Starting phenix.real_space_refine on Thu Mar 13 18:06:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6meo_9108/03_2025/6meo_9108.cif Found real_map, /net/cci-nas-00/data/ceres_data/6meo_9108/03_2025/6meo_9108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6meo_9108/03_2025/6meo_9108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6meo_9108/03_2025/6meo_9108.map" model { file = "/net/cci-nas-00/data/ceres_data/6meo_9108/03_2025/6meo_9108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6meo_9108/03_2025/6meo_9108.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2562 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 109 Unusual residues: {'BMA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'A2G': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.55, per 1000 atoms: 0.74 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: 2.75 Conformation dependent library (CDL) restraints added in 900.8 milliseconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 13 sheets defined 36.1% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 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: 1.90 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2057 1.34 - 1.46: 1629 1.46 - 1.58: 3876 1.58 - 1.70: 2 1.70 - 1.82: 60 Bond restraints: 7624 Sorted by residual: bond pdb=" O3 TYS B 10 " pdb=" S TYS B 10 " ideal model delta sigma weight residual 1.458 1.634 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" O2 TYS B 14 " pdb=" S TYS B 14 " ideal model delta sigma weight residual 1.461 1.635 -0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" OH TYS B 10 " pdb=" S TYS B 10 " ideal model delta sigma weight residual 1.679 1.531 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" OH TYS B 14 " pdb=" S TYS B 14 " ideal model delta sigma weight residual 1.679 1.542 0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" N ARG B 60 " pdb=" CA ARG B 60 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.01e+01 ... (remaining 7619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 9955 2.31 - 4.62: 324 4.62 - 6.94: 63 6.94 - 9.25: 13 9.25 - 11.56: 6 Bond angle restraints: 10361 Sorted by residual: angle pdb=" C ASN G 280 " pdb=" CA ASN G 280 " pdb=" CB ASN G 280 " ideal model delta sigma weight residual 111.73 119.20 -7.47 1.42e+00 4.96e-01 2.77e+01 angle pdb=" C THR G 460 " pdb=" N THR G 461 " pdb=" CA THR G 461 " ideal model delta sigma weight residual 121.91 132.31 -10.40 2.03e+00 2.43e-01 2.62e+01 angle pdb=" C ALA G 72 " pdb=" N CYS G 73 " pdb=" CA CYS G 73 " ideal model delta sigma weight residual 122.19 133.75 -11.56 2.30e+00 1.89e-01 2.53e+01 angle pdb=" C ILE B 23 " pdb=" N ASN B 24 " pdb=" CA ASN B 24 " ideal model delta sigma weight residual 120.28 127.01 -6.73 1.34e+00 5.57e-01 2.52e+01 angle pdb=" N ALA B 92 " pdb=" CA ALA B 92 " pdb=" C ALA B 92 " ideal model delta sigma weight residual 110.80 120.48 -9.68 2.13e+00 2.20e-01 2.07e+01 ... (remaining 10356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.25: 4772 22.25 - 44.49: 137 44.49 - 66.73: 17 66.73 - 88.98: 30 88.98 - 111.22: 16 Dihedral angle restraints: 4972 sinusoidal: 2392 harmonic: 2580 Sorted by residual: dihedral pdb=" CB CYS G 118 " pdb=" SG CYS G 118 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -172.00 86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS G 376 " pdb=" SG CYS G 376 " pdb=" SG CYS G 440 " pdb=" CB CYS G 440 " ideal model delta sinusoidal sigma weight residual 93.00 162.04 -69.04 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CA ALA G 317 " pdb=" C ALA G 317 " pdb=" N THR G 318 " pdb=" CA THR G 318 " ideal model delta harmonic sigma weight residual 180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 4969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 1268 0.197 - 0.394: 14 0.394 - 0.591: 1 0.591 - 0.788: 2 0.788 - 0.985: 1 Chirality restraints: 1286 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-02 2.50e+03 2.43e+03 chirality pdb=" C1 BMA G 612 " pdb=" O6 BMA E 3 " pdb=" C2 BMA G 612 " pdb=" O5 BMA G 612 " both_signs ideal model delta sigma weight residual False -2.40 -3.14 0.74 2.00e-02 2.50e+03 1.37e+03 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN G 301 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 1283 not shown) Planarity restraints: 1271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.163 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" C7 NAG K 2 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.217 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 A2G B 401 " 0.158 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" C7 A2G B 401 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A2G B 401 " 0.116 2.00e-02 2.50e+03 pdb=" N2 A2G B 401 " -0.213 2.00e-02 2.50e+03 pdb=" O7 A2G B 401 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 384 " 0.113 2.00e-02 2.50e+03 1.20e-01 1.80e+02 pdb=" CG ASN G 384 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN G 384 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN G 384 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.155 2.00e-02 2.50e+03 ... (remaining 1268 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 45 2.57 - 3.15: 5661 3.15 - 3.73: 10416 3.73 - 4.32: 14377 4.32 - 4.90: 