638 Evaluate side-chains 195 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12280 Z= 0.267 Angle : 0.463 5.037 16656 Z= 0.256 Chirality : 0.034 0.130 1996 Planarity : 0.003 0.040 2040 Dihedral : 3.443 12.607 1660 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.82 % Allowed : 15.50 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.21), residues: 1508 helix: 2.63 (0.13), residues: 1256 sheet: 0.26 (0.67), residues: 48 loop : -1.53 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.002 0.001 HIS A 286 PHE 0.035 0.002 PHE D 422 TYR 0.008 0.001 TYR A 56 ARG 0.006 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.940 Fit side-chains REVERT: A 57 ARG cc_start: 0.6290 (tpt170) cc_final: 0.5090 (tpp-160) REVERT: A 59 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6027 (mp) REVERT: A 78 VAL cc_start: 0.7161 (t) cc_final: 0.6783 (p) REVERT: A 120 ASN cc_start: 0.6815 (p0) cc_final: 0.5893 (t160) REVERT: A 276 ASP cc_start: 0.7219 (t0) cc_final: 0.6881 (m-30) REVERT: A 328 TRP cc_start: 0.5547 (m100) cc_final: 0.4910 (m-10) REVERT: A 399 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.6839 (mtt180) REVERT: B 57 ARG cc_start: 0.6319 (tpt170) cc_final: 0.5086 (tpp-160) REVERT: B 59 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6026 (mp) REVERT: B 78 VAL cc_start: 0.7161 (t) cc_final: 0.6784 (p) REVERT: B 120 ASN cc_start: 0.6813 (p0) cc_final: 0.5892 (t160) REVERT: B 276 ASP cc_start: 0.7220 (t0) cc_final: 0.6881 (m-30) REVERT: B 328 TRP cc_start: 0.5547 (m100) cc_final: 0.4911 (m-10) REVERT: B 399 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.6842 (mtt180) REVERT: C 57 ARG cc_start: 0.6290 (tpt170) cc_final: 0.5089 (tpp-160) REVERT: C 59 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6027 (mp) REVERT: C 78 VAL cc_start: 0.7163 (t) cc_final: 0.6786 (p) REVERT: C 120 ASN cc_start: 0.6815 (p0) cc_final: 0.5892 (t160) REVERT: C 276 ASP cc_start: 0.7219 (t0) cc_final: 0.6882 (m-30) REVERT: C 328 TRP cc_start: 0.5548 (m100) cc_final: 0.4912 (m-10) REVERT: C 399 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.6835 (mtt90) REVERT: D 57 ARG cc_start: 0.6289 (tpt170) cc_final: 0.5089 (tpp-160) REVERT: D 59 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6028 (mp) REVERT: D 78 VAL cc_start: 0.7161 (t) cc_final: 0.6784 (p) REVERT: D 120 ASN cc_start: 0.6816 (p0) cc_final: 0.5894 (t160) REVERT: D 276 ASP cc_start: 0.7221 (t0) cc_final: 0.6883 (m-30) REVERT: D 328 TRP cc_start: 0.5548 (m100) cc_final: 0.4911 (m-10) REVERT: D 399 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.6841 (mtt180) outliers start: 24 outliers final: 12 residues processed: 200 average time/residue: 2.5197 time to fit residues: 549.6973 Evaluate side-chains 200 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 0.0270 chunk 133 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12280 Z= 0.166 Angle : 0.425 4.637 16656 Z= 0.234 Chirality : 0.033 0.124 1996 Planarity : 0.003 0.036 2040 Dihedral : 3.302 11.362 1660 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.22 % Allowed : 16.41 % Favored : 82.37 % 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: 3.48 (0.21), residues: 1508 helix: 2.90 (0.14), residues: 1256 sheet: 0.34 (0.68), residues: 48 loop : -1.36 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.001 0.000 HIS D 349 PHE 0.031 0.001 PHE D 422 TYR 0.006 0.001 TYR D 56 ARG 0.005 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 2.007 Fit side-chains REVERT: A 57 ARG cc_start: 0.6264 (tpt170) cc_final: 0.5068 (tpp-160) REVERT: A 67 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7345 (tt) REVERT: A 78 VAL cc_start: 0.7157 (t) cc_final: 0.6772 (p) REVERT: A 159 GLN cc_start: 0.5864 (pt0) cc_final: 0.5488 (mt0) REVERT: A 276 ASP cc_start: 0.7214 (t0) cc_final: 0.6876 (m-30) REVERT: A 328 TRP cc_start: 0.5527 (m100) cc_final: 0.4912 (m-10) REVERT: A 399 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.6805 (mtt90) REVERT: B 57 ARG cc_start: 0.6266 (tpt170) cc_final: 0.5069 (tpp-160) REVERT: B 67 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7346 (tt) REVERT: B 78 VAL cc_start: 0.7159 (t) cc_final: 0.6774 (p) REVERT: B 159 GLN cc_start: 0.5865 (pt0) cc_final: 0.5488 (mt0) REVERT: B 276 ASP cc_start: 0.7214 (t0) cc_final: 0.6876 (m-30) REVERT: B 328 TRP cc_start: 0.5528 (m100) cc_final: 0.4913 (m-10) REVERT: B 399 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.6819 (mtt180) REVERT: C 57 ARG cc_start: 0.6267 (tpt170) cc_final: 0.5070 (tpp-160) REVERT: C 67 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7345 (tt) REVERT: C 78 VAL cc_start: 0.7160 (t) cc_final: 0.6776 (p) REVERT: C 159 GLN cc_start: 0.5865 (pt0) cc_final: 0.5489 (mt0) REVERT: C 276 ASP cc_start: 0.7214 (t0) cc_final: 0.6876 (m-30) REVERT: C 328 TRP cc_start: 0.5529 (m100) cc_final: 0.4914 (m-10) REVERT: C 399 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.6804 (mtt90) REVERT: D 57 ARG cc_start: 0.6266 (tpt170) cc_final: 0.5068 (tpp-160) REVERT: D 67 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7345 (tt) REVERT: D 78 VAL cc_start: 0.7159 (t) cc_final: 0.6775 (p) REVERT: D 159 GLN cc_start: 0.5865 (pt0) cc_final: 0.5488 (mt0) REVERT: D 276 ASP cc_start: 0.7217 (t0) cc_final: 0.6878 (m-30) REVERT: D 328 TRP cc_start: 0.5530 (m100) cc_final: 0.4913 (m-10) REVERT: D 399 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.6803 (mtt90) outliers start: 16 outliers final: 8 residues processed: 196 average time/residue: 2.4051 time to fit residues: 517.3389 Evaluate side-chains 196 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0770 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12280 Z= 0.311 Angle : 0.477 4.851 16656 Z= 0.264 Chirality : 0.035 0.131 1996 Planarity : 0.003 0.033 2040 Dihedral : 3.492 12.770 1660 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.82 % Allowed : 15.05 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.21), residues: 1508 helix: 2.58 (0.13), residues: 1256 sheet: 0.19 (0.67), residues: 48 loop : -1.53 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.003 0.001 HIS A 286 PHE 0.037 0.002 PHE D 422 TYR 0.015 0.001 TYR A 182 ARG 0.004 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 1.867 Fit side-chains REVERT: A 57 ARG cc_start: 0.6319 (tpt170) cc_final: 0.5071 (tpp-160) REVERT: A 59 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.6001 (mp) REVERT: A 78 VAL cc_start: 0.7175 (t) cc_final: 0.6802 (p) REVERT: A 120 ASN cc_start: 0.6822 (p0) cc_final: 0.5861 (t160) REVERT: A 129 ARG cc_start: 0.6882 (ttm-80) cc_final: 0.6659 (ttm110) REVERT: A 159 GLN cc_start: 0.5858 (pt0) cc_final: 0.5487 (mt0) REVERT: A 276 ASP cc_start: 0.7253 (t0) cc_final: 0.6925 (m-30) REVERT: A 328 TRP cc_start: 0.5540 (m100) cc_final: 0.4967 (m-10) REVERT: A 399 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.6855 (mtt90) REVERT: B 57 ARG cc_start: 0.6318 (tpt170) cc_final: 0.5071 (tpp-160) REVERT: B 59 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.6000 (mp) REVERT: B 78 VAL cc_start: 0.7176 (t) cc_final: 0.6803 (p) REVERT: B 120 ASN cc_start: 0.6820 (p0) cc_final: 0.5860 (t160) REVERT: B 129 ARG cc_start: 0.6848 (ttm-80) cc_final: 0.6624 (ttm110) REVERT: B 159 GLN cc_start: 0.5860 (pt0) cc_final: 0.5488 (mt0) REVERT: B 276 ASP cc_start: 0.7253 (t0) cc_final: 0.6924 (m-30) REVERT: B 328 TRP cc_start: 0.5541 (m100) cc_final: 0.4969 (m-10) REVERT: B 399 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.6855 (mtt90) REVERT: C 57 ARG cc_start: 0.6319 (tpt170) cc_final: 0.5072 (tpp-160) REVERT: C 59 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6002 (mp) REVERT: C 78 VAL cc_start: 0.7178 (t) cc_final: 0.6805 (p) REVERT: C 120 ASN cc_start: 0.6821 (p0) cc_final: 0.5860 (t160) REVERT: C 129 ARG cc_start: 0.6884 (ttm-80) cc_final: 0.6660 (ttm110) REVERT: C 159 GLN cc_start: 0.5860 (pt0) cc_final: 0.5489 (mt0) REVERT: C 276 ASP cc_start: 0.7253 (t0) cc_final: 0.6925 (m-30) REVERT: C 328 TRP cc_start: 0.5543 (m100) cc_final: 0.4970 (m-10) REVERT: C 399 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.6854 (mtt90) REVERT: D 57 ARG cc_start: 0.6319 (tpt170) cc_final: 0.5071 (tpp-160) REVERT: D 59 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.6001 (mp) REVERT: D 78 VAL cc_start: 0.7175 (t) cc_final: 0.6803 (p) REVERT: D 120 ASN cc_start: 0.6823 (p0) cc_final: 0.5862 (t160) REVERT: D 129 ARG cc_start: 0.6882 (ttm-80) cc_final: 0.6658 (ttm110) REVERT: D 159 GLN cc_start: 0.5859 (pt0) cc_final: 0.5488 (mt0) REVERT: D 276 ASP cc_start: 0.7254 (t0) cc_final: 0.6926 (m-30) REVERT: D 328 TRP cc_start: 0.5543 (m100) cc_final: 0.4969 (m-10) REVERT: D 399 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.6854 (mtt90) outliers start: 24 outliers final: 12 residues processed: 210 average time/residue: 2.6916 time to fit residues: 618.9757 Evaluate side-chains 206 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12280 Z= 0.217 Angle : 0.454 6.111 16656 Z= 0.249 Chirality : 0.033 0.127 1996 Planarity : 0.003 0.032 2040 Dihedral : 3.416 12.429 1660 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.52 % Allowed : 15.50 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.21), residues: 1508 helix: 2.73 (0.14), residues: 1256 sheet: 0.25 (0.67), residues: 48 loop : -1.46 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.002 0.001 HIS A 278 PHE 0.041 0.002 PHE D 422 TYR 0.008 0.001 TYR A 182 ARG 0.005 0.000 ARG C 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6283 (tpt170) cc_final: 0.5082 (tpp-160) REVERT: A 59 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6022 (mp) REVERT: A 67 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7361 (tt) REVERT: A 78 VAL cc_start: 0.7155 (t) cc_final: 0.6777 (p) REVERT: A 159 GLN cc_start: 0.5855 (pt0) cc_final: 0.5480 (mt0) REVERT: A 276 ASP cc_start: 0.7229 (t0) cc_final: 0.6893 (m-30) REVERT: A 328 TRP cc_start: 0.5503 (m100) cc_final: 0.4941 (m-10) REVERT: A 399 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7232 (mtm110) REVERT: B 57 ARG cc_start: 0.6312 (tpt170) cc_final: 0.5079 (tpp-160) REVERT: B 67 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7361 (tt) REVERT: B 78 VAL cc_start: 0.7155 (t) cc_final: 0.6778 (p) REVERT: B 159 GLN cc_start: 0.5856 (pt0) cc_final: 0.5481 (mt0) REVERT: B 276 ASP cc_start: 0.7229 (t0) cc_final: 0.6894 (m-30) REVERT: B 328 TRP cc_start: 0.5504 (m100) cc_final: 0.4942 (m-10) REVERT: B 399 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.7232 (mtm110) REVERT: C 57 ARG cc_start: 0.6312 (tpt170) cc_final: 0.5079 (tpp-160) REVERT: C 59 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6021 (mp) REVERT: C 67 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7361 (tt) REVERT: C 78 VAL cc_start: 0.7157 (t) cc_final: 0.6779 (p) REVERT: C 159 GLN cc_start: 0.5856 (pt0) cc_final: 0.5480 (mt0) REVERT: C 276 ASP cc_start: 0.7230 (t0) cc_final: 0.6894 (m-30) REVERT: C 328 TRP cc_start: 0.5505 (m100) cc_final: 0.4953 (m-10) REVERT: C 399 ARG cc_start: 0.7500 (mtm-85) cc_final: 0.7233 (mtm110) REVERT: D 57 ARG cc_start: 0.6283 (tpt170) cc_final: 0.5082 (tpp-160) REVERT: D 59 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6022 (mp) REVERT: D 67 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7360 (tt) REVERT: D 78 VAL cc_start: 0.7155 (t) cc_final: 0.6777 (p) REVERT: D 159 GLN cc_start: 0.5856 (pt0) cc_final: 0.5481 (mt0) REVERT: D 276 ASP cc_start: 0.7231 (t0) cc_final: 0.6895 (m-30) REVERT: D 328 TRP cc_start: 0.5505 (m100) cc_final: 0.4943 (m-10) REVERT: D 399 ARG cc_start: 0.7498 (mtm-85) cc_final: 0.7233 (mtm110) outliers start: 20 outliers final: 8 residues processed: 196 average time/residue: 2.5532 time to fit residues: 546.3924 Evaluate side-chains 199 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.100667 restraints weight = 37544.478| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.91 r_work: 0.2991 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12280 Z= 0.149 Angle : 0.420 5.711 16656 Z= 0.231 Chirality : 0.032 0.123 1996 Planarity : 0.003 0.031 2040 Dihedral : 3.213 10.616 1660 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.30 % Allowed : 16.72 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.21), residues: 1508 helix: 3.02 (0.14), residues: 1260 sheet: 0.34 (0.68), residues: 48 loop : -1.09 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.001 0.000 HIS C 278 PHE 0.032 0.001 PHE D 422 TYR 0.005 0.001 TYR B 56 ARG 0.005 0.000 ARG C 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9311.54 seconds wall clock time: 163 minutes 2.99 seconds (9782.99 seconds total)