Starting phenix.real_space_refine on Mon Nov 17 23:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6meo_9108/11_2025/6meo_9108.cif Found real_map, /net/cci-nas-00/data/ceres_data/6meo_9108/11_2025/6meo_9108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6meo_9108/11_2025/6meo_9108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6meo_9108/11_2025/6meo_9108.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6meo_9108/11_2025/6meo_9108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6meo_9108/11_2025/6meo_9108.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1602 atoms to isotropic. 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 47 5.16 5 C 4767 2.51 5 N 1208 2.21 5 O 1443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7465 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3103 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2562 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 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: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "G" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 109 Unusual residues: {'BMA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'A2G': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.84, per 1000 atoms: 0.25 Number of scatterers: 7465 At special positions: 0 Unit cell: (114.372, 146.142, 111.195, 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 47 16.00 O 1443 8.00 N 1208 7.00 C 4767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 73 " distance=2.03 Simple disulfide: pdb=" SG CYS G 118 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 125 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 330 " distance=2.03 Simple disulfide: pdb=" SG CYS G 376 " - pdb=" SG CYS G 440 " distance=2.03 Simple disulfide: pdb=" SG CYS G 383 " - pdb=" SG CYS G 413 " distance=2.03 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 84 " distance=2.04 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 178 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " BETA1-6 " BMA E 3 " - " BMA G 612 " NAG-ASN " NAG C 1 " - " ASN G 234 " " NAG D 1 " - " ASN G 241 " " NAG E 1 " - " ASN G 262 " " NAG F 1 " - " ASN G 276 " " NAG G 601 " - " ASN G 87 " " NAG G 619 " - " ASN G 338 " " NAG G 620 " - " ASN G 354 " " NAG G 626 " - " ASN G 395 " " NAG G 627 " - " ASN G 459 " " NAG G 628 " - " ASN G 197 " " NAG G 631 " - " ASN G 390 " " NAG H 1 " - " ASN G 295 " " NAG I 1 " - " ASN G 331 " " NAG J 1 " - " ASN G 301 " " NAG K 1 " - " ASN G 384 " " NAG L 1 " - " ASN G 443 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 363.8 milliseconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 13 sheets defined 36.1% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.713A pdb=" N GLU G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE G 108 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU G 115 " --> pdb=" O TRP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 353 removed outlier: 4.686A pdb=" N ASP G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR G 340 " --> pdb=" O GLN G 336 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR G 346 " --> pdb=" O SER G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 371 removed outlier: 3.623A pdb=" N PHE G 371 " --> pdb=" O PRO G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 389 removed outlier: 3.841A pdb=" N PHE G 389 " --> pdb=" O THR G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 477 removed outlier: 3.737A pdb=" N SER G 477 " --> pdb=" O ASP G 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 removed outlier: 4.208A pdb=" N ASP A 63 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.777A pdb=" N SER A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 32 through 58 removed outlier: 3.599A pdb=" N LEU B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 81 Processing helix chain 'B' and resid 82 through 91 removed outlier: 3.903A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 131 removed outlier: 3.836A pdb=" N GLY B 106 " --> pdb=" O GLN B 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 140 removed outlier: 3.621A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.580A pdb=" N ASN B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.509A pdb=" N GLY B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 260 removed outlier: 3.553A pdb=" N HIS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.677A pdb=" N THR B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 288 removed outlier: 3.771A pdb=" N GLN B 277 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.897A pdb=" N ILE B 295 " --> pdb=" O CYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 