23635 Nonbonded interactions: 54134 Sorted by model distance: nonbonded pdb=" CG2 THR G 209 " pdb=" O4 MAN E 4 " model vdw 1.985 3.460 nonbonded pdb=" O LEU G 277 " pdb=" OG1 THR G 278 " model vdw 2.063 3.040 nonbonded pdb=" O GLU G 268 " pdb=" OD1 ASP G 269 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" OD2 ASP B 125 " model vdw 2.222 3.040 nonbonded pdb=" NH2 ARG G 313 " pdb=" OH TYR B 251 " model vdw 2.227 3.120 ... (remaining 54129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.240 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.176 7624 Z= 0.420 Angle : 1.036 11.561 10361 Z= 0.544 Chirality : 0.073 0.985 1286 Planarity : 0.010 0.135 1255 Dihedral : 14.049 111.225 3264 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.01 % Allowed : 1.52 % Favored : 97.47 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.002 TRP B 86 HIS 0.004 0.001 HIS G 372 PHE 0.029 0.002 PHE G 380 TYR 0.015 0.002 TYR B 3 ARG 0.004 0.000 ARG B 140 *********************** 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 : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 210 PHE cc_start: 0.6984 (t80) cc_final: 0.5844 (t80) REVERT: G 315 PHE cc_start: 0.4822 (m-80) cc_final: 0.4336 (m-80) REVERT: G 322 ILE cc_start: 0.8420 (pt) cc_final: 0.8159 (pt) REVERT: G 470 ASP cc_start: 0.6391 (t0) cc_final: 0.5916 (t0) REVERT: G 487 ILE cc_start: 0.4023 (OUTLIER) cc_final: 0.3415 (pt) REVERT: A 37 LEU cc_start: 0.8051 (mt) cc_final: 0.7801 (mt) REVERT: A 78 ASP cc_start: 0.7533 (m-30) cc_final: 0.7211 (m-30) REVERT: A 100 LEU cc_start: 0.8114 (tp) cc_final: 0.7695 (pp) REVERT: A 148 GLN cc_start: 0.7991 (mt0) cc_final: 0.7744 (tp40) REVERT: A 161 VAL cc_start: 0.9200 (t) cc_final: 0.8976 (t) REVERT: B 9 ILE cc_start: 0.6726 (tp) cc_final: 0.6418 (mt) REVERT: B 77 LEU cc_start: 0.6587 (mt) cc_final: 0.6244 (mt) REVERT: B 244 TYR cc_start: 0.6150 (t80) cc_final: 0.5928 (t80) outliers start: 8 outliers final: 1 residues processed: 344 average time/residue: 0.2402 time to fit residues: 106.7459 Evaluate side-chains 163 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 73 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS G 246 GLN G 279 ASN G 302 ASN G 417 GLN G 420 ASN A 163 GLN B 181 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.117000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096593 restraints weight = 23706.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097530 restraints weight = 15320.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097903 restraints weight = 11989.258| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7624 Z= 0.310 Angle : 0.800 9.610 10361 Z= 0.405 Chirality : 0.049 0.443 1286 Planarity : 0.006 0.048 1255 Dihedral : 12.299 75.205 1607 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.93 % Allowed : 16.35 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.25), residues: 871 helix: -0.60 (0.28), residues: 302 sheet: -2.30 (0.39), residues: 152 loop : -3.12 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 86 HIS 0.013 0.002 HIS G 308 PHE 0.030 0.002 PHE B 118 TYR 0.016 0.002 TYR B 68 ARG 0.006 0.001 ARG B 60 *********************** 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: 31 poor density : 182 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 375 ASN cc_start: 0.8007 (t0) cc_final: 0.7395 (t0) REVERT: G 472 ARG cc_start: 0.8296 (mtt90) cc_final: 0.8088 (mtt90) REVERT: G 487 ILE cc_start: 0.4885 (OUTLIER) cc_final: 0.4643 (pp) REVERT: A 56 ASP cc_start: 0.7116 (m-30) cc_final: 0.6846 (m-30) REVERT: A 78 ASP cc_start: 0.7828 (m-30) cc_final: 0.7561 (m-30) REVERT: B 53 LEU cc_start: 0.8286 (mt) cc_final: 0.7528 (tp) REVERT: B 205 LEU cc_start: 0.8876 (mp) cc_final: 0.8671 (mp) REVERT: B 210 MET cc_start: 0.8187 (tmm) cc_final: 0.7908 (tmm) REVERT: B 288 THR cc_start: 0.9300 (p) cc_final: 0.8974 (t) outliers start: 31 outliers final: 19 residues processed: 201 average time/residue: 0.2888 time to fit residues: 77.7923 Evaluate side-chains 150 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 386 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN G 308 HIS ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.113258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092440 restraints weight = 23837.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.093242 restraints weight = 15459.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.093535 restraints weight = 12204.225| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7624 Z= 0.274 Angle : 0.756 10.218 10361 Z= 0.379 Chirality : 0.049 0.399 1286 Planarity : 0.005 0.043 1255 Dihedral : 8.627 50.198 1607 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.82 % Allowed : 18.76 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.27), residues: 871 helix: -0.04 (0.30), residues: 295 sheet: -2.20 (0.38), residues: 170 loop : -2.77 (0.26), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 86 HIS 0.012 0.002 HIS A 27 PHE 0.027 0.002 PHE B 118 TYR 0.019 0.002 TYR B 108 ARG 0.006 0.001 ARG G 476 *********************** 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 181 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 280 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7849 (p0) REVERT: G 316 TYR cc_start: 0.8035 (m-10) cc_final: 0.7771 (m-10) REVERT: G 375 ASN cc_start: 0.8330 (t0) cc_final: 0.8063 (t0) REVERT: A 78 ASP cc_start: 0.8207 (m-30) cc_final: 0.7936 (m-30) REVERT: B 26 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8014 (mtpt) REVERT: B 109 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7132 (t80) REVERT: B 210 MET cc_start: 0.8180 (tmm) cc_final: 0.7905 (tmm) REVERT: B 288 THR cc_start: 0.9288 (p) cc_final: 0.8991 (t) outliers start: 38 outliers final: 25 residues processed: 170 average time/residue: 0.1622 time to fit residues: 38.4069 Evaluate side-chains 150 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 221 LEU 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 15 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.104116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083260 restraints weight = 24156.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.083370 restraints weight = 16348.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083792 restraints weight = 14379.837| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 7624 Z= 0.499 Angle : 0.938 13.335 10361 Z= 0.459 Chirality : 0.055 0.421 1286 Planarity : 0.006 0.052 1255 Dihedral : 8.454 56.164 1605 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 7.48 % Allowed : 19.39 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.26), residues: 871 helix: -0.15 (0.29), residues: 294 sheet: -2.09 (0.36), residues: 183 loop : -2.74 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP B 86 HIS 0.008 0.002 HIS G 65 PHE 0.035 0.003 PHE G 210 TYR 0.016 0.002 TYR B 187 ARG 0.009 0.001 ARG A 134 *********************** 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 187 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: G 44 TRP cc_start: 0.6521 (m-10) cc_final: 0.6161 (m-10) REVERT: G 375 ASN cc_start: 0.8806 (t0) cc_final: 0.8512 (t0) REVERT: G 480 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8581 (p90) REVERT: B 166 PHE cc_start: 0.6984 (t80) cc_final: 0.6651 (t80) REVERT: B 175 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.6210 (m-70) REVERT: B 196 LEU cc_start: 0.8075 (pt) cc_final: 0.7456 (mp) REVERT: B 214 TYR cc_start: 0.7658 (t80) cc_final: 0.7368 (t80) outliers start: 59 outliers final: 41 residues processed: 169 average time/residue: 0.1645 time to fit residues: 40.9851 Evaluate side-chains 148 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 392 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 480 TYR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 PHE 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 154 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 HIS 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 285 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 29 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.105624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085060 restraints weight = 23739.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085151 restraints weight = 14746.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086032 restraints weight = 13537.167| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.7630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7624 Z= 0.263 Angle : 0.751 10.912 10361 Z= 0.365 Chirality : 0.049 0.418 1286 Planarity : 0.004 0.045 1255 Dihedral : 7.588 48.112 1605 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.08 % Favored : 93.80 % Rotamer: Outliers : 6.08 % Allowed : 22.05 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.27), residues: 871 helix: 0.09 (0.29), residues: 300 sheet: -2.01 (0.36), residues: 185 loop : -2.63 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 86 HIS 0.005 0.001 HIS A 27 PHE 0.025 0.002 PHE B 118 TYR 0.028 0.002 TYR B 297 ARG 0.005 0.001 ARG G 472 *********************** 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 180 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 44 TRP cc_start: 0.6218 (m-10) cc_final: 0.5779 (m-10) REVERT: G 211 GLU cc_start: 0.7693 (tp30) cc_final: 0.7461 (tp30) REVERT: G 304 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6868 (ttm170) REVERT: G 320 ASP cc_start: 0.7865 (m-30) cc_final: 0.7484 (p0) REVERT: G 487 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.6052 (pp) REVERT: A 156 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8277 (t) REVERT: B 109 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7045 (t80) REVERT: B 196 LEU cc_start: 0.7984 (pt) cc_final: 0.7623 (mp) REVERT: B 241 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8165 (tpp) outliers start: 48 outliers final: 35 residues processed: 167 average time/residue: 0.1402 time to fit residues: 34.4288 Evaluate side-chains 159 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 209 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 304 ARG Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 PHE 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 231 HIS Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.105463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084833 restraints weight = 23697.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.084859 restraints weight = 14283.