Starting phenix.real_space_refine on Fri Sep 11 11:12:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6meo_9108/09_2026/6meo_9108.cif Found real_map, /net/cci-nas-00/data/ceres_data/6meo_9108/09_2026/6meo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6meo_9108/09_2026/6meo_9108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6meo_9108/09_2026/6meo_9108.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6meo_9108/09_2026/6meo_9108.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6meo_9108/09_2026/6meo_9108.cif" model { file = "/net/cci-nas-00/data/ceres_data/6meo_9108/09_2026/6meo_9108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6meo_9108/09_2026/6meo_9108.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 1.35, per 1000 atoms: 0.18 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: 0.70 Conformation dependent library (CDL) restraints added in 385.3 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: 0.17 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: 1.01 Time building geometry restraints manager: 0.96 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 - 17.20: 4147 17.20 - 34.40: 127 34.40 - 51.60: 30 51.60 - 68.80: 2 68.80 - 86.00: 6 Dihedral angle restraints: 4312 sinusoidal: 1732 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 4309 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 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 : 9.238 77.113 2604 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/Z covalent geometry : bond 0.00696 / 0.37 ( 7624) covalent geometry : angle 1.03591 / 0.54 (10361) SS BOND : bond 0.00312 / 0.22 ( 12) SS BOND : angle 1.46525 / 0.92 ( 24) hydrogen bonds : bond 0.28852 / 18.65 ( 262) hydrogen bonds : angle 9.98287 / 6.94 ( 720) Misc. bond : bond 0.43380 / 22.83 ( 1) link_ALPHA1-2 : bond 0.00372 / 0.20 ( 1) link_ALPHA1-2 : angle 2.76447 / 2.11 ( 3) link_ALPHA1-3 : bond 0.00682 / 0.36 ( 1) link_ALPHA1-3 : angle 1.10851 / 0.96 ( 3) link_BETA1-4 : bond 0.05408 / 3.39 ( 12) link_BETA1-4 : angle 3.73927 / 2.55 ( 36) link_BETA1-6 : bond 0.47836 / 25.18 ( 1) link_BETA1-6 : angle 41.66026 / 23.18 ( 3) link_NAG-ASN : bond 0.01068 / 0.70 ( 16) link_NAG-ASN : angle 5.41654 / 4.14 ( 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 : 0.266 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: 0.5856 (t80) REVERT: G 315 PHE cc_start: 0.4822 (m-80) cc_final: 0.4364 (m-80) REVERT: G 322 ILE cc_start: 0.8421 (pt) cc_final: 0.8162 (pt) REVERT: G 470 ASP cc_start: 0.6390 (t0) cc_final: 0.5900 (t0) REVERT: G 487 ILE cc_start: 0.4023 (OUTLIER) cc_final: 0.3416 (pt) REVERT: A 37 LEU cc_start: 0.8051 (mt) cc_final: 0.7805 (mt) REVERT: A 78 ASP cc_start: 0.7533 (m-30) cc_final: 0.7214 (m-30) REVERT: A 100 LEU cc_start: 0.8114 (tp) cc_final: 0.7694 (pp) REVERT: A 148 GLN cc_start: 0.7991 (mt0) cc_final: 0.7745 (tp40) REVERT: A 161 VAL cc_start: 0.9200 (t) cc_final: 0.8977 (t) REVERT: B 9 ILE cc_start: 0.6726 (tp) cc_final: 0.6417 (mt) REVERT: B 77 LEU cc_start: 0.6587 (mt) cc_final: 0.6241 (mt) REVERT: B 244 TYR cc_start: 0.6150 (t80) cc_final: 0.5929 (t80) outliers start: 8 outliers final: 1 residues processed: 344 average time/residue: 0.0985 time to fit residues: 44.2711 Evaluate side-chains 162 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0010 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 71 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.115775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.095113 restraints weight = 23997.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.095906 restraints weight = 15422.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.096350 restraints weight = 12165.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.096615 restraints weight = 11521.