Starting phenix.real_space_refine on Fri Dec 8 18:00:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/12_2023/7pvd_13667_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/12_2023/7pvd_13667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/12_2023/7pvd_13667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/12_2023/7pvd_13667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/12_2023/7pvd_13667_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/12_2023/7pvd_13667_updated.pdb" } resolution = 3.7 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 5570 2.51 5 N 1455 2.21 5 O 1793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8902 Number of models: 1 Model: "" Number of chains: 22 Chain: "a" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1298 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "b" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1298 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "c" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1298 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "A" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1484 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "B" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1484 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "C" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1484 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 136 Unusual residues: {'BDP': 6, 'XYS': 7} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 12 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.32, per 1000 atoms: 0.60 Number of scatterers: 8902 At special positions: 0 Unit cell: (86.154, 92.382, 96.534, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 1793 8.00 N 1455 7.00 C 5570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.02 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.02 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 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 Links applied ALPHA1-3 " BDP M 2 " - " XYS M 3 " " BDP M 4 " - " XYS M 5 " " BDP M 6 " - " XYS M 7 " " BDP M 8 " - " XYS M 9 " " BDP M 10 " - " XYS M 11 " " BDP M 12 " - " XYS M 13 " BETA1-3 " XYS M 1 " - " BDP M 2 " " XYS M 3 " - " BDP M 4 " " XYS M 5 " - " BDP M 6 " " XYS M 7 " - " BDP M 8 " " XYS M 9 " - " BDP M 10 " " XYS M 11 " - " BDP M 12 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG A 302 " - " ASN A 109 " " NAG B 301 " - " ASN B 99 " " NAG B 302 " - " ASN B 109 " " NAG C 301 " - " ASN C 99 " " NAG C 302 " - " ASN C 109 " " NAG D 1 " - " ASN A 119 " " NAG E 1 " - " ASN A 167 " " NAG F 1 " - " ASN A 79 " " NAG G 1 " - " ASN B 119 " " NAG H 1 " - " ASN B 167 " " NAG I 1 " - " ASN B 79 " " NAG J 1 " - " ASN C 119 " " NAG K 1 " - " ASN C 167 " " NAG L 1 " - " ASN C 79 " " NAG a 601 " - " ASN a 365 " " NAG a 602 " - " ASN a 395 " " NAG b 601 " - " ASN b 365 " " NAG b 602 " - " ASN b 395 " " NAG c 601 " - " ASN c 365 " " NAG c 602 " - " ASN c 395 " Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.6 seconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 3 sheets defined 32.8% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'a' and resid 295 through 302 removed outlier: 4.565A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN a 302 " --> pdb=" O VAL a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 309 through 325 Processing helix chain 'a' and resid 334 through 344 removed outlier: 5.397A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 349 through 359 Processing helix chain 'a' and resid 400 through 418 Processing helix chain 'b' and resid 295 through 302 removed outlier: 4.564A pdb=" N CYS b 301 " --> pdb=" O ALA b 297 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN b 302 " --> pdb=" O VAL b 298 " (cutoff:3.500A) Processing helix chain 'b' and resid 309 through 325 Processing helix chain 'b' and resid 334 through 344 removed outlier: 5.398A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 349 through 359 Processing helix chain 'b' and resid 400 through 418 Processing helix chain 'c' and resid 295 through 302 removed outlier: 4.564A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN c 302 " --> pdb=" O VAL c 298 " (cutoff:3.500A) Processing helix chain 'c' and resid 309 through 325 Processing helix chain 'c' and resid 334 through 344 removed outlier: 5.397A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 349 through 359 Processing helix chain 'c' and resid 400 through 418 Processing helix chain 'A' and resid 75 through 78 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.762A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.763A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 239 through 247 removed outlier: 3.762A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.623A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.623A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.623A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) 270 hydrogen bonds defined for protein. 