removed outlier: 3.585A pdb=" N VAL B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.527A pdb=" N LYS G 45 " --> pdb=" O ARG G 486 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS G 483 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 55 Processing sheet with id=AA3, first strand: chain 'G' and resid 196 through 202 removed outlier: 3.609A pdb=" N VAL G 119 " --> pdb=" O MET G 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 271 through 273 Processing sheet with id=AA5, first strand: chain 'G' and resid 408 through 414 removed outlier: 3.580A pdb=" N LEU G 332 " --> pdb=" O ILE G 409 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 413 " --> pdb=" O ALA G 328 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA G 328 " --> pdb=" O CYS G 413 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN G 295 " --> pdb=" O ASN G 331 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE G 294 " --> pdb=" O SER G 442 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 357 through 359 Processing sheet with id=AA7, first strand: chain 'G' and resid 372 through 376 Processing sheet with id=AA8, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.531A pdb=" N VAL A 12 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 71 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.961A pdb=" N TRP A 28 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AB3, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB4, first strand: chain 'A' and resid 128 through 131 262 hydrogen bonds defined for protein. 720 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: 0.89 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2057 1.34 - 1.46: 1629 1.46 - 1.58: 3876 1.58 - 1.70: 2 1.70 - 1.82: 60 Bond restraints: 7624 Sorted by residual: bond pdb=" O3 TYS B 10 " pdb=" S TYS B 10 " ideal model delta sigma weight residual 1.458 1.634 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" O2 TYS B 14 " pdb=" S TYS B 14 " ideal model delta sigma weight residual 1.461 1.635 -0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" OH TYS B 10 " pdb=" S TYS B 10 " ideal model delta sigma weight residual 1.679 1.531 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" OH TYS B 14 " pdb=" S TYS B 14 " ideal model delta sigma weight residual 1.679 1.542 0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" N ARG B 60 " pdb=" CA ARG B 60 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.01e+01 ... (remaining 7619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 9955 2.31 - 4.62: 324 4.62 - 6.94: 63 6.94 - 9.25: 13 9.25 - 11.56: 6 Bond angle restraints: 10361 Sorted by residual: angle pdb=" C ASN G 280 " pdb=" CA ASN G 280 " pdb=" CB ASN G 280 " ideal model delta sigma weight residual 111.73 119.20 -7.47 1.42e+00 4.96e-01 2.77e+01 angle pdb=" C THR G 460 " pdb=" N THR G 461 " pdb=" CA THR G 461 " ideal model delta sigma weight residual 121.91 132.31 -10.40 2.03e+00 2.43e-01 2.62e+01 angle pdb=" C ALA G 72 " pdb=" N CYS G 73 " pdb=" CA CYS G 73 " ideal model delta sigma weight residual 122.19 133.75 -11.56 2.30e+00 1.89e-01 2.53e+01 angle pdb=" C ILE B 23 " pdb=" N ASN B 24 " pdb=" CA ASN B 24 " ideal model delta sigma weight residual 120.28 127.01 -6.73 1.34e+00 5.57e-01 2.52e+01 angle pdb=" N ALA B 92 " pdb=" CA ALA B 92 " pdb=" C ALA B 92 " ideal model delta sigma weight residual 110.80 120.48 -9.68 2.13e+00 2.20e-01 2.07e+01 ... (remaining 10356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.25: 4772 22.25 - 44.49: 137 44.49 - 66.73: 17 66.73 - 88.98: 30 88.98 - 111.22: 16 Dihedral angle restraints: 4972 sinusoidal: 2392 harmonic: 2580 Sorted by residual: dihedral pdb=" CB CYS G 118 " pdb=" SG CYS G 118 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -172.00 86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS G 376 " pdb=" SG CYS G 376 " pdb=" SG CYS G 440 " pdb=" CB CYS G 440 " ideal model delta sinusoidal sigma weight residual 93.00 162.04 -69.04 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CA ALA G 317 " pdb=" C ALA G 317 " pdb=" N THR G 318 " pdb=" CA THR G 318 " ideal model delta harmonic sigma weight residual 180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 4969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 1268 0.197 - 0.394: 14 0.394 - 0.591: 1 0.591 - 0.788: 2 0.788 - 0.985: 1 Chirality restraints: 1286 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-02 2.50e+03 2.43e+03 chirality pdb=" C1 BMA G 612 " pdb=" O6 BMA E 3 " pdb=" C2 BMA G 612 " pdb=" O5 BMA G 612 " both_signs ideal model delta sigma weight residual False -2.40 -3.14 0.74 2.00e-02 2.50e+03 1.37e+03 