Starting phenix.real_space_refine on Fri Jan 19 15:01:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/01_2024/6vwj_21418.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/01_2024/6vwj_21418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/01_2024/6vwj_21418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/01_2024/6vwj_21418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/01_2024/6vwj_21418.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwj_21418/01_2024/6vwj_21418.pdb" } resolution = 4.21 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= 0.001 sd= 0.021 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 42 5.16 5 C 3802 2.51 5 N 1044 2.21 5 O 1122 1.98 5 H 5789 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 824": "OE1" <-> "OE2" Residue "A GLU 844": "OE1" <-> "OE2" Residue "A ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 150": "OD1" <-> "OD2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 636": "OD1" <-> "OD2" Residue "B GLU 779": "OE1" <-> "OE2" Residue "B GLU 799": "OE1" <-> "OE2" Residue "B GLU 815": "OE1" <-> "OE2" Residue "B PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 824": "OE1" <-> "OE2" Residue "B GLU 844": "OE1" <-> "OE2" Residue "B ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 11799 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 3865 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 20, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 7934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7934 Classifications: {'peptide': 507} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 471} Chain breaks: 4 Time building chain proxies: 5.74, per 1000 atoms: 0.49 Number of scatterers: 11799 At special positions: 0 Unit cell: (92.22, 113.42, 103.88, 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 42 16.00 O 1122 8.00 N 1044 7.00 C 3802 6.00 H 5789 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.04 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.02 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 849 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.04 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: 9.01 Conformation dependent library (CDL) restraints added in 1.3 seconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 12.0% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 686 through 700 removed outlier: 4.725A pdb=" N PHE A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 15 through 22 removed outlier: 4.349A pdb=" N ASN B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.749A pdb=" N ILE B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 625 through 630 removed outlier: 4.346A pdb=" N ARG B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 625 through 630' Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 593 removed outlier: 4.999A pdb=" N ASP A 586 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A 602 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 592 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLN A 596 " --> pdb=" O ASN A 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 752 removed outlier: 3.800A pdb=" N TYR A 614 " --> pdb=" O VAL A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 813 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.745A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 875 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TRP A 886 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA A 877 " --> pdb=" O GLY A 884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.745A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.691A pdb=" N ILE B 76 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.840A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 85 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG B 112 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 87 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLU B 114 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE B 89 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AB1, first strand: chain 'B' and resid 205 through 209 removed outlier: 4.097A pdb=" N ALA B 220 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER B 208 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N CYS B 218 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB3, first strand: chain 'B' and resid 245 through 248 removed outlier: 8.084A pdb=" N CYS B 273 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B 240 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AB5, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.145A pdb=" N ASP B 586 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN B 602 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 747 through 751 Processing sheet with id=AB7, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AB8, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.700A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.700A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 528 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: 4.41 Time building geometry restraints manager: 9.