765 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: 2.17 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2784 1.34 - 1.46: 2297 1.46 - 1.58: 3866 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 9079 Sorted by residual: bond pdb=" C3 BDP M 6 " pdb=" O3 BDP M 6 " ideal model delta sigma weight residual 1.411 1.520 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C3 BDP M 10 " pdb=" O3 BDP M 10 " ideal model delta sigma weight residual 1.411 1.518 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C3 BDP M 2 " pdb=" O3 BDP M 2 " ideal model delta sigma weight residual 1.411 1.517 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C3 BDP M 4 " pdb=" O3 BDP M 4 " ideal model delta sigma weight residual 1.411 1.517 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C3 BDP M 8 " pdb=" O3 BDP M 8 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.72e+01 ... (remaining 9074 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.12: 150 106.12 - 113.09: 5172 113.09 - 120.06: 3066 120.06 - 127.03: 3780 127.03 - 134.00: 107 Bond angle restraints: 12275 Sorted by residual: angle pdb=" C LEU C 103 " pdb=" N GLU C 104 " pdb=" CA GLU C 104 " ideal model delta sigma weight residual 121.42 127.02 -5.60 1.43e+00 4.89e-01 1.53e+01 angle pdb=" C LEU B 103 " pdb=" N GLU B 104 " pdb=" CA GLU B 104 " ideal model delta sigma weight residual 121.42 126.99 -5.57 1.43e+00 4.89e-01 1.52e+01 angle pdb=" C LEU A 103 " pdb=" N GLU A 104 " pdb=" CA GLU A 104 " ideal model delta sigma weight residual 121.42 126.96 -5.54 1.43e+00 4.89e-01 1.50e+01 angle pdb=" C ILE A 222 " pdb=" N GLN A 223 " pdb=" CA GLN A 223 " ideal model delta sigma weight residual 121.75 115.86 5.89 1.73e+00 3.34e-01 1.16e+01 angle pdb=" C ILE C 222 " pdb=" N GLN C 223 " pdb=" CA GLN C 223 " ideal model delta sigma weight residual 121.75 115.87 5.88 1.73e+00 3.34e-01 1.16e+01 ... (remaining 12270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 5485 27.97 - 55.95: 279 55.95 - 83.92: 21 83.92 - 111.90: 48 111.90 - 139.87: 7 Dihedral angle restraints: 5840 sinusoidal: 2816 harmonic: 3024 Sorted by residual: dihedral pdb=" CB CYS b 301 " pdb=" SG CYS b 301 " pdb=" SG CYS b 310 " pdb=" CB CYS b 310 " ideal model delta sinusoidal sigma weight residual 93.00 142.75 -49.75 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS c 301 " pdb=" SG CYS c 301 " pdb=" SG CYS c 310 " pdb=" CB CYS c 310 " ideal model delta sinusoidal sigma weight residual 93.00 142.74 -49.74 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS a 301 " pdb=" SG CYS a 301 " pdb=" SG CYS a 310 " pdb=" CB CYS a 310 " ideal model delta sinusoidal sigma weight residual 93.00 142.71 -49.71 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 5837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1306 0.078 - 0.156: 151 0.156 - 0.234: 11 0.234 - 0.312: 0 0.312 - 0.390: 3 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 79 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 79 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 79 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 1468 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 104 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C GLU C 104 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU C 104 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU C 105 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 104 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C GLU B 104 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU B 104 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 105 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 104 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C GLU A 104 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU A 104 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 105 " 0.010 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 206 2.69 - 3.24: 9032 3.24 - 3.79: 13800 3.79 - 4.35: 18547 4.35 - 4.90: 29747 Nonbonded interactions: 71332 Sorted by model distance: nonbonded pdb=" OE2 GLU b 396 " pdb=" OH TYR B 62 " model vdw 2.134 2.440 nonbonded pdb=" OE1 GLU C 100 " pdb=" OG1 THR C 101 " model vdw 2.175 2.440 nonbonded pdb=" OE1 GLU B 100 " pdb=" OG1 THR B 101 " model vdw 2.175 2.440 nonbonded pdb=" OE1 GLU A 100 " pdb=" OG1 THR A 101 " model vdw 2.175 2.440 nonbonded pdb=" OD1 ASP c 347 " pdb=" OG SER C 246 " model vdw 2.206 2.440 ... (remaining 71327 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.680 Find NCS groups from input model: 0.610 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 : 0.007 0.109 9079 Z= 0.438 Angle : 0.826 8.936 12275 Z= 0.393 Chirality : 0.051 0.390 1471 Planarity : 0.004 0.040 1497 Dihedral : 18.571 139.869 3836 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.32 % Allowed : 2.04 % Favored : 97.64 % 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: -1.16 (0.24), residues: 1011 helix: -0.36 (0.27), residues: 351 sheet: -0.45 (0.42), residues: 150 loop : -1.09 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 227 HIS 0.005 0.001 HIS a 305 PHE 0.009 0.001 PHE B 191 TYR 0.021 0.002 TYR A 253 ARG 0.003 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 