Starting phenix.real_space_refine on Mon Mar 11 19:23:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/03_2024/7pvd_13667_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/03_2024/7pvd_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_13667/03_2024/7pvd_13667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/03_2024/7pvd_13667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/03_2024/7pvd_13667_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pvd_13667/03_2024/7pvd_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-dev-5265/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: 36 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: 5.08, per 1000 atoms: 0.57 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: 3.84 Conformation dependent library (CDL) restraints added in 1.8 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: 2.12 Time building geometry restraints manager: 4.04 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: 5595 27.97 - 55.95: 291 55.95 - 83.92: 22 83.92 - 111.90: 51 111.90 - 139.87: 7 Dihedral angle restraints: 5966 sinusoidal: 2942 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 5963 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.160 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 26.430 Find NCS groups from input model: 0.550 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- 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 : 18.683 139.869 3962 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 : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7114 (t0) cc_final: 0.6897 (t0) REVERT: a 417 LYS cc_start: 0.6310 (mptm) cc_final: 0.6076 (mptt) REVERT: b 312 MET cc_start: 0.7583 (mmm) cc_final: 0.7308 (mmt) REVERT: b 357 ASP cc_start: 0.8004 (t0) cc_final: 0.7760 (t0) REVERT: b 414 MET cc_start: 0.6694 (ttm) cc_final: 0.6481 (ttm) REVERT: c 357 ASP cc_start: 0.8182 (t0) cc_final: 0.7845 (t0) REVERT: A 228 GLU cc_start: 0.6696 (mp0) cc_final: 0.6433 (mt-10) REVERT: A 255 SER cc_start: 0.7468 (m) cc_final: 0.7088 (t) REVERT: B 255 SER cc_start: 0.7950 (m) cc_final: 0.7693 (t) REVERT: C 68 LEU cc_start: 0.8077 (tp) cc_final: 0.7827 (tp) outliers start: 3 outliers final: 0 residues processed: 288 average time/residue: 0.2611 time to fit residues: 98.1336 Evaluate side-chains 163 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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: 0.0770 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 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: 0.5978 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9079 Z= 0.199 Angle : 0.721 11.095 12275 Z= 0.352 Chirality : 0.047 0.298 1471 Planarity : 0.004 0.054 1497 Dihedral : 14.798 127.741 1967 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.79 % Allowed : 11.15 % Favored : 86.07 % 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: -0.90 (0.24), residues: 1011 helix: 0.00 (0.27), residues: 348 sheet: -0.50 (0.46), residues: 108 loop : -0.98 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 370 HIS 0.009 0.001 HIS A 141 PHE 0.009 0.002 PHE C 233 TYR 0.020 0.002 TYR C 62 ARG 0.008 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 211 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7331 (t0) cc_final: 0.7111 (t0) REVERT: b 312 MET cc_start: 0.7694 (mmm) cc_final: 0.7477 (mmp) REVERT: b 405 GLN cc_start: 0.7330 (tp40) cc_final: 0.7123 (tt0) REVERT: c 357 ASP cc_start: 0.8082 (t0) cc_final: 0.7848 (t0) REVERT: A 62 TYR cc_start: 0.5370 (m-80) cc_final: 0.4918 (m-80) REVERT: A 249 THR cc_start: 0.8825 (p) cc_final: 0.8624 (p) REVERT: A 255 SER cc_start: 0.7754 (m) cc_final: 0.7385 (t) outliers start: 26 outliers final: 15 residues processed: 197 average time/residue: 0.2134 time to fit residues: 57.6142 Evaluate side-chains 184 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain a residue 412 THR Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 127 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN C 92 HIS C 127 ASN C 146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9079 Z= 0.286 Angle : 0.748 8.245 12275 Z= 0.363 Chirality : 0.048 0.227 1471 Planarity : 0.004 0.037 1497 Dihedral : 11.301 124.085 1967 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.00 % Allowed : 13.93 % Favored : 83.07 % 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: -0.55 (0.25), residues: 1011 helix: 0.24 (0.28), residues: 324 sheet: -0.57 (0.47), residues: 120 loop : -0.62 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP b 386 HIS 0.008 0.002 HIS B 230 PHE 0.025 0.002 PHE C 191 TYR 0.020 