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5789 1.03 - 1.23: 471 1.23 - 1.44: 2236 1.44 - 1.64: 3410 1.64 - 1.84: 50 Bond restraints: 11956 Sorted by residual: bond pdb=" N VAL A 580 " pdb=" CA VAL A 580 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" N VAL A 580 " pdb=" H VAL A 580 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" CB LYS A 897 " pdb=" CG LYS A 897 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CB CYS A 785 " pdb=" SG CYS A 785 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.57e+00 ... (remaining 11951 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.40: 269 106.40 - 113.32: 13639 113.32 - 120.23: 3880 120.23 - 127.14: 3668 127.14 - 134.05: 97 Bond angle restraints: 21553 Sorted by residual: angle pdb=" N ASN B 11 " pdb=" CA ASN B 11 " pdb=" C ASN B 11 " ideal model delta sigma weight residual 110.80 119.30 -8.50 2.13e+00 2.20e-01 1.59e+01 angle pdb=" CA LYS B 600 " pdb=" CB LYS B 600 " pdb=" CG LYS B 600 " ideal model delta sigma weight residual 114.10 107.58 6.52 2.00e+00 2.50e-01 1.06e+01 angle pdb=" N ASP B 12 " pdb=" CA ASP B 12 " pdb=" C ASP B 12 " ideal model delta sigma weight residual 109.06 114.51 -5.45 1.70e+00 3.46e-01 1.03e+01 angle pdb=" CA TYR A 628 " pdb=" CB TYR A 628 " pdb=" CG TYR A 628 " ideal model delta sigma weight residual 113.90 119.60 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" CA LYS A 862 " pdb=" CB LYS A 862 " pdb=" CG LYS A 862 " ideal model delta sigma weight residual 114.10 107.84 6.26 2.00e+00 2.50e-01 9.80e+00 ... (remaining 21548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5187 17.48 - 34.96: 326 34.96 - 52.45: 78 52.45 - 69.93: 64 69.93 - 87.41: 7 Dihedral angle restraints: 5662 sinusoidal: 3045 harmonic: 2617 Sorted by residual: dihedral pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -145.73 59.73 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CA SER B 788 " pdb=" C SER B 788 " pdb=" N ASN B 789 " pdb=" CA ASN B 789 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA SER A 788 " pdb=" C SER A 788 " pdb=" N ASN A 789 " pdb=" CA ASN A 789 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 5659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 456 0.035 - 0.070: 245 0.070 - 0.105: 110 0.105 - 0.140: 52 0.140 - 0.175: 11 Chirality restraints: 874 Sorted by residual: chirality pdb=" CA GLN B 14 " pdb=" N GLN B 14 " pdb=" C GLN B 14 " pdb=" CB GLN B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ASN B 11 " pdb=" N ASN B 11 " pdb=" C ASN B 11 " pdb=" CB ASN B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE A 832 " pdb=" N ILE A 832 " pdb=" C ILE A 832 " pdb=" CB ILE A 832 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 871 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 112 " -0.099 9.50e-02 1.11e+02 4.89e-02 3.05e+01 pdb=" NE ARG B 112 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 112 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG B 112 " 0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG B 112 " 0.039 2.00e-02 2.50e+03 pdb="HH11 ARG B 112 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG B 112 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 112 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 112 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 865 " 0.032 9.50e-02 1.11e+02 3.24e-02 2.12e+01 pdb=" NE ARG A 865 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 865 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG A 865 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 865 " 0.041 2.00e-02 2.50e+03 pdb="HH11 ARG A 865 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 865 " 0.027 2.00e-02 2.50e+03 pdb="HH21 ARG A 865 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 865 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 269 " -0.001 2.00e-02 2.50e+03 2.84e-02 1.81e+01 pdb=" CG HIS B 269 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS B 269 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS B 269 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS B 269 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS B 269 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 HIS B 269 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS B 269 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 HIS B 269 " 0.041 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 335 2.09 - 2.72: 20056 2.72 - 3.35: 33407 3.35 - 3.97: 41862 3.97 - 4.60: 65099 Nonbonded interactions: 160759 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 635 " pdb=" OE2 GLU B 836 " model vdw 1.463 1.850 nonbonded pdb=" HH TYR B 171 " pdb=" O LEU B 880 " model vdw 1.471 1.850 nonbonded pdb="HH11 ARG B 874 " pdb=" O THR B 887 " model vdw 1.484 1.850 nonbonded pdb=" O ASN A 610 " pdb=" H HIS A 778 " model vdw 1.507 1.850 nonbonded pdb=" OD2 ASP A 586 " pdb="HD21 ASN A 602 " model vdw 1.527 1.850 ... (remaining 160754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 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: 0.180 Extract box with map and model: 13.580 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 39.760 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6167 Z= 0.321 Angle : 0.989 8.496 8370 Z= 0.561 Chirality : 0.055 0.175 874 Planarity : 0.006 0.060 1101 Dihedral : 13.450 80.669 2316 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.79 % Favored : 94.80 % Rotamer: Outliers : 1.20 % Allowed : 4.19 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.29), residues: 731 helix: -3.55 (0.43), residues: 65 sheet: 0.23 (0.36), residues: 212 loop : -0.87 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 176 HIS 0.017 0.003 HIS B 269 PHE 0.020 0.003 PHE B 90 TYR 0.025 0.006 TYR A 628 ARG 0.089 0.009 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.062 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: symmetry clash 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: 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 870 ASN cc_start: 0.4986 (m-40) cc_final: 0.4719 (m-40) REVERT: B 131 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7257 (pp) REVERT: B 878 THR cc_start: 0.8570 (m) cc_final: 0.8307 (p) outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 0.4011 time to fit residues: 56.2059 Evaluate side-chains 68 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN B 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6167 Z= 0.278 Angle : 0.708 5.338 8370 Z= 0.386 Chirality : 0.048 0.160 874 Planarity : 0.005 0.047 1101 Dihedral : 6.834 31.892 831 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.10 % Favored : 95.62 % Rotamer: Outliers : 0.15 % Allowed : 3.14 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.30), residues: 731 helix: -2.63 (0.50), residues: 63 sheet: -0.23 (0.36), residues: 196 loop : -0.60 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 618 HIS 0.008 0.002 HIS B 778 PHE 0.019 0.002 PHE B 45 TYR 0.018 0.002 TYR A 858 ARG 0.006 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.910 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: 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 602 ASN cc_start: 0.9115 (m110) cc_final: 0.8711 (m-40) REVERT: A 610 ASN cc_start: 0.8269 (m110) cc_final: 0.7961 (m110) REVERT: A 854 GLU cc_start: 0.8337 (tp30) cc_final: 0.8114 (tp30) REVERT: B 852 ARG cc_start: 0.6557 (ttt-90) cc_final: 0.6174 (ptm160) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.3518 time to fit residues: 33.9681 Evaluate side-chains 48 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.6770 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6167 Z= 0.240 Angle : 0.643 6.142 8370 Z= 0.348 Chirality : 0.047 0.151 874 Planarity : 0.005 0.037 1101 Dihedral : 6.426 31.964 831 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.06 % Favored : 94.80 % Rotamer: Outliers : 0.30 % Allowed : 1.20 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.30), residues: 731 helix: -2.24 (0.58), residues: 63 sheet: -0.59 (0.36), residues: 196 loop : -0.53 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 618 HIS 0.006 0.001 HIS A 774 PHE 0.019 0.002 PHE A 892 TYR 0.014 0.002 TYR B 239 ARG 0.004 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.052 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASN cc_start: 0.9007 (m110) cc_final: 0.8528 (m-40) REVERT: A 693 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6951 (tm-30) REVERT: A 854 GLU cc_start: 0.8192 (tp30) cc_final: 0.7988 (tp30) REVERT: B 602 ASN cc_start: 0.8834 (t0) cc_final: 0.8270 (t0) REVERT: B 608 ASN cc_start: 0.5656 (OUTLIER) cc_final: 0.2521 (t0) REVERT: B 852 ARG cc_start: 0.6597 (ttt-90) cc_final: 0.6276 (ptm160) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.3649 time to fit residues: 34.1335 Evaluate side-chains 57 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.6772 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6167 Z= 0.197 Angle : 0.597 5.600 8370 Z= 0.322 Chirality : 0.047 0.162 874 Planarity : 0.005 0.033 1101 Dihedral : 6.070 30.729 831 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.61 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.30), residues: 731 helix: -1.94 (0.65), residues: 57 sheet: -0.70 (0.35), residues: 208 loop : -0.59 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 244 HIS 0.009 0.002 HIS A 774 PHE 0.012 0.001 PHE B 45 TYR 0.016 0.002 TYR B 13 ARG 0.003 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.878 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 602 ASN cc_start: 0.8998 (m110) cc_final: 0.8599 (m-40) REVERT: A 624 ASP cc_start: 0.8123 (m-30) cc_final: 0.7668 (t0) REVERT: A 693 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6988 (tm-30) REVERT: A 854 GLU cc_start: 0.8146 (tp30) cc_final: 0.7902 (tp30) REVERT: B 810 TRP cc_start: 0.5637 (p-90) cc_final: 0.5336 (p-90) REVERT: B 852 ARG cc_start: 0.6443 (ttt-90) cc_final: 0.5929 (ptm160) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3236 time to fit residues: 30.6126 Evaluate side-chains 54 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 ASN B 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6167 Z= 0.192 Angle : 0.576 5.481 8370 Z= 0.311 Chirality : 0.046 0.144 874 Planarity : 0.004 0.035 1101 Dihedral : 5.823 30.109 831 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.57 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.30), residues: 731 helix: -1.30 (0.68), residues: 54 sheet: -0.86 (0.34), residues: 209 loop : -0.43 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 618 HIS 0.008 0.001 HIS A 774 PHE 0.011 0.001 PHE B 748 TYR 0.012 0.001 TYR B 13 ARG 0.004 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.053 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: symmetry clash 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: symmetry clash REVERT: A 602 ASN cc_start: 0.9016 (m110) cc_final: 0.8648 (m-40) REVERT: A 624 ASP cc_start: 0.8023 (m-30) cc_final: 0.7509 (t0) REVERT: A 693 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 810 TRP cc_start: 0.5667 (p-90) cc_final: 0.5348 (p-90) REVERT: B 852 ARG cc_start: 0.6561 (ttt180) cc_final: 0.6196 (ptm160) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3202 time to fit residues: 30.0732 Evaluate side-chains 53 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.0170 chunk 37 optimal weight: 3.