Starting phenix.real_space_refine on Wed Apr 30 02:10:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6meo_9108/04_2025/6meo_9108.cif Found real_map, /net/cci-nas-00/data/ceres_data/6meo_9108/04_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_9108/04_2025/6meo_9108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6meo_9108/04_2025/6meo_9108.map" model { file = "/net/cci-nas-00/data/ceres_data/6meo_9108/04_2025/6meo_9108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6meo_9108/04_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-5669/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: 4.68, per 1000 atoms: 0.63 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: 2.57 Conformation dependent library (CDL) restraints added in 868.4 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: 0.82 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: 1.95 Time building geometry restraints manager: 2.90 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: 1.780 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.050 Find NCS groups from input model: 0.110 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.478 7668 Z= 0.684 Angle : 1.322 67.875 10478 Z= 0.608 Chirality : 0.073 0.985 1286 Planarity : 0.010 0.135 1255 Dihedral : 14.049 111.225 3264 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.01 % Allowed : 1.52 % Favored : 97.47 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.01068 ( 16) link_NAG-ASN : angle 5.41654 ( 48) link_BETA1-4 : bond 0.05408 ( 12) link_BETA1-4 : angle 3.73927 ( 36) link_ALPHA1-2 : bond 0.00372 ( 1) link_ALPHA1-2 : angle 2.76447 ( 3) link_ALPHA1-3 : bond 0.00682 ( 1) link_ALPHA1-3 : angle 1.10851 ( 3) hydrogen bonds : bond 0.28852 ( 262) hydrogen bonds : angle 9.98287 ( 720) link_BETA1-6 : bond 0.47836 ( 1) link_BETA1-6 : angle 41.66026 ( 3) SS BOND : bond 0.00312 ( 12) SS BOND : angle 1.46525 ( 24) covalent geometry : bond 0.00696 ( 7624) covalent geometry : angle 1.03591 (10361) Misc. bond : bond 0.43380 ( 1) *********************** 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 : 0.827 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: 0.2261 time to fit residues: 99.7724 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 : 0.861 ------------------------------------------------------------------------------- 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: 0.9990 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: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.117856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097360 restraints weight = 23719.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.098492 restraints weight = 15851.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098953 restraints weight = 11933.575| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7668 Z= 0.197 Angle : 0.855 10.751 10478 Z= 0.419 Chirality : 0.049 0.427 1286 Planarity : 0.006 0.049 1255 Dihedral : 11.817 71.630 1607 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.06 % Allowed : 15.84 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.25), residues: 871 helix: -0.51 (0.28), residues: 295 sheet: -2.27 (0.40), residues: 150 loop : -3.10 (0.25), residues: 426 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 0.031 0.002 PHE B 118 TYR 0.017 0.002 TYR B 68 ARG 0.007 0.001 ARG B 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 16) link_NAG-ASN : angle 3.39958 ( 48) link_BETA1-4 : bond 0.00434 ( 12) link_BETA1-4 : angle 2.02988 ( 36) link_ALPHA1-2 : bond 0.00986 ( 1) link_ALPHA1-2 : angle 3.42439 ( 3) link_ALPHA1-3 : bond 0.01337 ( 1) link_ALPHA1-3 : angle 1.84404 ( 3) hydrogen bonds : bond 0.06033 ( 262) hydrogen bonds : angle 6.47636 ( 720) link_BETA1-6 : bond 0.00175 ( 1) link_BETA1-6 : angle 4.20788 ( 3) SS BOND : bond 0.00447 ( 12) SS BOND : angle 1.14437 ( 24) covalent geometry : bond 0.00445 ( 7624) covalent geometry : angle 0.81224 (10361) Misc. bond : bond 0.00227 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 472 ARG cc_start: 0.8248 (mtt90) cc_final: 0.8011 (mtt90) REVERT: G 487 ILE cc_start: 0.4860 (OUTLIER) cc_final: 0.4626 (pp) REVERT: A 37 LEU cc_start: 0.8215 (mt) cc_final: 0.8012 (mt) REVERT: A 56 ASP cc_start: 0.7078 (m-30) cc_final: 0.6813 (m-30) REVERT: A 78 ASP cc_start: 0.7798 (m-30) cc_final: 0.7519 (m-30) REVERT: B 205 LEU cc_start: 0.8872 (mp) cc_final: 0.8671 (mp) REVERT: B 288 THR cc_start: 0.9287 (p) cc_final: 0.8970 (t) outliers start: 32 outliers final: 18 residues processed: 206 average time/residue: 0.1981 time to fit residues: 54.9732 Evaluate side-chains 149 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 386 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 308 HIS A 148 GLN B 71 ASN B 231 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.116459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.095594 restraints weight = 23813.