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN G 301 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 1283 not shown) Planarity restraints: 1271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.163 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" C7 NAG K 2 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.217 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 A2G B 401 " 0.158 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" C7 A2G B 401 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A2G B 401 " 0.116 2.00e-02 2.50e+03 pdb=" N2 A2G B 401 " -0.213 2.00e-02 2.50e+03 pdb=" O7 A2G B 401 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 384 " 0.113 2.00e-02 2.50e+03 1.20e-01 1.80e+02 pdb=" CG ASN G 384 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN G 384 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN G 384 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.155 2.00e-02 2.50e+03 ... (remaining 1268 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 45 2.57 - 3.15: 5661 3.15 - 3.73: 10416 3.73 - 4.32: 14377 4.32 - 4.90: 23635 Nonbonded interactions: 54134 Sorted by model distance: nonbonded pdb=" CG2 THR G 209 " pdb=" O4 MAN E 4 " model vdw 1.985 3.460 nonbonded pdb=" O LEU G 277 " pdb=" OG1 THR G 278 " model vdw 2.063 3.040 nonbonded pdb=" O GLU G 268 " pdb=" OD1 ASP G 269 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" OD2 ASP B 125 " model vdw 2.222 3.040 nonbonded pdb=" NH2 ARG G 313 " pdb=" OH TYR B 251 " model vdw 2.227 3.120 ... (remaining 54129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'J' } 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 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 : 0.010 0.478 7668 Z= 0.684 Angle : 1.322 67.875 10478 Z= 0.608 Chirality : 0.073 0.985 1286 Planarity : 0.010 0.135 1255 Dihedral : 14.049 111.225 3264 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.01 % Allowed : 1.52 % Favored : 97.47 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.22), residues: 871 helix: -1.99 (0.25), residues: 281 sheet: -2.96 (0.38), residues: 140 loop : -3.42 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 140 TYR 0.015 0.002 TYR B 3 PHE 0.029 0.002 PHE G 380 TRP 0.034 0.002 TRP B 86 HIS 0.004 0.001 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 7624) covalent geometry : angle 1.03591 (10361) SS BOND : bond 0.00312 ( 12) SS BOND : angle 1.46525 ( 24) hydrogen bonds : bond 0.28852 ( 262) hydrogen bonds : angle 9.98287 ( 720) Misc. bond : bond 0.43380 ( 1) link_ALPHA1-2 : bond 0.00372 ( 1) link_ALPHA1-2 : angle 2.76447 ( 3) link_ALPHA1-3 : bond 0.00682 ( 1) link_ALPHA1-3 : angle 1.10851 ( 3) link_BETA1-4 : bond 0.05408 ( 12) link_BETA1-4 : angle 3.73927 ( 36) link_BETA1-6 : bond 0.47836 ( 1) link_BETA1-6 : angle 41.66026 ( 3) link_NAG-ASN : bond 0.01068 ( 16) link_NAG-ASN : angle 5.41654 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 337 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 210 PHE cc_start: 0.6984 (t80) cc_final: 0.5844 (t80) REVERT: G 315 PHE cc_start: 0.4822 (m-80) cc_final: 0.4336 (m-80) REVERT: G 322 ILE cc_start: 0.8420 (pt) cc_final: 0.8159 (pt) REVERT: G 470 ASP cc_start: 0.6391 (t0) cc_final: 0.5916 (t0) REVERT: G 487 ILE cc_start: 0.4023 (OUTLIER) cc_final: 0.3415 (pt) REVERT: A 37 LEU cc_start: 0.8051 (mt) cc_final: 0.7801 (mt) REVERT: A 78 ASP cc_start: 0.7533 (m-30) cc_final: 0.7211 (m-30) REVERT: A 100 LEU cc_start: 0.8114 (tp) cc_final: 0.7695 (pp) REVERT: A 148 GLN cc_start: 0.7991 (mt0) cc_final: 0.7744 (tp40) REVERT: A 161 VAL cc_start: 0.9200 (t) cc_final: 0.8976 (t) REVERT: B 9 ILE cc_start: 0.6726 (tp) cc_final: 0.6418 (mt) REVERT: B 77 LEU cc_start: 0.6587 (mt) cc_final: 0.6244 (mt) REVERT: B 244 TYR cc_start: 0.6150 (t80) cc_final: 0.5928 (t80) outliers start: 8 outliers final: 1 residues processed: 344 average time/residue: 0.0952 time to fit residues: 42.2306 Evaluate side-chains 163 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 487 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.0010 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS G 246 GLN G 279 ASN G 302 ASN G 417 GLN G 420 ASN A 163 GLN B 181 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.118288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.097806 restraints weight = 23971.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098994 restraints weight = 15687.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.099471 restraints weight = 11752.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.099565 restraints weight = 11331.