286 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 288 average time/residue: 0.2580 time to fit residues: 98.9604 Evaluate side-chains 157 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 405 GLN A 127 ASN A 146 ASN A 170 HIS B 127 ASN B 131 HIS B 170 HIS C 127 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9079 Z= 0.259 Angle : 0.773 10.340 12275 Z= 0.377 Chirality : 0.049 0.327 1471 Planarity : 0.004 0.055 1497 Dihedral : 13.813 126.953 1841 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.89 % Allowed : 11.90 % Favored : 85.21 % 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: -0.76 (0.25), residues: 1011 helix: 0.24 (0.27), residues: 324 sheet: -0.92 (0.44), residues: 120 loop : -0.80 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP a 386 HIS 0.010 0.002 HIS A 141 PHE 0.012 0.002 PHE C 191 TYR 0.021 0.002 TYR C 62 ARG 0.009 0.001 ARG a 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 199 average time/residue: 0.2329 time to fit residues: 62.6373 Evaluate side-chains 179 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0884 time to fit residues: 3.7255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 0.0770 chunk 63 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.0070 chunk 31 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 398 HIS b 405 GLN B 127 ASN B 170 HIS B 189 GLN C 92 HIS C 127 ASN C 146 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9079 Z= 0.161 Angle : 0.647 9.056 12275 Z= 0.316 Chirality : 0.045 0.224 1471 Planarity : 0.003 0.036 1497 Dihedral : 10.708 125.151 1841 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.29 % Allowed : 14.47 % Favored : 84.24 % 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: -0.75 (0.25), residues: 1011 helix: 0.07 (0.27), residues: 348 sheet: -0.65 (0.47), residues: 120 loop : -0.77 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 210 HIS 0.007 0.001 HIS A 141 PHE 0.021 0.001 PHE C 191 TYR 0.014 0.001 TYR B 62 ARG 0.006 0.001 ARG a 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 176 average time/residue: 0.2271 time to fit residues: 54.5111 Evaluate side-chains 165 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0943 time to fit residues: 1.7080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN A 146 ASN B 127 ASN C 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9079 Z= 0.262 Angle : 0.703 9.791 12275 Z= 0.345 Chirality : 0.047 0.235 1471 Planarity : 0.004 0.045 1497 Dihedral : 9.635 121.994 1841 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.71 % Allowed : 16.08 % Favored : 82.21 % 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: -0.39 (0.26), residues: 1011 helix: 0.47 (0.28), residues: 324 sheet: -0.41 (0.44), residues: 144 loop : -0.60 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 227 HIS 0.007 0.001 HIS B 230 PHE 0.017 0.002 PHE C 191 TYR 0.018 0.002 TYR A 253 ARG 0.009 0.001 ARG a 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 182 average time/residue: 0.2214 time to fit residues: 55.3850 Evaluate side-chains 159 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0890 time to fit residues: 2.3098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 0.0060 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN B 127 ASN B 170 HIS B 209 ASN C 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9079 Z= 0.255 Angle : 0.689 9.422 12275 Z= 0.340 Chirality : 0.045 0.223 1471 Planarity : 0.004 0.035 1497 Dihedral : 9.443 119.995 1841 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.47 % Allowed : 16.51 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.26), residues: 1011 helix: 0.79 (0.29), residues: 318 sheet: -0.28 (0.44), residues: 144 loop : -0.72 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 210 HIS 0.008 0.001 HIS A 93 PHE 0.018 0.002 PHE C 191 TYR 0.018 0.002 TYR A 253 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 181 average time/residue: 0.2319 time to fit residues: 57.3040 Evaluate side-chains 167 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1245 time to fit residues: 3.7180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 51 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN b 406 GLN c 390 ASN C 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9079 Z= 0.171 Angle : 0.631 9.559 12275 Z= 0.309 Chirality : 0.043 0.228 1471 Planarity : 0.003 0.034 1497 Dihedral : 9.117 117.664 1841 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 18.11 % Favored : 80.49 % 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: -0.14 (0.27), residues: 1011 helix: 0.92 (0.30), residues: 321 sheet: -0.16 (0.45), residues: 144 loop : -0.65 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 210 HIS 0.005 0.001 HIS A 141 PHE 0.022 0.001 PHE C 191 TYR 0.010 0.001 TYR A 253 ARG 0.003 0.000 ARG a 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 170 average time/residue: 0.2227 time to fit residues: 52.0249 Evaluate side-chains 156 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0898 time to fit residues: 1.9746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 