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085484 restraints weight = 13524.689| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.7891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7624 Z= 0.237 Angle : 0.760 16.155 10361 Z= 0.363 Chirality : 0.048 0.399 1286 Planarity : 0.004 0.042 1255 Dihedral : 7.178 47.725 1605 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.00 % Favored : 92.88 % Rotamer: Outliers : 5.32 % Allowed : 22.43 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.27), residues: 871 helix: 0.33 (0.30), residues: 303 sheet: -1.76 (0.37), residues: 179 loop : -2.62 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 157 HIS 0.015 0.001 HIS B 231 PHE 0.036 0.002 PHE B 166 TYR 0.021 0.002 TYR B 297 ARG 0.008 0.001 ARG G 313 *********************** 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 165 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 44 TRP cc_start: 0.6268 (m-10) cc_final: 0.5842 (m-10) REVERT: G 211 GLU cc_start: 0.7787 (tp30) cc_final: 0.7546 (tp30) REVERT: G 304 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7761 (ptp90) REVERT: G 487 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6101 (pp) REVERT: A 156 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8326 (t) REVERT: B 109 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7022 (t80) REVERT: B 196 LEU cc_start: 0.8134 (pt) cc_final: 0.7902 (mp) REVERT: B 210 MET cc_start: 0.8173 (tmm) cc_final: 0.7729 (tpp) outliers start: 42 outliers final: 31 residues processed: 156 average time/residue: 0.1426 time to fit residues: 32.5971 Evaluate side-chains 147 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 256 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 71 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.0980 chunk 40 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.106192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.085971 restraints weight = 23884.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085037 restraints weight = 16457.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.085483 restraints weight = 14904.978| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.8056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7624 Z= 0.218 Angle : 0.739 14.457 10361 Z= 0.353 Chirality : 0.047 0.389 1286 Planarity : 0.004 0.040 1255 Dihedral : 6.901 47.357 1605 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 5.20 % Allowed : 23.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.28), residues: 871 helix: 0.66 (0.30), residues: 297 sheet: -1.59 (0.38), residues: 179 loop : -2.56 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 157 HIS 0.005 0.001 HIS G 65 PHE 0.022 0.001 PHE B 118 TYR 0.023 0.002 TYR B 297 ARG 0.003 0.000 ARG A 134 *********************** 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 164 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7741 (tp30) cc_final: 0.7498 (tp30) REVERT: G 487 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6167 (pp) REVERT: B 109 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.6924 (t80) REVERT: B 172 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7517 (mp0) REVERT: B 196 LEU cc_start: 0.8225 (pt) cc_final: 0.7885 (mp) REVERT: B 210 MET cc_start: 0.8104 (tmm) cc_final: 0.7808 (tpp) outliers start: 41 outliers final: 31 residues processed: 155 average time/residue: 0.1355 time to fit residues: 31.4457 Evaluate side-chains 154 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 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 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 85 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.104493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084604 restraints weight = 23885.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083626 restraints weight = 15658.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083993 restraints weight = 15227.487| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.8342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7624 Z= 0.284 Angle : 0.808 18.824 10361 Z= 0.381 Chirality : 0.049 0.393 1286 Planarity : 0.004 0.043 1255 Dihedral : 7.053 47.303 1605 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.46 % Favored : 92.42 % Rotamer: Outliers : 5.07 % Allowed : 23.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.28), residues: 871 helix: 0.50 (0.30), residues: 300 sheet: -1.63 (0.37), residues: 179 loop : -2.55 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 157 HIS 0.007 0.001 HIS G 65 PHE 0.019 0.001 PHE B 118 TYR 0.023 0.002 TYR B 214 ARG 0.003 0.000 ARG G 476 *********************** 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 164 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7835 (tp30) cc_final: 0.7580 (tp30) REVERT: G 487 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6192 (pp) REVERT: A 156 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8250 (t) REVERT: B 109 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6997 (t80) REVERT: B 196 LEU cc_start: 0.8261 (pt) cc_final: 0.7905 (mp) outliers start: 40 outliers final: 34 residues processed: 152 average time/residue: 0.1410 time to fit residues: 32.4656 Evaluate side-chains 148 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 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 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 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 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 109 PHE 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 231 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 74 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 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 = 0.3744 r_free = 0.3744 target = 0.105068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084855 restraints weight = 24014.