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.096744 restraints weight = 10808.524| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 7668 Z= 0.216 Angle : 0.864 10.454 10478 Z= 0.425 Chirality : 0.049 0.400 1286 Planarity : 0.006 0.047 1255 Dihedral : 5.670 46.717 947 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.44 % Allowed : 16.48 % Favored : 79.09 % 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: -3.13 (0.25), residues: 871 helix: -0.63 (0.28), residues: 296 sheet: -2.37 (0.38), residues: 157 loop : -3.09 (0.25), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 60 TYR 0.015 0.002 TYR B 108 PHE 0.028 0.003 PHE B 118 TRP 0.019 0.002 TRP B 86 HIS 0.012 0.002 HIS G 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 ( 7624) covalent geometry : angle 0.82495 / 0.42 (10361) SS BOND : bond 0.00535 / 0.40 ( 12) SS BOND : angle 1.38863 / 0.90 ( 24) hydrogen bonds : bond 0.05720 / 3.76 ( 262) hydrogen bonds : angle 6.41303 / 4.51 ( 720) Misc. bond : bond 0.00786 / 0.41 ( 1) link_ALPHA1-2 : bond 0.01235 / 0.65 ( 1) link_ALPHA1-2 : angle 3.08477 / 2.48 ( 3) link_ALPHA1-3 : bond 0.01065 / 0.56 ( 1) link_ALPHA1-3 : angle 0.92187 / 0.81 ( 3) link_BETA1-4 : bond 0.00467 / 0.25 ( 12) link_BETA1-4 : angle 1.89448 / 1.09 ( 36) link_BETA1-6 : bond 0.00535 / 0.28 ( 1) link_BETA1-6 : angle 3.41114 / 2.01 ( 3) link_NAG-ASN : bond 0.00407 / 0.21 ( 16) link_NAG-ASN : angle 3.34170 / 2.24 ( 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 213 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 210 PHE cc_start: 0.6934 (t80) cc_final: 0.6637 (t80) REVERT: G 375 ASN cc_start: 0.8137 (t0) cc_final: 0.7513 (t0) REVERT: G 472 ARG cc_start: 0.8329 (mtt90) cc_final: 0.8083 (mtt90) REVERT: G 487 ILE cc_start: 0.4798 (OUTLIER) cc_final: 0.4458 (pp) REVERT: A 78 ASP cc_start: 0.7999 (m-30) cc_final: 0.6679 (m-30) REVERT: B 210 MET cc_start: 0.8266 (tmm) cc_final: 0.8034 (tmm) REVERT: B 288 THR cc_start: 0.9309 (p) cc_final: 0.9000 (t) outliers start: 35 outliers final: 22 residues processed: 203 average time/residue: 0.0866 time to fit residues: 23.8052 Evaluate side-chains 150 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 LYS 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 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 156 THR 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 125 ASP 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: 2.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 HIS A 148 GLN B 231 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.114730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.092612 restraints weight = 23517.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094471 restraints weight = 15286.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.095471 restraints weight = 11662.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096301 restraints weight = 10042.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.096731 restraints weight = 9047.888| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7668 Z= 0.161 Angle : 0.776 9.342 10478 Z= 0.376 Chirality : 0.047 0.349 1286 Planarity : 0.004 0.042 1255 Dihedral : 5.466 51.454 947 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.69 % Allowed : 18.63 % Favored : 76.68 % 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: -2.60 (0.27), residues: 871 helix: -0.11 (0.30), residues: 295 sheet: -2.21 (0.38), residues: 170 loop : -2.77 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 476 TYR 0.013 0.002 TYR B 108 PHE 0.027 0.002 PHE B 118 TRP 0.036 0.002 TRP B 86 HIS 0.005 0.002 HIS G 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 7624) covalent geometry : angle 0.73927 / 0.37 (10361) SS BOND : bond 0.00489 / 0.38 ( 12) SS BOND : angle 1.98794 / 1.18 ( 24) hydrogen bonds : bond 0.05026 / 3.30 ( 262) hydrogen bonds : angle 5.85637 / 4.14 ( 720) Misc. bond : bond 0.00129 / 0.07 ( 1) link_ALPHA1-2 : bond 0.00849 / 0.45 ( 1) link_ALPHA1-2 : angle 2.45908 / 1.77 ( 3) link_ALPHA1-3 : bond 0.00801 / 0.42 ( 1) link_ALPHA1-3 : angle 1.39866 / 0.91 ( 3) link_BETA1-4 : bond 0.00445 / 0.27 ( 12) link_BETA1-4 : angle 1.58337 / 0.94 ( 36) link_BETA1-6 : bond 0.00564 / 0.30 ( 1) link_BETA1-6 : angle 1.82363 / 1.55 ( 3) link_NAG-ASN : bond 0.00422 / 0.23 ( 16) link_NAG-ASN : angle 2.96775 / 2.02 ( 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 177 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: G 44 TRP cc_start: 0.6467 (m-90) cc_final: 0.6261 (m-10) REVERT: G 375 ASN cc_start: 0.8231 (t0) cc_final: 0.7701 (t0) REVERT: B 26 LYS cc_start: 0.8264 (mtpt) cc_final: 0.8026 (mtpt) REVERT: B 210 MET cc_start: 0.8295 (tmm) cc_final: 0.8019 (tmm) REVERT: B 288 THR cc_start: 0.9281 (p) cc_final: 0.8957 (t) outliers start: 37 outliers final: 28 residues processed: 165 average time/residue: 0.0629 time to fit residues: 15.3515 Evaluate side-chains 149 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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 260 LEU Chi-restraints excluded: chain G residue 272 ILE 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 114 LEU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 25 VAL 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 116 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3792 r_free = 0.3792 target = 0.107950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.087172 restraints weight = 23901.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087362 restraints weight = 16533.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088201 restraints weight = 13496.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088373 restraints weight = 12496.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088751 restraints weight = 11660.533| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7668 Z= 0.257 Angle : 0.864 11.407 10478 Z= 0.417 Chirality : 0.050 0.356 1286 Planarity : 0.005 0.039 1255 Dihedral : 5.350 48.712 945 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.81 % Favored : 91.96 % Rotamer: Outliers : 5.96 % Allowed : 18.76 % Favored : 75.29 % 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: -2.38 (0.27), residues: 871 helix: 0.07 (0.30), residues: 294 sheet: -2.02 (0.38), residues: 175 loop : -2.66 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 472 TYR 0.018 0.002 TYR G 217 PHE 0.031 0.002 PHE B 118 TRP 0.045 0.003 TRP B 86 HIS 0.038 0.003 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.26 ( 7624) covalent geometry : angle 0.82802 / 0.41 (10361) SS BOND : bond 0.00640 / 0.44 ( 12) SS BOND : angle 1.53210 / 0.95 ( 24) hydrogen bonds : bond 0.04863 / 3.18 ( 262) hydrogen bonds : angle 5.74144 / 4.08 ( 720) Misc. bond : bond 0.00180 / 0.09 ( 1) link_ALPHA1-2 : bond 0.00694 / 0.37 ( 1) link_ALPHA1-2 : angle 2.49145 / 1.76 ( 3) link_ALPHA1-3 : bond 0.00844 / 0.44 ( 1) link_ALPHA1-3 : angle 1.07232 / 0.77 ( 3) link_BETA1-4 : bond 0.00408 / 0.24 ( 12) link_BETA1-4 : angle 1.88761 / 1.09 ( 36) link_BETA1-6 : bond 0.00387 / 0.20 ( 1) link_BETA1-6 : angle 1.42673 / 1.05 ( 3) link_NAG-ASN : bond 0.00405 / 0.22 ( 16) link_NAG-ASN : angle 3.22370 / 2.21 ( 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 180 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7631 (tp30) cc_final: 0.7352 (tp30) REVERT: G 316 TYR cc_start: 0.8259 (m-10) cc_final: 0.7849 (m-10) REVERT: G 375 ASN cc_start: 0.8637 (t0) cc_final: 0.8241 (t0) REVERT: G 478 GLU cc_start: 0.7988 (tt0) cc_final: 0.7753 (tt0) REVERT: B 26 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7872 (tttt) REVERT: B 196 LEU cc_start: 0.7977 (pt) cc_final: 0.7267 (mp) REVERT: B 214 TYR cc_start: 0.7588 (t80) cc_final: 0.7163 (t80) outliers start: 47 outliers final: 38 residues processed: 164 average time/residue: 0.0683 time to fit residues: 16.3311 Evaluate side-chains 153 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 119 VAL 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 236 THR Chi-restraints excluded: chain G residue 272 ILE 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 G residue 479 LEU Chi-restraints excluded: chain A residue 53 ASP 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 114 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 145 SER 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 39 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 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 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: 0.0870 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 10.9990 chunk 25 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 14 optimal weight: 0.1980 chunk 2 optimal weight: 0.0370 chunk 71 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN ** G 372 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 = 0.3837 r_free = 0.3837 target = 0.110643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.090187 restraints weight = 23675.