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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: 0.6774 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6167 Z= 0.165 Angle : 0.566 6.726 8370 Z= 0.304 Chirality : 0.046 0.145 874 Planarity : 0.004 0.036 1101 Dihedral : 5.707 28.503 831 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.57 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.93 (0.31), residues: 731 helix: -1.22 (0.74), residues: 48 sheet: -0.89 (0.34), residues: 209 loop : -0.34 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 618 HIS 0.008 0.001 HIS A 774 PHE 0.015 0.001 PHE A 695 TYR 0.015 0.001 TYR B 13 ARG 0.013 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.926 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: symmetry clash 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: symmetry clash REVERT: A 602 ASN cc_start: 0.9015 (m110) cc_final: 0.8655 (m-40) REVERT: A 693 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6831 (tm-30) REVERT: B 810 TRP cc_start: 0.5596 (p-90) cc_final: 0.5274 (p-90) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3907 time to fit residues: 36.3756 Evaluate side-chains 52 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6167 Z= 0.189 Angle : 0.570 5.043 8370 Z= 0.306 Chirality : 0.046 0.154 874 Planarity : 0.005 0.056 1101 Dihedral : 5.648 27.370 831 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.30), residues: 731 helix: -1.53 (0.70), residues: 54 sheet: -0.91 (0.34), residues: 209 loop : -0.42 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 618 HIS 0.009 0.002 HIS A 774 PHE 0.014 0.001 PHE B 747 TYR 0.015 0.001 TYR B 13 ARG 0.009 0.001 ARG B 852 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.934 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: 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 602 ASN cc_start: 0.9029 (m110) cc_final: 0.8677 (m-40) REVERT: A 693 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6945 (tm-30) REVERT: B 810 TRP cc_start: 0.5627 (p-90) cc_final: 0.5261 (p-90) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3209 time to fit residues: 30.8723 Evaluate side-chains 48 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6167 Z= 0.218 Angle : 0.582 4.617 8370 Z= 0.314 Chirality : 0.046 0.155 874 Planarity : 0.005 0.038 1101 Dihedral : 5.744 25.665 831 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.15 % Allowed : 0.90 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.30), residues: 731 helix: -1.60 (0.71), residues: 54 sheet: -1.04 (0.33), residues: 217 loop : -0.54 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 618 HIS 0.008 0.002 HIS A 774 PHE 0.012 0.001 PHE B 45 TYR 0.013 0.002 TYR B 13 ARG 0.008 0.001 ARG B 852 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.972 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: 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 693 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6953 (tm-30) REVERT: B 810 TRP cc_start: 0.5671 (p-90) cc_final: 0.5297 (p-90) REVERT: B 833 LEU cc_start: 0.9149 (mm) cc_final: 0.8616 (tp) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.3462 time to fit residues: 31.4768 Evaluate side-chains 53 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6167 Z= 0.187 Angle : 0.566 4.542 8370 Z= 0.304 Chirality : 0.046 0.168 874 Planarity : 0.005 0.037 1101 Dihedral : 5.647 24.783 831 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.31), residues: 731 helix: -1.47 (0.72), residues: 54 sheet: -0.88 (0.34), residues: 214 loop : -0.53 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 618 HIS 0.008 0.002 HIS A 774 PHE 0.011 0.001 PHE B 45 TYR 0.012 0.001 TYR B 13 ARG 0.004 0.001 ARG B 757 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.992 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASN cc_start: 0.9043 (m110) cc_final: 0.8843 (m-40) REVERT: A 693 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6956 (tm-30) REVERT: B 810 TRP cc_start: 0.5678 (p-90) cc_final: 0.5306 (p-90) REVERT: B 833 LEU cc_start: 0.9183 (mm) cc_final: 0.8581 (tp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3625 time to fit residues: 32.0638 Evaluate side-chains 45 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6167 Z= 0.182 Angle : 0.554 4.483 8370 Z= 0.299 Chirality : 0.046 0.147 874 Planarity : 0.005 0.038 1101 Dihedral : 5.566 24.317 831 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.31), residues: 731 helix: -1.33 (0.74), residues: 54 sheet: -0.81 (0.34), residues: 214 loop : -0.54 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 618 HIS 0.008 0.002 HIS A 774 PHE 0.012 0.001 PHE B 45 TYR 0.012 0.001 TYR B 13 ARG 0.003 0.000 ARG A 813 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.940 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: 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 693 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6931 (tm-30) REVERT: B 810 TRP cc_start: 0.5689 (p-90) cc_final: 0.5284 (p-90) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.3508 time to fit residues: 28.7401 Evaluate side-chains 46 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 16 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.094951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.081637 restraints weight = 108623.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.083804 restraints weight = 58857.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.085333 restraints weight = 39027.312| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6167 Z= 0.181 Angle : 0.551 4.488 8370 Z= 0.297 Chirality : 0.046 0.149 874 Planarity : 0.005 0.038 1101 Dihedral : 5.525 23.427 831 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.31), residues: 731 helix: -1.31 (0.74), residues: 54 sheet: -0.88 (0.32), residues: 230 loop : -0.51 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 822 HIS 0.012 0.002 HIS A 774 PHE 0.012 0.001 PHE B 45 TYR 0.012 0.001 TYR A 835 ARG 0.006 0.000 ARG B 852 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.43 seconds wall clock time: 59 minutes 53.59 seconds (3593.59 seconds total)