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.099785 restraints weight = 10594.018| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 7668 Z= 0.195 Angle : 0.833 9.957 10478 Z= 0.409 Chirality : 0.049 0.420 1286 Planarity : 0.006 0.046 1255 Dihedral : 11.913 72.437 1607 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.06 % Allowed : 15.72 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.25), residues: 871 helix: -0.60 (0.28), residues: 296 sheet: -2.26 (0.40), residues: 150 loop : -3.10 (0.25), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 60 TYR 0.015 0.002 TYR B 68 PHE 0.030 0.002 PHE B 118 TRP 0.017 0.002 TRP B 86 HIS 0.012 0.002 HIS G 308 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 7624) covalent geometry : angle 0.78944 (10361) SS BOND : bond 0.00818 ( 12) SS BOND : angle 1.26382 ( 24) hydrogen bonds : bond 0.06393 ( 262) hydrogen bonds : angle 6.48125 ( 720) Misc. bond : bond 0.00161 ( 1) link_ALPHA1-2 : bond 0.01140 ( 1) link_ALPHA1-2 : angle 3.60868 ( 3) link_ALPHA1-3 : bond 0.01593 ( 1) link_ALPHA1-3 : angle 2.02000 ( 3) link_BETA1-4 : bond 0.00515 ( 12) link_BETA1-4 : angle 2.01410 ( 36) link_BETA1-6 : bond 0.00018 ( 1) link_BETA1-6 : angle 3.07762 ( 3) link_NAG-ASN : bond 0.00430 ( 16) link_NAG-ASN : angle 3.38047 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 371 PHE cc_start: 0.6983 (m-10) cc_final: 0.6764 (m-10) REVERT: G 375 ASN cc_start: 0.7941 (t0) cc_final: 0.7303 (t0) REVERT: G 472 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7954 (mtt90) REVERT: G 487 ILE cc_start: 0.4836 (OUTLIER) cc_final: 0.4608 (pp) REVERT: A 37 LEU cc_start: 0.8194 (mt) cc_final: 0.7989 (mt) REVERT: A 78 ASP cc_start: 0.7764 (m-30) cc_final: 0.7496 (m-30) REVERT: B 205 LEU cc_start: 0.8869 (mp) cc_final: 0.8665 (mp) REVERT: B 210 MET cc_start: 0.8215 (tmm) cc_final: 0.7950 (tmm) REVERT: B 288 THR cc_start: 0.9284 (p) cc_final: 0.8963 (t) outliers start: 32 outliers final: 18 residues processed: 205 average time/residue: 0.0843 time to fit residues: 23.3685 Evaluate side-chains 152 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 386 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 0.3980 chunk 49 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 HIS A 148 GLN ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.114157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093361 restraints weight = 23645.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.094621 restraints weight = 16354.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.095114 restraints weight = 12108.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.095163 restraints weight = 11340.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095313 restraints weight = 10859.476| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7668 Z= 0.177 Angle : 0.789 9.760 10478 Z= 0.384 Chirality : 0.049 0.394 1286 Planarity : 0.005 0.042 1255 Dihedral : 8.281 52.108 1607 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.44 % Allowed : 18.12 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.26), residues: 871 helix: -0.17 (0.30), residues: 294 sheet: -2.13 (0.39), residues: 164 loop : -2.79 (0.26), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 131 TYR 0.016 0.002 TYR B 108 PHE 0.026 0.002 PHE B 118 TRP 0.040 0.002 TRP B 86 HIS 0.006 0.002 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7624) covalent geometry : angle 0.74999 (10361) SS BOND : bond 0.00714 ( 12) SS BOND : angle 1.98404 ( 24) hydrogen bonds : bond 0.04895 ( 262) hydrogen bonds : angle 5.78842 ( 720) Misc. bond : bond 0.00124 ( 1) link_ALPHA1-2 : bond 0.00608 ( 1) link_ALPHA1-2 : angle 2.82683 ( 3) link_ALPHA1-3 : bond 0.01223 ( 1) link_ALPHA1-3 : angle 1.60326 ( 3) link_BETA1-4 : bond 0.00443 ( 12) link_BETA1-4 : angle 1.89366 ( 36) link_BETA1-6 : bond 0.00638 ( 1) link_BETA1-6 : angle 1.66524 ( 3) link_NAG-ASN : bond 0.00359 ( 16) link_NAG-ASN : angle 3.02582 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 375 ASN cc_start: 0.8287 (t0) cc_final: 0.7965 (t0) REVERT: A 78 ASP cc_start: 0.8167 (m-30) cc_final: 0.6685 (m-30) REVERT: B 196 LEU cc_start: 0.7722 (pt) cc_final: 0.7177 (pp) REVERT: B 288 THR cc_start: 0.9256 (p) cc_final: 0.8948 (t) outliers start: 35 outliers final: 25 residues processed: 171 average time/residue: 0.0685 time to fit residues: 16.6007 Evaluate side-chains 155 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.107084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.086503 restraints weight = 24190.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086312 restraints weight = 16264.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.087295 restraints weight = 14297.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087444 restraints weight = 12570.