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089728 restraints weight = 17681.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.090471 restraints weight = 13864.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090738 restraints weight = 12772.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.091079 restraints weight = 11449.713| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.6872 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= 0.131 Angle : 0.745 10.280 10478 Z= 0.350 Chirality : 0.046 0.319 1286 Planarity : 0.004 0.035 1255 Dihedral : 5.087 47.840 945 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.49 % Rotamer: Outliers : 4.56 % Allowed : 21.29 % Favored : 74.14 % 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: -2.16 (0.27), residues: 871 helix: 0.28 (0.30), residues: 300 sheet: -1.87 (0.38), residues: 168 loop : -2.61 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 472 TYR 0.023 0.001 TYR B 297 PHE 0.022 0.001 PHE B 118 TRP 0.024 0.002 TRP B 86 HIS 0.005 0.001 HIS G 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7624) covalent geometry : angle 0.71398 / 0.34 (10361) SS BOND : bond 0.00664 / 0.44 ( 12) SS BOND : angle 1.66576 / 1.08 ( 24) hydrogen bonds : bond 0.04529 / 3.02 ( 262) hydrogen bonds : angle 5.42904 / 3.84 ( 720) Misc. bond : bond 0.00073 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00579 / 0.30 ( 1) link_ALPHA1-2 : angle 2.26280 / 1.63 ( 3) link_ALPHA1-3 : bond 0.00655 / 0.34 ( 1) link_ALPHA1-3 : angle 1.37436 / 1.16 ( 3) link_BETA1-4 : bond 0.00440 / 0.29 ( 12) link_BETA1-4 : angle 1.42052 / 0.81 ( 36) link_BETA1-6 : bond 0.00371 / 0.20 ( 1) link_BETA1-6 : angle 1.36853 / 1.16 ( 3) link_NAG-ASN : bond 0.00432 / 0.23 ( 16) link_NAG-ASN : angle 2.78937 / 1.93 ( 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 166 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7468 (tp30) cc_final: 0.7114 (tp30) REVERT: G 375 ASN cc_start: 0.8449 (t0) cc_final: 0.8214 (t0) REVERT: G 487 ILE cc_start: 0.6078 (OUTLIER) cc_final: 0.5504 (pp) REVERT: B 196 LEU cc_start: 0.7821 (pt) cc_final: 0.7342 (mp) REVERT: B 214 TYR cc_start: 0.7237 (t80) cc_final: 0.6963 (t80) REVERT: B 296 ILE cc_start: 0.9026 (pt) cc_final: 0.8636 (tp) outliers start: 36 outliers final: 21 residues processed: 154 average time/residue: 0.0642 time to fit residues: 14.6586 Evaluate side-chains 145 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 200 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 344 ILE 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 114 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 231 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN ** G 372 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 = 0.3800 r_free = 0.3800 target = 0.108219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087480 restraints weight = 23833.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087371 restraints weight = 15536.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.088302 restraints weight = 13637.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.088478 restraints weight = 11968.