0.002 TYR A 94 ARG 0.012 0.001 ARG C 193 *********************** 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 214 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 357 ASP cc_start: 0.7194 (t0) cc_final: 0.6852 (t0) REVERT: a 359 MET cc_start: 0.8168 (mtm) cc_final: 0.7718 (mtm) REVERT: a 419 TYR cc_start: 0.1729 (m-80) cc_final: 0.1066 (m-80) REVERT: b 312 MET cc_start: 0.7884 (mmm) cc_final: 0.7621 (mmp) REVERT: b 335 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7200 (mt0) REVERT: c 283 TRP cc_start: 0.5197 (m-10) cc_final: 0.4954 (m100) REVERT: c 357 ASP cc_start: 0.8135 (t0) cc_final: 0.7843 (t0) REVERT: A 229 ASP cc_start: 0.6998 (t70) cc_final: 0.6780 (t70) REVERT: A 255 SER cc_start: 0.7958 (m) cc_final: 0.7652 (t) REVERT: B 122 ASP cc_start: 0.7782 (t0) cc_final: 0.7494 (t0) REVERT: C 125 LYS cc_start: 0.8697 (tptt) cc_final: 0.7771 (ttmm) REVERT: C 227 TRP cc_start: 0.6661 (OUTLIER) cc_final: 0.6347 (t60) outliers start: 28 outliers final: 17 residues processed: 201 average time/residue: 0.2118 time to fit residues: 58.5866 Evaluate side-chains 180 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 419 TYR Chi-restraints excluded: chain c residue 344 LEU Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 227 TRP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 252 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 A 146 ASN B 127 ASN B 170 HIS C 127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4131 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= 0.211 Angle : 0.653 9.686 12275 Z= 0.324 Chirality : 0.044 0.233 1471 Planarity : 0.004 0.041 1497 Dihedral : 10.123 121.600 1967 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.75 % Allowed : 14.58 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1011 helix: 0.79 (0.29), residues: 318 sheet: -0.51 (0.48), residues: 120 loop : -0.56 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 210 HIS 0.008 0.001 HIS A 93 PHE 0.016 0.001 PHE A 191 TYR 0.016 0.002 TYR C 94 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 203 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 357 ASP cc_start: 0.7285 (t0) cc_final: 0.6955 (t0) REVERT: a 359 MET cc_start: 0.8344 (mtm) cc_final: 0.7907 (mtm) REVERT: a 419 TYR cc_start: 0.1856 (m-80) cc_final: 0.0521 (m-80) REVERT: c 357 ASP cc_start: 0.8124 (t0) cc_final: 0.7869 (t0) REVERT: A 229 ASP cc_start: 0.7090 (t70) cc_final: 0.6790 (t70) REVERT: A 255 SER cc_start: 0.8004 (m) cc_final: 0.7794 (t) REVERT: B 193 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7694 (mmm-85) REVERT: C 125 LYS cc_start: 0.8621 (tptt) cc_final: 0.7750 (ttmm) REVERT: C 227 TRP cc_start: 0.6594 (OUTLIER) cc_final: 0.6289 (t60) REVERT: C 252 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.9011 (pt) REVERT: C 253 TYR cc_start: 0.8635 (m-10) cc_final: 0.8349 (m-10) outliers start: 35 outliers final: 19 residues processed: 185 average time/residue: 0.2125 time to fit residues: 54.0215 Evaluate side-chains 181 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 405 GLN Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 TRP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 252 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.0010 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** c 390 ASN B 127 ASN B 170 HIS C 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9079 Z= 0.167 Angle : 0.617 8.486 12275 Z= 0.304 Chirality : 0.043 0.231 1471 Planarity : 0.003 0.034 1497 Dihedral : 9.647 120.393 1967 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.68 % Allowed : 17.58 % Favored : 79.74 % 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: -0.34 (0.26), residues: 1011 helix: 0.55 (0.29), residues: 339 sheet: -0.31 (0.44), residues: 144 loop : -0.66 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 210 HIS 0.005 0.001 HIS A 141 PHE 0.006 0.001 PHE c 399 TYR 0.035 0.001 TYR A 94 ARG 0.003 0.000 ARG C 193 *********************** 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 195 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 357 ASP cc_start: 0.7320 (t0) cc_final: 0.7009 (t0) REVERT: b 361 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8237 (mt) REVERT: c 357 ASP cc_start: 0.8166 (t0) cc_final: 0.7837 (t0) REVERT: A 229 ASP cc_start: 0.7009 (t70) cc_final: 0.6743 (t70) REVERT: A 255 SER cc_start: 0.7899 (m) cc_final: 0.7656 (t) REVERT: B 122 ASP cc_start: 0.7823 (t0) cc_final: 0.7518 (t0) REVERT: C 125 LYS cc_start: 0.8600 (tptt) cc_final: 0.7742 (ttmm) REVERT: C 227 TRP cc_start: 0.6554 (OUTLIER) cc_final: 0.6335 (t60) outliers start: 