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087670 restraints weight = 11730.673| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 7668 Z= 0.297 Angle : 0.896 12.091 10478 Z= 0.427 Chirality : 0.052 0.413 1286 Planarity : 0.005 0.045 1255 Dihedral : 7.719 53.650 1605 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 6.34 % Allowed : 19.26 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.26), residues: 871 helix: -0.02 (0.30), residues: 294 sheet: -1.98 (0.38), residues: 168 loop : -2.74 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 472 TYR 0.014 0.002 TYR B 3 PHE 0.025 0.003 PHE B 118 TRP 0.042 0.003 TRP B 86 HIS 0.008 0.002 HIS G 372 Details of bonding type rmsd covalent geometry : bond 0.00673 ( 7624) covalent geometry : angle 0.85616 (10361) SS BOND : bond 0.00542 ( 12) SS BOND : angle 1.62159 ( 24) hydrogen bonds : bond 0.04978 ( 262) hydrogen bonds : angle 5.83182 ( 720) Misc. bond : bond 0.00173 ( 1) link_ALPHA1-2 : bond 0.00836 ( 1) link_ALPHA1-2 : angle 2.61201 ( 3) link_ALPHA1-3 : bond 0.01217 ( 1) link_ALPHA1-3 : angle 2.23268 ( 3) link_BETA1-4 : bond 0.00414 ( 12) link_BETA1-4 : angle 2.08070 ( 36) link_BETA1-6 : bond 0.00205 ( 1) link_BETA1-6 : angle 1.99109 ( 3) link_NAG-ASN : bond 0.00388 ( 16) link_NAG-ASN : angle 3.37325 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 375 ASN cc_start: 0.8632 (t0) cc_final: 0.8402 (t0) REVERT: B 214 TYR cc_start: 0.7496 (t80) cc_final: 0.7089 (t80) outliers start: 50 outliers final: 37 residues processed: 169 average time/residue: 0.0693 time to fit residues: 16.6252 Evaluate side-chains 147 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 392 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 69 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 85 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.109064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088056 restraints weight = 23858.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088151 restraints weight = 16941.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089045 restraints weight = 13802.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.089339 restraints weight = 12428.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.089627 restraints weight = 11778.423| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7668 Z= 0.148 Angle : 0.797 15.499 10478 Z= 0.370 Chirality : 0.049 0.391 1286 Planarity : 0.004 0.038 1255 Dihedral : 7.124 47.986 1605 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.97 % Favored : 93.92 % Rotamer: Outliers : 5.58 % Allowed : 22.56 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.27), residues: 871 helix: 0.14 (0.30), residues: 300 sheet: -1.86 (0.40), residues: 158 loop : -2.60 (0.26), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 54 TYR 0.025 0.001 TYR B 297 PHE 0.023 0.002 PHE B 118 TRP 0.025 0.002 TRP B 86 HIS 0.014 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7624) covalent geometry : angle 0.76235 (10361) SS BOND : bond 0.00397 ( 12) SS BOND : angle 1.61754 ( 24) hydrogen bonds : bond 0.04660 ( 262) hydrogen bonds : angle 5.48027 ( 720) Misc. bond : bond 0.00081 ( 1) link_ALPHA1-2 : bond 0.00567 ( 1) link_ALPHA1-2 : angle 2.49077 ( 3) link_ALPHA1-3 : bond 0.01161 ( 1) link_ALPHA1-3 : angle 1.82885 ( 3) link_BETA1-4 : bond 0.00476 ( 12) link_BETA1-4 : angle 1.75958 ( 36) link_BETA1-6 : bond 0.00115 ( 1) link_BETA1-6 : angle 2.54436 ( 3) link_NAG-ASN : bond 0.00413 ( 16) link_NAG-ASN : angle 2.94018 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 210 PHE cc_start: 0.7554 (t80) cc_final: 0.6967 (t80) REVERT: G 375 ASN cc_start: 0.8560 (t0) cc_final: 0.8249 (t0) REVERT: B 196 LEU cc_start: 0.8041 (pt) cc_final: 0.7489 (mp) REVERT: B 214 TYR cc_start: 0.7407 (t80) cc_final: 0.7164 (t80) outliers start: 44 outliers final: 29 residues processed: 159 average time/residue: 0.0590 time to fit residues: 14.0631 Evaluate side-chains 147 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 0.0050 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.109150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088163 restraints weight = 23780.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088184 restraints weight = 16948.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.088743 restraints weight = 13753.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088940 restraints weight = 12917.