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.088743 restraints weight = 11372.664| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.7215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7668 Z= 0.168 Angle : 0.761 15.966 10478 Z= 0.359 Chirality : 0.047 0.428 1286 Planarity : 0.004 0.035 1255 Dihedral : 5.058 47.440 945 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.31 % Favored : 93.57 % Rotamer: Outliers : 5.58 % Allowed : 21.04 % Favored : 73.38 % 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: -1.91 (0.28), residues: 871 helix: 0.47 (0.31), residues: 299 sheet: -1.38 (0.41), residues: 168 loop : -2.63 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 230 TYR 0.029 0.002 TYR B 297 PHE 0.019 0.001 PHE B 118 TRP 0.016 0.002 TRP A 157 HIS 0.021 0.002 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 7624) covalent geometry : angle 0.73078 / 0.35 (10361) SS BOND : bond 0.00509 / 0.35 ( 12) SS BOND : angle 1.47401 / 0.98 ( 24) hydrogen bonds : bond 0.04405 / 2.95 ( 262) hydrogen bonds : angle 5.38988 / 3.82 ( 720) Misc. bond : bond 0.00108 / 0.06 ( 1) link_ALPHA1-2 : bond 0.00560 / 0.29 ( 1) link_ALPHA1-2 : angle 2.23383 / 1.62 ( 3) link_ALPHA1-3 : bond 0.00689 / 0.36 ( 1) link_ALPHA1-3 : angle 1.20622 / 0.96 ( 3) link_BETA1-4 : bond 0.00323 / 0.20 ( 12) link_BETA1-4 : angle 1.54136 / 0.89 ( 36) link_BETA1-6 : bond 0.00396 / 0.21 ( 1) link_BETA1-6 : angle 1.36935 / 1.09 ( 3) link_NAG-ASN : bond 0.00335 / 0.16 ( 16) link_NAG-ASN : angle 2.76454 / 1.93 ( 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 169 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.292 Fit side-chains REVERT: G 211 GLU cc_start: 0.7528 (tp30) cc_final: 0.7197 (tp30) REVERT: G 375 ASN cc_start: 0.8520 (t0) cc_final: 0.8163 (t0) REVERT: G 471 MET cc_start: 0.8908 (mmt) cc_final: 0.8546 (mmp) REVERT: G 476 ARG cc_start: 0.8560 (mtt-85) cc_final: 0.8273 (mtt-85) REVERT: G 487 ILE cc_start: 0.6110 (OUTLIER) cc_final: 0.5559 (pp) REVERT: A 156 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8115 (t) REVERT: B 196 LEU cc_start: 0.7984 (pt) cc_final: 0.7737 (mp) outliers start: 44 outliers final: 30 residues processed: 157 average time/residue: 0.0661 time to fit residues: 15.3993 Evaluate side-chains 145 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 307 ILE 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 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 70 LEU Chi-restraints excluded: chain B residue 103 LEU 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 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: 0.9990 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 ASN ** G 372 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 = 0.3820 r_free = 0.3820 target = 0.109801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.089094 restraints weight = 23768.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088887 restraints weight = 15418.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089475 restraints weight = 13304.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.089734 restraints weight = 12237.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089944 restraints weight = 11118.578| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.7383 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= 0.131 Angle : 0.766 15.646 10478 Z= 0.355 Chirality : 0.046 0.358 1286 Planarity : 0.004 0.034 1255 Dihedral : 4.937 46.452 945 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.63 % Favored : 94.14 % Rotamer: Outliers : 4.56 % Allowed : 22.18 % Favored : 73.26 % 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: 0.54 (0.30), residues: 304 sheet: -1.24 (0.41), residues: 168 loop : -2.58 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 313 TYR 0.026 0.001 TYR B 297 PHE 0.019 0.001 PHE B 118 TRP 0.013 0.001 TRP A 157 HIS 0.014 0.001 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7624) covalent geometry : angle 0.73949 / 0.35 (10361) SS BOND : bond 0.00454 / 0.33 ( 12) SS BOND : angle 1.61765 / 1.08 ( 24) hydrogen bonds : bond 0.04227 / 2.83 ( 262) hydrogen bonds : angle 5.28562 / 3.75 ( 720) Misc. bond : bond 0.00076 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00367 / 0.19 ( 1) link_ALPHA1-2 : angle 2.12290 / 1.58 ( 3) link_ALPHA1-3 : bond 0.00681 / 0.36 ( 1) link_ALPHA1-3 : angle 1.32774 / 1.12 ( 3) link_BETA1-4 : bond 0.00376 / 0.24 ( 12) link_BETA1-4 : angle 1.40990 / 0.81 ( 36) link_BETA1-6 : bond 0.00363 / 0.19 ( 1) link_BETA1-6 : angle 1.29430 / 1.07 ( 3) link_NAG-ASN : bond 0.00383 / 0.20 ( 16) link_NAG-ASN : angle 2.57370 / 1.80 ( 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: 