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.096885 restraints weight = 16254.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.097372 restraints weight = 11972.711| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7668 Z= 0.153 Angle : 0.758 8.259 10478 Z= 0.369 Chirality : 0.047 0.388 1286 Planarity : 0.005 0.044 1255 Dihedral : 8.429 49.501 1607 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.07 % Allowed : 17.74 % Favored : 77.19 % 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: -2.59 (0.27), residues: 871 helix: -0.09 (0.30), residues: 295 sheet: -2.23 (0.38), residues: 170 loop : -2.76 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 86 HIS 0.005 0.001 HIS B 231 PHE 0.027 0.002 PHE B 118 TYR 0.018 0.002 TYR B 108 ARG 0.006 0.001 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 16) link_NAG-ASN : angle 2.94753 ( 48) link_BETA1-4 : bond 0.00471 ( 12) link_BETA1-4 : angle 1.83791 ( 36) link_ALPHA1-2 : bond 0.00813 ( 1) link_ALPHA1-2 : angle 2.80731 ( 3) link_ALPHA1-3 : bond 0.01419 ( 1) link_ALPHA1-3 : angle 1.62707 ( 3) hydrogen bonds : bond 0.04917 ( 262) hydrogen bonds : angle 5.82172 ( 720) link_BETA1-6 : bond 0.00512 ( 1) link_BETA1-6 : angle 1.71253 ( 3) SS BOND : bond 0.00732 ( 12) SS BOND : angle 1.88438 ( 24) covalent geometry : bond 0.00332 ( 7624) covalent geometry : angle 0.71858 (10361) Misc. bond : bond 0.00071 ( 1) *********************** 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 191 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 44 TRP cc_start: 0.6562 (m-90) cc_final: 0.6351 (m-10) REVERT: A 78 ASP cc_start: 0.8050 (m-30) cc_final: 0.7721 (m-30) REVERT: B 109 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7059 (t80) REVERT: B 288 THR cc_start: 0.9213 (p) cc_final: 0.8890 (t) outliers start: 40 outliers final: 25 residues processed: 175 average time/residue: 0.1635 time to fit residues: 40.5074 Evaluate side-chains 153 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 272 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 123 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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** B 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.114388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.092415 restraints weight = 23738.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.094234 restraints weight = 15214.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.095437 restraints weight = 11587.839| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7668 Z= 0.151 Angle : 0.749 9.821 10478 Z= 0.355 Chirality : 0.046 0.388 1286 Planarity : 0.004 0.038 1255 Dihedral : 6.848 47.580 1605 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.94 % Allowed : 20.79 % Favored : 74.27 % 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: -2.27 (0.27), residues: 871 helix: 0.22 (0.31), residues: 294 sheet: -2.03 (0.38), residues: 170 loop : -2.62 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 86 HIS 0.017 0.002 HIS B 231 PHE 0.023 0.002 PHE B 118 TYR 0.014 0.001 TYR G 217 ARG 0.006 0.001 ARG G 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 16) link_NAG-ASN : angle 2.87631 ( 48) link_BETA1-4 : bond 0.00415 ( 12) link_BETA1-4 : angle 1.81810 ( 36) link_ALPHA1-2 : bond 0.00683 ( 1) link_ALPHA1-2 : angle 2.55030 ( 3) link_ALPHA1-3 : bond 0.01033 ( 1) link_ALPHA1-3 : angle 1.59159 ( 3) hydrogen bonds : bond 0.04464 ( 262) hydrogen bonds : angle 5.65443 ( 720) link_BETA1-6 : bond 0.00359 ( 1) link_BETA1-6 : angle 1.55248 ( 3) SS BOND : bond 0.00493 ( 12) SS BOND : angle 1.45118 ( 24) covalent geometry : bond 0.00346 ( 7624) covalent geometry : angle 0.71328 (10361) Misc. bond : bond 0.00064 ( 1) *********************** 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 173 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 375 ASN cc_start: 0.8268 (t0) cc_final: 0.7988 (t0) REVERT: A 78 ASP cc_start: 0.8257 (m-30) cc_final: 0.7883 (m-30) REVERT: A 156 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7917 (t) REVERT: B 109 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7126 (t80) REVERT: B 214 TYR cc_start: 0.7352 (t80) cc_final: 0.6966 (t80) REVERT: B 287 MET cc_start: 0.8528 (mmm) cc_final: 0.8294 (tpp) REVERT: B 288 THR cc_start: 0.9268 (p) cc_final: 0.8956 (t) outliers start: 39 outliers final: 28 residues processed: 161 average time/residue: 0.1587 time to fit residues: 37.5517 Evaluate side-chains 153 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain 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 128 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 77 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 255 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 31 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** A 25 GLN A 27 HIS B 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.114442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092335 restraints weight = 23614.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.094196 restraints weight = 15243.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.095303 restraints weight = 11659.874| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7668 Z= 0.133 Angle : 0.732 12.271 10478 Z= 0.346 Chirality : 0.046 0.377 1286 Planarity : 0.004 0.035 1255 Dihedral : 6.377 47.649 1605 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.32 % Allowed : 21.04 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.28), residues: 871 helix: 0.45 (0.31), residues: 294 sheet: -1.95 (0.38), residues: 170 loop : -2.54 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 86 HIS 0.003 0.001 HIS G 249 PHE 0.017 0.001 PHE B 118 TYR 0.021 0.001 TYR B 297 ARG 0.006 0.001 ARG G 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 16) link_NAG-ASN : angle 2.71791 ( 48) link_BETA1-4 : bond 0.00430 ( 12) link_BETA1-4 : angle 1.67784 ( 36) link_ALPHA1-2 : bond 0.00511 ( 1) link_ALPHA1-2 : angle 2.43607 ( 3) link_ALPHA1-3 : bond 0.01043 ( 1) link_ALPHA1-3 : angle 1.51881 ( 3) hydrogen bonds : bond 0.04347 ( 262) hydrogen bonds : angle 5.55988 ( 720) link_BETA1-6 : bond 0.00325 ( 1) link_BETA1-6 : angle 1.78549 ( 3) SS BOND : bond 0.00520 ( 12) SS BOND : angle 1.76674 ( 24) covalent geometry : bond 0.00297 ( 7624) covalent geometry : angle 0.69811 (10361) Misc. bond : bond 0.00055 ( 1) *********************** 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 177 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 471 MET cc_start: 0.8908 (mmt) cc_final: 0.8448 (mmp) REVERT: G 476 ARG cc_start: 0.8484 (mtt-85) cc_final: 0.8176 (mtt-85) REVERT: A 78 ASP cc_start: 0.8324 (m-30) cc_final: 0.7897 (m-30) REVERT: A 156 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8066 (t) REVERT: B 196 LEU cc_start: 0.7907 (pt) cc_final: 0.7284 (mp) REVERT: B 214 TYR cc_start: 0.7468 (t80) cc_final: 0.7220 (t80) REVERT: B 288 THR cc_start: 0.9254 (p) cc_final: 0.8934 (t) outliers start: 42 outliers final: 24 residues processed: 165 average time/residue: 0.1701 time to fit residues: 40.8695 Evaluate side-chains 142 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 483 LYS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 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: 9.9990 chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 0.0470 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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** A 25 GLN B 71 ASN ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.113951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.091693 restraints weight = 23564.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093568 restraints weight = 15029.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094670 restraints weight = 11417.201| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7668 Z= 0.130 Angle : 0.727 12.498 10478 Z= 0.342 Chirality : 0.046 0.371 1286 Planarity : 0.004 0.034 1255 Dihedral : 6.077 46.297 1605 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.14 % Rotamer: Outliers : 5.45 % Allowed : 21.29 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.28), residues: 871 helix: 0.49 (0.31), residues: 303 sheet: -1.71 (0.39), residues: 170 loop : -2.53 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 86 HIS 0.003 0.001 HIS G 249 PHE 0.018 0.001 PHE A 26 TYR 0.025 0.001 TYR B 297 ARG 0.007 0.001 