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.089024 restraints weight = 11445.180| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.7244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7668 Z= 0.138 Angle : 0.753 15.066 10478 Z= 0.352 Chirality : 0.047 0.381 1286 Planarity : 0.004 0.036 1255 Dihedral : 6.683 47.877 1605 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 5.32 % Allowed : 23.07 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.28), residues: 871 helix: 0.35 (0.30), residues: 304 sheet: -1.52 (0.40), residues: 168 loop : -2.56 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 131 TYR 0.022 0.001 TYR B 297 PHE 0.032 0.001 PHE B 166 TRP 0.013 0.002 TRP A 157 HIS 0.004 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7624) covalent geometry : angle 0.71846 (10361) SS BOND : bond 0.00483 ( 12) SS BOND : angle 1.91295 ( 24) hydrogen bonds : bond 0.04368 ( 262) hydrogen bonds : angle 5.35955 ( 720) Misc. bond : bond 0.00081 ( 1) link_ALPHA1-2 : bond 0.00388 ( 1) link_ALPHA1-2 : angle 2.43866 ( 3) link_ALPHA1-3 : bond 0.01050 ( 1) link_ALPHA1-3 : angle 1.70701 ( 3) link_BETA1-4 : bond 0.00479 ( 12) link_BETA1-4 : angle 1.59345 ( 36) link_BETA1-6 : bond 0.00224 ( 1) link_BETA1-6 : angle 2.18131 ( 3) link_NAG-ASN : bond 0.00400 ( 16) link_NAG-ASN : angle 2.77478 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 210 PHE cc_start: 0.7493 (t80) cc_final: 0.6832 (t80) REVERT: G 375 ASN cc_start: 0.8515 (t0) cc_final: 0.8155 (t0) REVERT: G 447 LEU cc_start: 0.9257 (mt) cc_final: 0.9003 (mt) REVERT: G 471 MET cc_start: 0.8838 (mmt) cc_final: 0.8475 (mmp) REVERT: G 487 ILE cc_start: 0.6503 (OUTLIER) cc_final: 0.6045 (pp) REVERT: A 156 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8065 (t) REVERT: B 196 LEU cc_start: 0.8076 (pt) cc_final: 0.7478 (mp) outliers start: 42 outliers final: 31 residues processed: 161 average time/residue: 0.0622 time to fit residues: 14.5214 Evaluate side-chains 152 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 15 optimal weight: 9.9990 chunk 58 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.0020 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 GLN A 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.110521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089938 restraints weight = 23705.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.089648 restraints weight = 15627.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090651 restraints weight = 13525.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.091011 restraints weight = 11703.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091290 restraints weight = 10946.509| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.7400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7668 Z= 0.128 Angle : 0.744 15.799 10478 Z= 0.348 Chirality : 0.047 0.369 1286 Planarity : 0.004 0.034 1255 Dihedral : 6.371 47.570 1605 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.86 % Favored : 94.03 % Rotamer: Outliers : 4.44 % Allowed : 23.95 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.28), residues: 871 helix: 0.48 (0.30), residues: 305 sheet: -1.32 (0.41), residues: 168 loop : -2.50 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 476 TYR 0.019 0.001 TYR B 297 PHE 0.025 0.001 PHE B 238 TRP 0.012 0.001 TRP A 157 HIS 0.007 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7624) covalent geometry : angle 0.71438 (10361) SS BOND : bond 0.00575 ( 12) SS BOND : angle 1.77806 ( 24) hydrogen bonds : bond 0.04256 ( 262) hydrogen bonds : angle 5.24899 ( 720) Misc. bond : bond 0.00073 ( 1) link_ALPHA1-2 : bond 0.00453 ( 1) link_ALPHA1-2 : angle 2.30301 ( 3) link_ALPHA1-3 : bond 0.00954 ( 1) link_ALPHA1-3 : angle 1.52503 ( 3) link_BETA1-4 : bond 0.00482 ( 12) link_BETA1-4 : angle 1.53146 ( 36) link_BETA1-6 : bond 0.00281 ( 1) link_BETA1-6 : angle 2.04797 ( 3) link_NAG-ASN : bond 0.00412 ( 16) link_NAG-ASN : angle 2.59370 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.289 Fit side-chains REVERT: G 210 PHE cc_start: 0.7425 (t80) cc_final: 0.6807 (t80) REVERT: G 320 ASP cc_start: 0.8044 (m-30) cc_final: 0.7735 (m-30) REVERT: G 375 ASN cc_start: 0.8514 (t0) cc_final: 0.8104 (t0) REVERT: G 447 LEU cc_start: 0.9232 (mt) cc_final: 0.9031 (mt) REVERT: G 487 ILE cc_start: 0.6411 (OUTLIER) cc_final: 0.6000 (pp) REVERT: A 156 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8029 (t) REVERT: B 196 LEU cc_start: 0.8049 (pt) cc_final: 0.7556 (mp) REVERT: B 241 MET cc_start: 0.8462 (tpp) cc_final: 0.8148 (tmm) outliers start: 35 outliers final: 26 residues processed: 162 average time/residue: 0.0725 time to fit residues: 16.9412 Evaluate side-chains 150 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 24 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.109432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088756 restraints weight = 24024.