0.0040 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN c 390 ASN A 127 ASN C 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9079 Z= 0.166 Angle : 0.637 9.294 12275 Z= 0.313 Chirality : 0.042 0.230 1471 Planarity : 0.004 0.057 1497 Dihedral : 8.895 117.232 1841 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.18 % Allowed : 18.97 % Favored : 79.85 % 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: -0.31 (0.27), residues: 1011 helix: 0.59 (0.29), residues: 345 sheet: -0.07 (0.46), residues: 144 loop : -0.75 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 210 HIS 0.005 0.001 HIS B 230 PHE 0.017 0.001 PHE C 191 TYR 0.009 0.001 TYR A 253 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 170 average time/residue: 0.2195 time to fit residues: 52.1454 Evaluate side-chains 154 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0937 time to fit residues: 1.5654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN b 405 GLN c 331 GLN c 390 ASN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN B 127 ASN C 127 ASN C 146 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9079 Z= 0.284 Angle : 0.703 9.472 12275 Z= 0.349 Chirality : 0.045 0.242 1471 Planarity : 0.004 0.030 1497 Dihedral : 8.903 116.590 1841 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.39 % Allowed : 19.51 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.27), residues: 1011 helix: 0.70 (0.29), residues: 336 sheet: 0.07 (0.46), residues: 141 loop : -0.97 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP B 210 HIS 0.013 0.001 HIS A 230 PHE 0.016 0.002 PHE C 191 TYR 0.023 0.002 TYR b 363 ARG 0.005 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 169 average time/residue: 0.2140 time to fit residues: 50.4957 Evaluate side-chains 160 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0949 time to fit residues: 2.5870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN c 390 ASN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN B 127 ASN C 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9079 Z= 0.192 Angle : 0.675 10.869 12275 Z= 0.333 Chirality : 0.044 0.221 1471 Planarity : 0.003 0.032 1497 Dihedral : 8.732 115.136 1841 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.43 % Allowed : 20.69 % Favored : 78.89 % 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: -0.20 (0.27), residues: 1011 helix: 1.06 (0.30), residues: 318 sheet: -0.24 (0.45), residues: 144 loop : -0.80 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP B 210 HIS 0.005 0.001 HIS B 230 PHE 0.019 0.001 PHE A 191 TYR 0.053 0.002 TYR A 94 ARG 0.003 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.086 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 outliers start: 4 outliers final: 2 residues processed: 167 average time/residue: 0.2115 time to fit residues: 49.4483 Evaluate side-chains 152 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0865 time to fit residues: 1.7052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN c 390 ASN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN B 127 ASN C 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9079 Z= 0.244 Angle : 0.700 11.626 12275 Z= 0.345 Chirality : 0.044 0.215 1471 Planarity : 0.003 0.033 1497 Dihedral : 8.927 115.431 1841 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.43 % Allowed : 21.76 % Favored : 77.81 % 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: -0.41 (0.27), residues: 1011 helix: 0.78 (0.29), residues: 333 sheet: -0.21 (0.46), residues: 144 loop : -0.95 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B 210 HIS 0.005 0.001 HIS B 230 PHE 0.016 0.001 PHE A 191 TYR 0.016 0.002 TYR A 94 ARG 0.003 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 156 average time/residue: 0.2175 time to fit residues: 47.0219 Evaluate side-chains 148 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1128 time to fit residues: 1.8146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.0670 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.0370 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN B 127 ASN C 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122287 restraints weight = 13866.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125034 restraints weight = 9513.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127073 restraints weight = 7497.021| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9079 Z= 0.190 Angle : 0.680 11.569 12275 Z= 0.335 Chirality : 0.044 0.228 1471 Planarity : 0.004 0.044 1497 Dihedral : 8.766 113.789 1841 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.43 % Allowed : 21.44 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.34 (0.27), residues: 1011 helix: 0.78 (0.29), residues: 336 sheet: -0.22 (0.46), residues: 144 loop : -0.86 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP B 210 HIS 0.005 0.001 HIS B 230 PHE 0.019 0.001 PHE A 191 TYR 0.023 0.001 TYR B 94 ARG 0.002 0.000 ARG C 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2077.46 seconds wall clock time: 38 minutes 48.09 seconds (2328.09 seconds total)