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 16) link_NAG-ASN : angle 2.56539 ( 48) link_BETA1-4 : bond 0.00411 ( 12) link_BETA1-4 : angle 1.55963 ( 36) link_ALPHA1-2 : bond 0.00399 ( 1) link_ALPHA1-2 : angle 2.23708 ( 3) link_ALPHA1-3 : bond 0.00997 ( 1) link_ALPHA1-3 : angle 1.33135 ( 3) hydrogen bonds : bond 0.04105 ( 262) hydrogen bonds : angle 5.43794 ( 720) link_BETA1-6 : bond 0.00334 ( 1) link_BETA1-6 : angle 1.94374 ( 3) SS BOND : bond 0.00460 ( 12) SS BOND : angle 1.35271 ( 24) covalent geometry : bond 0.00297 ( 7624) covalent geometry : angle 0.69854 (10361) Misc. bond : bond 0.00053 ( 1) *********************** 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 179 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 471 MET cc_start: 0.8878 (mmt) cc_final: 0.8535 (mmp) REVERT: G 476 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.8014 (mtt-85) REVERT: A 78 ASP cc_start: 0.8239 (m-30) cc_final: 0.7828 (m-30) REVERT: B 196 LEU cc_start: 0.7842 (pt) cc_final: 0.7423 (mp) outliers start: 43 outliers final: 26 residues processed: 167 average time/residue: 0.1675 time to fit residues: 39.5013 Evaluate side-chains 151 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain A residue 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 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 291 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 81 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.0702 ------------------------------------------------------------------------------- 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** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 231 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 = 0.3864 r_free = 0.3864 target = 0.112544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090276 restraints weight = 23546.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.092169 restraints weight = 14737.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093291 restraints weight = 11078.494| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7668 Z= 0.146 Angle : 0.770 18.153 10478 Z= 0.357 Chirality : 0.046 0.370 1286 Planarity : 0.004 0.034 1255 Dihedral : 6.056 45.276 1605 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.08 % Favored : 93.80 % Rotamer: Outliers : 4.31 % Allowed : 22.43 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.28), residues: 871 helix: 0.42 (0.31), residues: 304 sheet: -1.65 (0.40), residues: 169 loop : -2.50 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 157 HIS 0.003 0.001 HIS G 249 PHE 0.034 0.001 PHE B 238 TYR 0.015 0.001 TYR B 297 ARG 0.006 0.001 ARG G 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 16) link_NAG-ASN : angle 2.53939 ( 48) link_BETA1-4 : bond 0.00379 ( 12) link_BETA1-4 : angle 1.56388 ( 36) link_ALPHA1-2 : bond 0.00163 ( 1) link_ALPHA1-2 : angle 2.26814 ( 3) link_ALPHA1-3 : bond 0.00951 ( 1) link_ALPHA1-3 : angle 1.35463 ( 3) hydrogen bonds : bond 0.04148 ( 262) hydrogen bonds : angle 5.34812 ( 720) link_BETA1-6 : bond 0.00144 ( 1) link_BETA1-6 : angle 1.94583 ( 3) SS BOND : bond 0.00546 ( 12) SS BOND : angle 1.43040 ( 24) covalent geometry : bond 0.00333 ( 7624) covalent geometry : angle 0.74416 (10361) Misc. bond : bond 0.00055 ( 1) *********************** 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 175 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 471 MET cc_start: 0.8898 (mmt) cc_final: 0.8556 (mmp) REVERT: A 78 ASP cc_start: 0.8299 (m-30) cc_final: 0.8086 (m-30) REVERT: B 196 LEU cc_start: 0.7875 (pt) cc_final: 0.7505 (mp) REVERT: B 210 MET cc_start: 0.7853 (tmm) cc_final: 0.7515 (tmm) outliers start: 34 outliers final: 28 residues processed: 164 average time/residue: 0.1604 time to fit residues: 36.9979 Evaluate side-chains 158 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain A residue 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 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 78 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN ** B 231 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 = 0.3852 r_free = 0.3852 target = 0.111726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.091051 restraints weight = 23555.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.090859 restraints weight = 15003.