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.088512 restraints weight = 15883.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088987 restraints weight = 14831.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089228 restraints weight = 12972.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.089331 restraints weight = 12050.668| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.7567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7668 Z= 0.135 Angle : 0.770 18.929 10478 Z= 0.352 Chirality : 0.047 0.370 1286 Planarity : 0.004 0.036 1255 Dihedral : 6.241 47.066 1605 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.63 % Favored : 94.26 % Rotamer: Outliers : 4.56 % Allowed : 23.45 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.28), residues: 871 helix: 0.49 (0.30), residues: 301 sheet: -1.34 (0.39), residues: 178 loop : -2.46 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 414 TYR 0.021 0.001 TYR B 214 PHE 0.016 0.001 PHE B 166 TRP 0.029 0.002 TRP A 157 HIS 0.004 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7624) covalent geometry : angle 0.74298 (10361) SS BOND : bond 0.00558 ( 12) SS BOND : angle 1.56855 ( 24) hydrogen bonds : bond 0.04115 ( 262) hydrogen bonds : angle 5.18709 ( 720) Misc. bond : bond 0.00078 ( 1) link_ALPHA1-2 : bond 0.00392 ( 1) link_ALPHA1-2 : angle 2.22209 ( 3) link_ALPHA1-3 : bond 0.00975 ( 1) link_ALPHA1-3 : angle 1.54053 ( 3) link_BETA1-4 : bond 0.00406 ( 12) link_BETA1-4 : angle 1.52878 ( 36) link_BETA1-6 : bond 0.00264 ( 1) link_BETA1-6 : angle 2.04226 ( 3) link_NAG-ASN : bond 0.00367 ( 16) link_NAG-ASN : angle 2.55246 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: G 210 PHE cc_start: 0.7570 (t80) cc_final: 0.6967 (t80) REVERT: G 320 ASP cc_start: 0.8094 (m-30) cc_final: 0.7872 (m-30) REVERT: G 375 ASN cc_start: 0.8572 (t0) cc_final: 0.8170 (t0) REVERT: G 447 LEU cc_start: 0.9186 (mt) cc_final: 0.8981 (mt) REVERT: G 487 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6064 (pp) REVERT: A 156 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8033 (t) REVERT: B 196 LEU cc_start: 0.8136 (pt) cc_final: 0.7769 (mp) REVERT: B 241 MET cc_start: 0.8512 (tpp) cc_final: 0.8186 (tmm) outliers start: 36 outliers final: 29 residues processed: 156 average time/residue: 0.0656 time to fit residues: 15.0365 Evaluate side-chains 153 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.105486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084592 restraints weight = 23923.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084930 restraints weight = 15046.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.085530 restraints weight = 14050.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085717 restraints weight = 11554.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.085771 restraints weight = 11114.126| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.8030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 7668 Z= 0.225 Angle : 0.863 15.372 10478 Z= 0.402 Chirality : 0.050 0.391 1286 Planarity : 0.005 0.060 1255 Dihedral : 6.879 48.947 1605 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 5.58 % Allowed : 22.69 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.28), residues: 871 helix: 0.44 (0.30), residues: 301 sheet: -1.43 (0.39), residues: 179 loop : -2.47 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 472 TYR 0.024 0.002 TYR B 297 PHE 0.017 0.002 PHE B 166 TRP 0.026 0.003 TRP A 157 HIS 0.015 0.002 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 7624) covalent geometry : angle 0.82874 (10361) SS BOND : bond 0.00587 ( 12) SS BOND : angle 2.31942 ( 24) hydrogen bonds : bond 0.04558 ( 262) hydrogen bonds : angle 5.45943 ( 720) Misc. bond : bond 0.00104 ( 1) link_ALPHA1-2 : bond 0.00632 ( 1) link_ALPHA1-2 : angle 2.33108 ( 3) link_ALPHA1-3 : bond 0.01242 ( 1) link_ALPHA1-3 : angle 2.05174 ( 3) link_BETA1-4 : bond 0.00358 ( 12) link_BETA1-4 : angle 1.72908 ( 36) link_BETA1-6 : bond 0.00212 ( 1) link_BETA1-6 : angle 2.24018 ( 3) link_NAG-ASN : bond 0.00395 ( 16) link_NAG-ASN : angle 2.92359 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7782 (tp30) cc_final: 0.7445 (tp30) REVERT: G 304 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7796 (ptp90) REVERT: G 375 ASN cc_start: 0.8743 (t0) cc_final: 0.8440 (t0) REVERT: G 471 MET cc_start: 0.8979 (mmt) cc_final: 0.8644 (mmp) REVERT: G 487 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6264 (pp) REVERT: B 116 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9066 (tp) REVERT: B 196 LEU cc_start: 0.8220 (pt) cc_final: 0.7789 (mp) REVERT: B 241 MET cc_start: 0.8502 (tpp) cc_final: 0.8209 (tmm) outliers start: 44 outliers final: 33 residues processed: 156 average time/residue: 0.0641 time to fit residues: 14.9682 Evaluate side-chains 147 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.107516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086782 restraints weight = 23750.