25 outliers final: 14 residues processed: 182 average time/residue: 0.2109 time to fit residues: 52.8841 Evaluate side-chains 174 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain c residue 310 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 227 TRP Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN C 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9079 Z= 0.183 Angle : 0.624 10.310 12275 Z= 0.306 Chirality : 0.043 0.230 1471 Planarity : 0.003 0.032 1497 Dihedral : 9.368 119.693 1967 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.11 % Allowed : 17.90 % Favored : 78.99 % 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: -0.27 (0.27), residues: 1011 helix: 0.64 (0.29), residues: 339 sheet: -0.11 (0.46), residues: 144 loop : -0.69 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 210 HIS 0.005 0.001 HIS A 93 PHE 0.006 0.001 PHE c 399 TYR 0.014 0.001 TYR A 94 ARG 0.004 0.000 ARG B 256 *********************** 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 191 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 312 MET cc_start: 0.7682 (mmt) cc_final: 0.7394 (mmt) REVERT: c 357 ASP cc_start: 0.8189 (t0) cc_final: 0.7831 (t0) REVERT: A 255 SER cc_start: 0.7909 (m) cc_final: 0.7672 (t) REVERT: B 122 ASP cc_start: 0.7883 (t0) cc_final: 0.7569 (t0) REVERT: B 193 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7731 (tpt-90) REVERT: C 125 LYS cc_start: 0.8705 (tptt) cc_final: 0.7899 (ttmm) outliers start: 29 outliers final: 21 residues processed: 181 average time/residue: 0.2087 time to fit residues: 52.4261 Evaluate side-chains 176 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 310 CYS Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain c residue 310 CYS Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 98 optimal weight: 0.0000 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 0.0770 chunk 45 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN C 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9079 Z= 0.150 Angle : 0.600 10.147 12275 Z= 0.294 Chirality : 0.042 0.231 1471 Planarity : 0.003 0.034 1497 Dihedral : 9.044 118.280 1967 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.57 % Allowed : 18.97 % Favored : 78.46 % 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: -0.22 (0.27), residues: 1011 helix: 0.73 (0.29), residues: 336 sheet: -0.03 (0.45), residues: 144 loop : -0.71 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 227 HIS 0.005 0.001 HIS B 230 PHE 0.005 0.001 PHE b 318 TYR 0.013 0.001 TYR A 94 ARG 0.003 0.000 ARG C 193 *********************** 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 188 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 329 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6362 (tp30) REVERT: c 357 ASP cc_start: 0.8166 (t0) cc_final: 0.7803 (t0) REVERT: A 255 SER cc_start: 0.7840 (m) cc_final: 0.7569 (t) REVERT: C 125 LYS cc_start: 0.8553 (tptt) cc_final: 0.7777 (ttmm) REVERT: C 194 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7382 (ttt) outliers start: 24 outliers final: 16 residues processed: 177 average time/residue: 0.2156 time to fit residues: 52.2942 Evaluate side-chains 176 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain b residue 329 GLU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain c residue 310 CYS Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN A 127 ASN B 127 ASN C 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9079 Z= 0.222 Angle : 0.644 10.203 12275 Z= 0.317 Chirality : 0.043 0.221 1471 Planarity : 0.003 0.033 1497 Dihedral : 8.873 117.896 1967 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.89 % Allowed : 19.19 % Favored : 77.92 % 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: -0.04 (0.27), residues: 1011 helix: 1.10 (0.30), residues: 315 sheet: 0.01 (0.46), residues: 144 loop : -0.68 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 210 HIS 0.005 0.001 HIS B 230 PHE 0.009 0.001 PHE a 316 TYR 0.023 0.002 TYR b 363 ARG 0.004 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 192 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 329 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6553 (tp30) REVERT: c 357 ASP cc_start: 0.8173 (t0) cc_final: 0.7739 (t0) REVERT: A 255 SER cc_start: 0.7883 (m) cc_final: 0.7647 (t) REVERT: B 122 ASP cc_start: 0.7948 (t0) cc_final: 0.7605 (t0) REVERT: C 86 CYS cc_start: 0.3148 (p) cc_final: 0.2529 (p) REVERT: C 125 LYS cc_start: 0.8724 (tptt) cc_final: 0.7991 (ttmm) REVERT: C 194 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7388 (ttt) REVERT: C 255 SER cc_start: 