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.091538 restraints weight = 13662.251| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.7230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7668 Z= 0.150 Angle : 0.794 17.043 10478 Z= 0.366 Chirality : 0.048 0.370 1286 Planarity : 0.004 0.035 1255 Dihedral : 6.116 44.527 1605 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.00 % Favored : 92.88 % Rotamer: Outliers : 4.18 % Allowed : 24.08 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.86 (0.28), residues: 871 helix: 0.46 (0.30), residues: 301 sheet: -1.57 (0.40), residues: 169 loop : -2.46 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 157 HIS 0.010 0.001 HIS B 181 PHE 0.049 0.002 PHE B 166 TYR 0.014 0.001 TYR B 297 ARG 0.006 0.001 ARG G 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 16) link_NAG-ASN : angle 2.50377 ( 48) link_BETA1-4 : bond 0.00409 ( 12) link_BETA1-4 : angle 1.56367 ( 36) link_ALPHA1-2 : bond 0.00334 ( 1) link_ALPHA1-2 : angle 2.18875 ( 3) link_ALPHA1-3 : bond 0.00924 ( 1) link_ALPHA1-3 : angle 1.32705 ( 3) hydrogen bonds : bond 0.04153 ( 262) hydrogen bonds : angle 5.31150 ( 720) link_BETA1-6 : bond 0.00091 ( 1) link_BETA1-6 : angle 2.50239 ( 3) SS BOND : bond 0.00465 ( 12) SS BOND : angle 1.75651 ( 24) covalent geometry : bond 0.00345 ( 7624) covalent geometry : angle 0.76790 (10361) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 320 ASP cc_start: 0.8013 (m-30) cc_final: 0.7703 (m-30) REVERT: G 471 MET cc_start: 0.8914 (mmt) cc_final: 0.8450 (mmp) REVERT: G 472 ARG cc_start: 0.8501 (mtt90) cc_final: 0.7568 (mtt90) REVERT: B 196 LEU cc_start: 0.7972 (pt) cc_final: 0.7602 (mp) REVERT: B 210 MET cc_start: 0.7880 (tmm) cc_final: 0.7575 (tmm) outliers start: 33 outliers final: 25 residues processed: 153 average time/residue: 0.1626 time to fit residues: 35.5832 Evaluate side-chains 143 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain 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 159 CYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 28 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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** B 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.106513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086773 restraints weight = 24030.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085536 restraints weight = 15925.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086145 restraints weight = 15399.309| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.7920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7668 Z= 0.234 Angle : 0.888 16.583 10478 Z= 0.412 Chirality : 0.051 0.399 1286 Planarity : 0.004 0.037 1255 Dihedral : 6.912 48.154 1605 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.69 % Favored : 92.19 % Rotamer: Outliers : 4.44 % Allowed : 23.45 % Favored : 72.12 % 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: -1.89 (0.28), residues: 871 helix: 0.22 (0.30), residues: 308 sheet: -1.30 (0.40), residues: 175 loop : -2.47 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 86 HIS 0.007 0.001 HIS G 216 PHE 0.034 0.002 PHE B 166 TYR 0.014 0.002 TYR B 3 ARG 0.005 0.001 ARG G 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 16) link_NAG-ASN : angle 2.97248 ( 48) link_BETA1-4 : bond 0.00332 ( 12) link_BETA1-4 : angle 1.80877 ( 36) link_ALPHA1-2 : bond 0.00715 ( 1) link_ALPHA1-2 : angle 2.46948 ( 3) link_ALPHA1-3 : bond 0.00886 ( 1) link_ALPHA1-3 : angle 2.04805 ( 3) hydrogen bonds : bond 0.04615 ( 262) hydrogen bonds : angle 5.50581 ( 720) link_BETA1-6 : bond 0.00094 ( 1) link_BETA1-6 : angle 2.26288 ( 3) SS BOND : bond 0.00580 ( 12) SS BOND : angle 1.93325 ( 24) covalent geometry : bond 0.00535 ( 7624) covalent geometry : angle 0.85561 (10361) Misc. bond : bond 0.00109 ( 1) *********************** 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 156 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7633 (tp30) cc_final: 0.7374 (tp30) REVERT: G 316 TYR cc_start: 0.8131 (m-10) cc_final: 0.7899 (m-10) REVERT: B 26 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7740 (tttt) REVERT: B 116 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8932 (tp) REVERT: B 196 LEU cc_start: 0.8329 (pt) cc_final: 0.7888 (mp) REVERT: B 210 MET cc_start: 0.7819 (tmm) cc_final: 0.7481 (tmm) REVERT: B 244 TYR cc_start: 0.7679 (t80) cc_final: 0.7237 (t80) outliers start: 35 outliers final: 29 residues processed: 145 average time/residue: 0.1626 time to fit residues: 33.7028 Evaluate side-chains 143 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 99 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain A residue 36 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 159 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.108588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088029 restraints weight = 23613.