36 poor density : 135 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7530 (tp30) cc_final: 0.7180 (tp30) REVERT: G 375 ASN cc_start: 0.8452 (t0) cc_final: 0.8167 (t0) REVERT: G 487 ILE cc_start: 0.6139 (OUTLIER) cc_final: 0.5600 (pp) REVERT: A 156 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8107 (t) REVERT: B 69 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8593 (mt) REVERT: B 196 LEU cc_start: 0.7909 (pt) cc_final: 0.7617 (mp) outliers start: 36 outliers final: 28 residues processed: 161 average time/residue: 0.0677 time to fit residues: 16.0533 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 : 0.301 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 307 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 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 B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 LEU 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 221 LEU Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 24 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 0.0060 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN B 71 ASN B 231 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.109911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089352 restraints weight = 23668.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.089246 restraints weight = 14497.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090027 restraints weight = 13138.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.090478 restraints weight = 11316.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.090615 restraints weight = 11057.845| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.7604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7668 Z= 0.134 Angle : 0.784 19.010 10478 Z= 0.360 Chirality : 0.046 0.341 1286 Planarity : 0.004 0.034 1255 Dihedral : 4.887 45.838 945 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 3.80 % Allowed : 23.70 % Favored : 72.50 % 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: 0.61 (0.31), residues: 294 sheet: -1.41 (0.38), residues: 188 loop : -2.52 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 472 TYR 0.021 0.002 TYR B 297 PHE 0.042 0.002 PHE B 166 TRP 0.025 0.001 TRP A 157 HIS 0.012 0.002 HIS B 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 7624) covalent geometry : angle 0.76131 / 0.35 (10361) SS BOND : bond 0.00463 / 0.32 ( 12) SS BOND : angle 1.51960 / 1.01 ( 24) hydrogen bonds : bond 0.04158 / 2.78 ( 262) hydrogen bonds : angle 5.22004 / 3.73 ( 720) Misc. bond : bond 0.00066 / 0.03 ( 1) link_ALPHA1-2 : bond 0.00363 / 0.19 ( 1) link_ALPHA1-2 : angle 2.05766 / 1.53 ( 3) link_ALPHA1-3 : bond 0.00690 / 0.36 ( 1) link_ALPHA1-3 : angle 1.31521 / 1.11 ( 3) link_BETA1-4 : bond 0.00386 / 0.24 ( 12) link_BETA1-4 : angle 1.38490 / 0.80 ( 36) link_BETA1-6 : bond 0.00293 / 0.15 ( 1) link_BETA1-6 : angle 1.25064 / 1.03 ( 3) link_NAG-ASN : bond 0.00379 / 0.19 ( 16) link_NAG-ASN : angle 2.46464 / 1.73 ( 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 162 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7484 (tp30) cc_final: 0.7211 (tp30) REVERT: G 320 ASP cc_start: 0.7987 (m-30) cc_final: 0.7742 (m-30) REVERT: G 375 ASN cc_start: 0.8522 (t0) cc_final: 0.8250 (t0) REVERT: G 472 ARG cc_start: 0.8582 (mtt90) cc_final: 0.7810 (mtt90) REVERT: G 476 ARG cc_start: 0.8535 (mtt-85) cc_final: 0.7939 (mtt-85) REVERT: A 156 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7897 (t) REVERT: B 196 LEU cc_start: 0.8158 (pt) cc_final: 0.7891 (mp) outliers start: 30 outliers final: 25 residues processed: 153 average time/residue: 0.0663 time to fit residues: 14.8893 Evaluate side-chains 147 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 344 ILE 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 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 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 70 LEU 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 221 LEU Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3796 r_free = 0.3796 target = 0.108243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088039 restraints weight = 23705.