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.084166 restraints weight = 16717.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084574 restraints weight = 14769.461| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.8512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7624 Z= 0.246 Angle : 0.814 15.998 10361 Z= 0.383 Chirality : 0.048 0.389 1286 Planarity : 0.004 0.040 1255 Dihedral : 6.970 47.423 1605 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 5.07 % Allowed : 24.33 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.28), residues: 871 helix: 0.72 (0.31), residues: 294 sheet: -1.59 (0.36), residues: 189 loop : -2.49 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP G 44 HIS 0.007 0.001 HIS G 65 PHE 0.014 0.001 PHE B 112 TYR 0.020 0.002 TYR B 214 ARG 0.003 0.000 ARG A 134 *********************** 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 155 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7776 (tp30) cc_final: 0.7530 (tp30) REVERT: G 487 ILE cc_start: 0.6544 (OUTLIER) cc_final: 0.6087 (pp) REVERT: A 156 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7920 (t) REVERT: B 109 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7100 (t80) REVERT: B 196 LEU cc_start: 0.8225 (pt) cc_final: 0.7886 (mp) outliers start: 40 outliers final: 34 residues processed: 144 average time/residue: 0.1360 time to fit residues: 29.0853 Evaluate side-chains 150 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 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 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 109 PHE 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 231 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.0270 chunk 37 optimal weight: 0.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 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 = 0.3757 r_free = 0.3757 target = 0.105885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084368 restraints weight = 23979.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085064 restraints weight = 17823.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.085769 restraints weight = 12994.687| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.8605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7624 Z= 0.216 Angle : 0.814 15.072 10361 Z= 0.388 Chirality : 0.048 0.378 1286 Planarity : 0.004 0.040 1255 Dihedral : 6.837 46.568 1605 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 4.31 % Allowed : 24.59 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.28), residues: 871 helix: 0.82 (0.31), residues: 288 sheet: -1.63 (0.35), residues: 189 loop : -2.40 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 44 HIS 0.005 0.001 HIS G 65 PHE 0.021 0.001 PHE B 166 TYR 0.020 0.002 TYR B 214 ARG 0.003 0.000 ARG A 134 ********************** 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 158 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7720 (tp30) cc_final: 0.7498 (tp30) REVERT: G 368 GLU cc_start: 0.8351 (mp0) cc_final: 0.8135 (mp0) REVERT: G 487 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.5993 (pp) REVERT: B 109 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.6997 (t80) REVERT: B 196 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7942 (mp) outliers start: 34 outliers final: 29 residues processed: 149 average time/residue: 0.1404 time to fit residues: 31.0017 Evaluate side-chains 147 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 231 HIS 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 10 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.105226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084870 restraints weight = 23648.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.084414 restraints weight = 15940.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084621 restraints weight = 15112.894| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.8765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7624 Z= 0.244 Angle : 0.830 14.662 10361 Z= 0.393 Chirality : 0.049 0.385 1286 Planarity : 0.004 0.040 1255 Dihedral : 6.778 46.191 1605 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.31 % Favored : 93.57 % Rotamer: Outliers : 4.56 % Allowed : 25.10 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.28), residues: 871 helix: 0.68 (0.30), residues: 299 sheet: -1.56 (0.36), residues: 189 loop : -2.38 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 44 HIS 0.006 0.001 HIS G 65 PHE 0.019 0.002 PHE B 78 TYR 0.020 0.002 TYR B 244 ARG 0.003 0.001 ARG G 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2916.35 seconds wall clock time: 53 minutes 8.36 seconds (3188.36 seconds total)