0.8418 (m) cc_final: 0.8086 (t) outliers start: 27 outliers final: 17 residues processed: 181 average time/residue: 0.2118 time to fit residues: 52.6208 Evaluate side-chains 175 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 324 GLN Chi-restraints excluded: chain b residue 329 GLU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 381 SER Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain c residue 310 CYS Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 0.0020 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 335 GLN A 127 ASN B 127 ASN C 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9079 Z= 0.177 Angle : 0.611 10.691 12275 Z= 0.300 Chirality : 0.042 0.220 1471 Planarity : 0.003 0.047 1497 Dihedral : 8.639 116.444 1967 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.68 % Allowed : 18.86 % Favored : 78.46 % 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 (0.27), residues: 1011 helix: 0.67 (0.29), residues: 342 sheet: 0.02 (0.46), residues: 144 loop : -0.80 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 227 HIS 0.005 0.001 HIS B 230 PHE 0.016 0.001 PHE A 191 TYR 0.010 0.001 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 185 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 312 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7279 (mmp) REVERT: b 329 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6417 (tp30) REVERT: c 357 ASP cc_start: 0.8175 (t0) cc_final: 0.7784 (t0) REVERT: C 86 CYS cc_start: 0.3040 (p) cc_final: 0.2402 (p) REVERT: C 125 LYS cc_start: 0.8682 (tptt) cc_final: 0.7965 (ttmm) REVERT: C 134 MET cc_start: 0.7920 (mmm) cc_final: 0.7634 (tpt) outliers start: 25 outliers final: 17 residues processed: 172 average time/residue: 0.2290 time to fit residues: 54.5559 Evaluate side-chains 174 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain a residue 381 SER Chi-restraints excluded: chain b residue 329 GLU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain c residue 310 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 C 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9079 Z= 0.197 Angle : 0.641 11.311 12275 Z= 0.315 Chirality : 0.043 0.209 1471 Planarity : 0.003 0.031 1497 Dihedral : 8.559 116.020 1967 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.93 % Allowed : 19.40 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 1011 helix: 0.70 (0.29), residues: 342 sheet: 0.04 (0.46), residues: 144 loop : -0.83 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 227 HIS 0.005 0.001 HIS B 230 PHE 0.015 0.001 PHE A 191 TYR 0.017 0.001 TYR a 363 ARG 0.005 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 172 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 312 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7519 (mmp) REVERT: b 329 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6404 (tp30) REVERT: c 331 GLN cc_start: 0.6778 (mt0) cc_final: 0.6573 (mm-40) REVERT: c 357 ASP cc_start: 0.8167 (t0) cc_final: 0.7811 (t0) REVERT: C 86 CYS cc_start: 0.3049 (p) cc_final: 0.2437 (p) REVERT: C 125 LYS cc_start: 0.8711 (tptt) cc_final: 0.8013 (ttmm) REVERT: C 134 MET cc_start: 0.7948 (mmm) cc_final: 0.7727 (tpt) REVERT: C 189 GLN cc_start: 0.7779 (mt0) cc_final: 0.7232 (mt0) outliers start: 18 outliers final: 16 residues processed: 162 average time/residue: 0.2197 time to fit residues: 48.7318 Evaluate side-chains 167 residues out of total 933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain b residue 329 GLU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain c residue 310 CYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 A 224 ASN C 127 ASN C 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118605 restraints weight = 13900.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121443 restraints weight = 9546.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123480 restraints weight = 7461.551| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9079 Z= 0.257 Angle : 0.682 10.774 12275 Z= 0.336 Chirality : 0.045 0.207 1471 Planarity : 0.003 0.032 1497 Dihedral : 8.574 115.472 1967 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.68 % Allowed : 19.29 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 1011 helix: 0.94 (0.29), residues: 318 sheet: -0.14 (0.45), residues: 144 loop : -0.82 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 283 HIS 0.006 0.001 HIS C 93 PHE 0.015 0.001 PHE A 191 TYR 0.017 0.002 TYR a 363 ARG 0.006 0.001 ARG C 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2040.44 seconds wall clock time: 38 minutes 9.42 seconds (2289.42 seconds total)