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087381 restraints weight = 15114.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087978 restraints weight = 14699.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088453 restraints weight = 11974.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088635 restraints weight = 11165.152| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.7830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7668 Z= 0.166 Angle : 0.806 16.035 10478 Z= 0.374 Chirality : 0.047 0.332 1286 Planarity : 0.004 0.035 1255 Dihedral : 5.062 45.697 945 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.89 % Favored : 93.00 % Rotamer: Outliers : 4.56 % Allowed : 23.95 % Favored : 71.48 % 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: -1.80 (0.28), residues: 871 helix: 0.54 (0.30), residues: 301 sheet: -1.30 (0.40), residues: 179 loop : -2.59 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 472 TYR 0.024 0.002 TYR B 214 PHE 0.030 0.001 PHE B 166 TRP 0.012 0.002 TRP A 28 HIS 0.007 0.001 HIS G 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 7624) covalent geometry : angle 0.77720 / 0.37 (10361) SS BOND : bond 0.00608 / 0.38 ( 12) SS BOND : angle 2.35020 / 1.26 ( 24) hydrogen bonds : bond 0.04205 / 2.82 ( 262) hydrogen bonds : angle 5.28085 / 3.78 ( 720) Misc. bond : bond 0.00085 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00563 / 0.30 ( 1) link_ALPHA1-2 : angle 2.01998 / 1.50 ( 3) link_ALPHA1-3 : bond 0.00711 / 0.37 ( 1) link_ALPHA1-3 : angle 1.31310 / 1.08 ( 3) link_BETA1-4 : bond 0.00304 / 0.19 ( 12) link_BETA1-4 : angle 1.49809 / 0.87 ( 36) link_BETA1-6 : bond 0.00353 / 0.19 ( 1) link_BETA1-6 : angle 1.29503 / 1.04 ( 3) link_NAG-ASN : bond 0.00347 / 0.17 ( 16) link_NAG-ASN : angle 2.56430 / 1.78 ( 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 165 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7599 (tp30) cc_final: 0.7333 (tp30) REVERT: G 375 ASN cc_start: 0.8615 (t0) cc_final: 0.8258 (t0) REVERT: G 471 MET cc_start: 0.8917 (mmt) cc_final: 0.8532 (mmp) REVERT: G 472 ARG cc_start: 0.8628 (mtt90) cc_final: 0.7888 (mtt90) REVERT: G 476 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.7984 (mtt-85) REVERT: G 487 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5700 (pp) REVERT: A 156 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7909 (t) REVERT: B 116 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9066 (tp) REVERT: B 196 LEU cc_start: 0.8221 (pt) cc_final: 0.7838 (mp) outliers start: 36 outliers final: 28 residues processed: 152 average time/residue: 0.0657 time to fit residues: 14.5320 Evaluate side-chains 151 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN 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 479 LEU 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 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 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 221 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 0.0000 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3808 r_free = 0.3808 target = 0.109063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088720 restraints weight = 23563.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088456 restraints weight = 14913.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089418 restraints weight = 13088.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089828 restraints weight = 11403.