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.088101 restraints weight = 14616.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.088977 restraints weight = 12960.929| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.8076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7668 Z= 0.141 Angle : 0.819 16.008 10478 Z= 0.379 Chirality : 0.047 0.382 1286 Planarity : 0.004 0.034 1255 Dihedral : 6.446 45.862 1605 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.97 % Favored : 93.92 % Rotamer: Outliers : 3.30 % Allowed : 24.46 % 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: -1.65 (0.28), residues: 871 helix: 0.64 (0.31), residues: 296 sheet: -1.26 (0.38), residues: 189 loop : -2.44 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 86 HIS 0.003 0.001 HIS A 27 PHE 0.023 0.002 PHE B 78 TYR 0.013 0.001 TYR B 108 ARG 0.013 0.001 ARG G 313 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 16) link_NAG-ASN : angle 2.67686 ( 48) link_BETA1-4 : bond 0.00434 ( 12) link_BETA1-4 : angle 1.55272 ( 36) link_ALPHA1-2 : bond 0.00474 ( 1) link_ALPHA1-2 : angle 2.21002 ( 3) link_ALPHA1-3 : bond 0.00873 ( 1) link_ALPHA1-3 : angle 1.59582 ( 3) hydrogen bonds : bond 0.04208 ( 262) hydrogen bonds : angle 5.32113 ( 720) link_BETA1-6 : bond 0.00254 ( 1) link_BETA1-6 : angle 2.03887 ( 3) SS BOND : bond 0.00432 ( 12) SS BOND : angle 1.79941 ( 24) covalent geometry : bond 0.00323 ( 7624) covalent geometry : angle 0.79112 (10361) Misc. bond : bond 0.00088 ( 1) ********************** 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 159 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: G 211 GLU cc_start: 0.7610 (tp30) cc_final: 0.7345 (tp30) REVERT: G 472 ARG cc_start: 0.8585 (mtt90) cc_final: 0.7983 (mtt90) REVERT: G 476 ARG cc_start: 0.8463 (mtt-85) cc_final: 0.7626 (mtt-85) REVERT: B 26 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7730 (tptm) REVERT: B 196 LEU cc_start: 0.8241 (pt) cc_final: 0.7893 (mp) outliers start: 26 outliers final: 20 residues processed: 153 average time/residue: 0.1885 time to fit residues: 39.9843 Evaluate side-chains 137 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 99 MET Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain G residue 442 SER Chi-restraints excluded: chain 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 159 CYS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 49 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.106913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086106 restraints weight = 23924.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086151 restraints weight = 15071.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086912 restraints weight = 14237.930| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.8251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 7668 Z= 0.181 Angle : 0.861 15.876 10478 Z= 0.401 Chirality : 0.048 0.390 1286 Planarity : 0.004 0.035 1255 Dihedral : 6.581 45.812 1605 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 3.17 % Allowed : 24.59 % 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: -1.63 (0.28), residues: 871 helix: 0.52 (0.30), residues: 307 sheet: -1.19 (0.39), residues: 189 loop : -2.41 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 28 HIS 0.005 0.001 HIS G 216 PHE 0.022 0.002 PHE B 166 TYR 0.014 0.002 TYR G 223 ARG 0.007 0.001 ARG G 472 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 16) link_NAG-ASN : angle 2.73861 ( 48) link_BETA1-4 : bond 0.00362 ( 12) link_BETA1-4 : angle 1.60499 ( 36) link_ALPHA1-2 : bond 0.00486 ( 1) link_ALPHA1-2 : angle 2.22050 ( 3) link_ALPHA1-3 : bond 0.00937 ( 1) link_ALPHA1-3 : angle 1.76514 ( 3) hydrogen bonds : bond 0.04249 ( 262) hydrogen bonds : angle 5.43656 ( 720) link_BETA1-6 : bond 0.00188 ( 1) link_BETA1-6 : angle 2.06958 ( 3) SS BOND : bond 0.00546 ( 12) SS BOND : angle 2.72519 ( 24) covalent geometry : bond 0.00425 ( 7624) covalent geometry : angle 0.82764 (10361) Misc. bond : bond 0.00098 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2737.63 seconds wall clock time: 48 minutes 49.62 seconds (2929.62 seconds total)