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086746 restraints weight = 14539.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087824 restraints weight = 13313.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.087904 restraints weight = 11345.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.087958 restraints weight = 10790.439| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.8153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7668 Z= 0.144 Angle : 0.839 15.656 10478 Z= 0.385 Chirality : 0.048 0.374 1286 Planarity : 0.004 0.036 1255 Dihedral : 6.597 48.476 1605 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.08 % Favored : 93.80 % Rotamer: Outliers : 4.06 % Allowed : 24.59 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.28), residues: 871 helix: 0.63 (0.31), residues: 301 sheet: -1.46 (0.37), residues: 189 loop : -2.42 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 472 TYR 0.021 0.001 TYR B 214 PHE 0.020 0.001 PHE B 78 TRP 0.026 0.002 TRP A 157 HIS 0.009 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7624) covalent geometry : angle 0.80689 (10361) SS BOND : bond 0.00407 ( 12) SS BOND : angle 2.07842 ( 24) hydrogen bonds : bond 0.04193 ( 262) hydrogen bonds : angle 5.27089 ( 720) Misc. bond : bond 0.00068 ( 1) link_ALPHA1-2 : bond 0.00421 ( 1) link_ALPHA1-2 : angle 2.21902 ( 3) link_ALPHA1-3 : bond 0.00958 ( 1) link_ALPHA1-3 : angle 1.63441 ( 3) link_BETA1-4 : bond 0.00399 ( 12) link_BETA1-4 : angle 1.53052 ( 36) link_BETA1-6 : bond 0.00379 ( 1) link_BETA1-6 : angle 2.04559 ( 3) link_NAG-ASN : bond 0.00404 ( 16) link_NAG-ASN : angle 2.89159 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7673 (tp30) cc_final: 0.7368 (tp30) REVERT: G 304 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7776 (ptp90) REVERT: G 375 ASN cc_start: 0.8659 (t0) cc_final: 0.8382 (t0) REVERT: G 471 MET cc_start: 0.8936 (mmt) cc_final: 0.8675 (mmp) REVERT: G 487 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6243 (pp) REVERT: A 13 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7848 (tm-30) REVERT: B 116 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9070 (tp) REVERT: B 196 LEU cc_start: 0.8375 (pt) cc_final: 0.7958 (mp) REVERT: B 241 MET cc_start: 0.8465 (tpp) cc_final: 0.8131 (tmm) outliers start: 32 outliers final: 27 residues processed: 148 average time/residue: 0.0653 time to fit residues: 14.3329 Evaluate side-chains 146 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.104774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.085606 restraints weight = 23985.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083682 restraints weight = 16067.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084297 restraints weight = 16769.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.084708 restraints weight = 13710.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084919 restraints weight = 12665.091| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.8427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7668 Z= 0.207 Angle : 0.865 14.764 10478 Z= 0.402 Chirality : 0.050 0.395 1286 Planarity : 0.004 0.041 1255 Dihedral : 6.893 48.714 1605 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.89 % Favored : 93.00 % Rotamer: Outliers : 4.06 % Allowed : 24.33 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.28), residues: 871 helix: 0.57 (0.30), residues: 305 sheet: -1.47 (0.37), residues: 189 loop : -2.34 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 472 TYR 0.023 0.002 TYR B 297 PHE 0.016 0.002 PHE B 166 TRP 0.023 0.002 TRP A 157 HIS 0.011 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 7624) covalent geometry : angle 0.82789 (10361) SS BOND : bond 0.00476 ( 12) SS BOND : angle 2.15975 ( 24) hydrogen bonds : bond 0.04333 ( 262) hydrogen bonds : angle 5.36915 ( 720) Misc. bond : bond 0.00091 ( 1) link_ALPHA1-2 : bond 0.00601 ( 1) link_ALPHA1-2 : angle 2.29240 ( 3) link_ALPHA1-3 : bond 0.00865 ( 1) link_ALPHA1-3 : angle 1.80732 ( 3) link_BETA1-4 : bond 0.00324 ( 12) link_BETA1-4 : angle 1.65865 ( 36) link_BETA1-6 : bond 0.00151 ( 1) link_BETA1-6 : angle 2.12618 ( 3) link_NAG-ASN : bond 0.00402 ( 16) link_NAG-ASN : angle 3.16888 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1360.02 seconds wall clock time: 24 minutes 16.02 seconds (1456.02 seconds total)