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.090026 restraints weight = 10730.300| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.7990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7668 Z= 0.139 Angle : 0.825 17.042 10478 Z= 0.380 Chirality : 0.047 0.324 1286 Planarity : 0.004 0.036 1255 Dihedral : 5.171 44.883 945 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 3.80 % Allowed : 23.95 % Favored : 72.24 % 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: -1.75 (0.28), residues: 871 helix: 0.55 (0.30), residues: 301 sheet: -1.27 (0.39), residues: 189 loop : -2.56 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 472 TYR 0.021 0.002 TYR B 214 PHE 0.023 0.001 PHE B 166 TRP 0.017 0.002 TRP G 475 HIS 0.005 0.001 HIS G 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7624) covalent geometry : angle 0.79941 / 0.37 (10361) SS BOND : bond 0.00398 / 0.30 ( 12) SS BOND : angle 1.89745 / 1.09 ( 24) hydrogen bonds : bond 0.04118 / 2.77 ( 262) hydrogen bonds : angle 5.22730 / 3.73 ( 720) Misc. bond : bond 0.00079 / 0.04 ( 1) link_ALPHA1-2 : bond 0.00468 / 0.25 ( 1) link_ALPHA1-2 : angle 1.98980 / 1.49 ( 3) link_ALPHA1-3 : bond 0.00615 / 0.32 ( 1) link_ALPHA1-3 : angle 1.36210 / 1.16 ( 3) link_BETA1-4 : bond 0.00356 / 0.23 ( 12) link_BETA1-4 : angle 1.39985 / 0.81 ( 36) link_BETA1-6 : bond 0.00414 / 0.22 ( 1) link_BETA1-6 : angle 1.28924 / 1.06 ( 3) link_NAG-ASN : bond 0.00386 / 0.19 ( 16) link_NAG-ASN : angle 2.63785 / 1.82 ( 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 156 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7582 (tp30) cc_final: 0.7338 (tp30) REVERT: G 375 ASN cc_start: 0.8537 (t0) cc_final: 0.8290 (t0) REVERT: G 471 MET cc_start: 0.8918 (mmt) cc_final: 0.8670 (mmp) REVERT: G 472 ARG cc_start: 0.8558 (mtt90) cc_final: 0.7841 (mtt90) REVERT: G 476 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.7875 (mtt-85) REVERT: G 487 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.5798 (pp) REVERT: A 156 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7791 (t) REVERT: B 116 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9029 (tp) REVERT: B 196 LEU cc_start: 0.8169 (pt) cc_final: 0.7829 (mp) REVERT: B 287 MET cc_start: 0.8188 (mmm) cc_final: 0.7929 (mmt) outliers start: 30 outliers final: 26 residues processed: 146 average time/residue: 0.0697 time to fit residues: 14.7848 Evaluate side-chains 148 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN 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 479 LEU 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 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 221 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3779 r_free = 0.3779 target = 0.107078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085620 restraints weight = 23742.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086818 restraints weight = 17184.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.087387 restraints weight = 12132.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.087460 restraints weight = 11292.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088022 restraints weight = 10541.587| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.8191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7668 Z= 0.181 Angle : 0.844 15.890 10478 Z= 0.391 Chirality : 0.048 0.326 1286 Planarity : 0.004 0.036 1255 Dihedral : 5.247 44.905 945 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 3.55 % Allowed : 24.46 % Favored : 71.99 % 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: -1.70 (0.28), residues: 871 helix: 0.55 (0.30), residues: 301 sheet: -1.11 (0.39), residues: 189 loop : -2.57 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 472 TYR 0.027 0.002 TYR B 297 PHE 0.020 0.001 PHE B 166 TRP 0.012 0.002 TRP A 28 HIS 0.006 0.001 HIS G 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 7624) covalent geometry : angle 0.81486 / 0.38 (10361) SS BOND : bond 0.00454 / 0.31 ( 12) SS BOND : angle 1.92286 / 1.09 ( 24) hydrogen bonds : bond 0.04150 / 2.77 ( 262) hydrogen bonds : angle 5.27396 / 3.76 ( 720) Misc. bond : bond 0.00093 / 0.05 ( 1) link_ALPHA1-2 : bond 0.00527 / 0.28 ( 1) link_ALPHA1-2 : angle 2.03607 / 1.52 ( 3) link_ALPHA1-3 : bond 0.00610 / 0.32 ( 1) link_ALPHA1-3 : angle 1.31198 / 1.08 ( 3) link_BETA1-4 : bond 0.00297 / 0.18 ( 12) link_BETA1-4 : angle 1.52438 / 0.90 ( 36) link_BETA1-6 : bond 0.00316 / 0.17 ( 1) link_BETA1-6 : angle 1.26680 / 1.02 ( 3) link_NAG-ASN : bond 0.00394 / 0.18 ( 16) link_NAG-ASN : angle 2.85073 / 2.02 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.02 seconds wall clock time: 25 minutes 24.82 seconds (1524.82 seconds total)