Starting phenix.real_space_refine on Sun Jun 8 09:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzr_41767/06_2025/8tzr_41767.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzr_41767/06_2025/8tzr_41767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tzr_41767/06_2025/8tzr_41767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzr_41767/06_2025/8tzr_41767.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzr_41767/06_2025/8tzr_41767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzr_41767/06_2025/8tzr_41767.cif" } resolution = 3.5 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= 0.006 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 72 5.16 5 C 5668 2.51 5 N 1479 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8821 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2453 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 12, 'TRANS': 300} Chain: "B" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 4010 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 21, 'TRANS': 471} Chain: "C" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2218 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain breaks: 1 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 6.13, per 1000 atoms: 0.69 Number of scatterers: 8821 At special positions: 0 Unit cell: (97.11, 121.18, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 1 15.00 O 1601 8.00 N 1479 7.00 C 5668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.02 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 105 " - pdb=" SG CYS C 137 " 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 D 4 " - " MAN D 5 " " MAN D 5 " - " MAN D 6 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 6 " - " GLC D 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN A 298 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 996.5 milliseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 43.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 61 through 81 removed outlier: 4.595A pdb=" N SER A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 81 " --> pdb=" O CYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.742A pdb=" N LEU A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 156 through 159 removed outlier: 3.903A pdb=" N ILE A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.612A pdb=" N ASN A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 178 through 198 Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.533A pdb=" N ILE A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'B' and resid 4 through 9 removed outlier: 3.782A pdb=" N ASN B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 4.031A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 121 through 125 removed outlier: 4.256A pdb=" N GLN B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.591A pdb=" N GLU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 258 removed outlier: 3.811A pdb=" N LYS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 295 through 321 removed outlier: 3.683A pdb=" N PHE B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 removed outlier: 3.599A pdb=" N GLY B 334 " --> pdb=" O HIS B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 335 through 358 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 359 through 362 Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'B' and resid 371 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.769A pdb=" N MET B 417 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 456 Processing helix chain 'B' and resid 469 through 492 Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.722A pdb=" N ILE C 305 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C 306 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 377 removed outlier: 4.587A pdb=" N VAL C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR C 350 " --> pdb=" O THR C 346 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA C 353 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 206 Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258 removed outlier: 3.661A pdb=" N TYR A 273 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 326 Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46 removed outlier: 3.615A pdb=" N HIS B 225 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 215 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET B 110 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU B 186 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE B 112 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.165A pdb=" N LYS B 49 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG B 200 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 132 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET B 134 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG B 155 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 136 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N HIS B 153 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 138 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 462 Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 25 Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 25 removed outlier: 4.272A pdb=" N PHE C 330 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN C 94 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE C 332 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 92 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR C 182 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER C 193 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 184 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.147A pdb=" N GLY C 312 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TRP C 319 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39 removed outlier: 5.147A pdb=" N GLY C 312 " --> pdb=" O PHE C 81 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1414 1.31 - 1.43: 2568 1.43 - 1.56: 4962 1.56 - 1.69: 6 1.69 - 1.81: 105 Bond restraints: 9055 Sorted by residual: bond pdb=" C21 POV B 601 " pdb=" O21 POV B 601 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb="C210 POV B 601 " pdb="C211 POV B 601 " ideal model delta sigma weight residual 1.497 1.557 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 1.528 1.586 -0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" N POV B 601 " pdb=" C14 POV B 601 " ideal model delta sigma weight residual 1.490 1.433 0.057 2.00e-02 2.50e+03 8.13e+00 ... (remaining 9050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 11997 2.66 - 5.33: 198 5.33 - 7.99: 23 7.99 - 10.65: 7 10.65 - 13.31: 3 Bond angle restraints: 12228 Sorted by residual: angle pdb=" CA PRO B 82 " pdb=" N PRO B 82 " pdb=" CD PRO B 82 " ideal model delta sigma weight residual 112.00 105.50 6.50 1.40e+00 5.10e-01 2.16e+01 angle pdb=" N PHE A 331 " pdb=" CA PHE A 331 " pdb=" C PHE A 331 " ideal model delta sigma weight residual 110.91 115.92 -5.01 1.17e+00 7.31e-01 1.83e+01 angle pdb=" CG ARG B 141 " pdb=" CD ARG B 141 " pdb=" NE ARG B 141 " ideal model delta sigma weight residual 112.00 120.80 -8.80 2.20e+00 2.07e-01 1.60e+01 angle pdb=" O13 POV B 601 " pdb=" P POV B 601 " pdb=" O14 POV B 601 " ideal model delta sigma weight residual 121.11 109.51 11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA LEU C 367 " pdb=" CB LEU C 367 " pdb=" CG LEU C 367 " ideal model delta sigma weight residual 116.30 129.61 -13.31 3.50e+00 8.16e-02 1.45e+01 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.66: 5027 23.66 - 47.33: 341 47.33 - 70.99: 68 70.99 - 94.65: 23 94.65 - 118.31: 4 Dihedral angle restraints: 5463 sinusoidal: 2354 harmonic: 3109 Sorted by residual: dihedral pdb=" CB CYS A 327 " pdb=" SG CYS A 327 " pdb=" SG CYS A 342 " pdb=" CB CYS A 342 " ideal model delta sinusoidal sigma weight residual 93.00 152.31 -59.31 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -144.59 58.59 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS A 297 " pdb=" SG CYS A 297 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual 93.00 146.62 -53.62 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 922 0.044 - 0.087: 283 0.087 - 0.131: 83 0.131 - 0.175: 9 0.175 - 0.219: 5 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA PRO B 82 " pdb=" N PRO B 82 " pdb=" C PRO B 82 " pdb=" CB PRO B 82 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.48 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 1299 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 81 " 0.062 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO B 82 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 36 " -0.042 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO B 37 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 37 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 37 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 252 " 0.008 2.00e-02 2.50e+03 1.46e-02 5.30e+00 pdb=" CG TRP A 252 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 252 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 252 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 252 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 252 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 252 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 252 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 252 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 252 " -0.001 2.00e-02 2.50e+03 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1537 2.76 - 3.30: 8693 3.30 - 3.83: 14697 3.83 - 4.37: 16452 4.37 - 4.90: 29010 Nonbonded interactions: 70389 Sorted by model distance: nonbonded pdb=" NE1 TRP C 319 " pdb=" O4 BMA D 3 " model vdw 2.229 3.120 nonbonded pdb=" N SER B 133 " pdb=" OD1 ASN B 210 " model vdw 2.283 3.120 nonbonded pdb=" NE2 HIS A 332 " pdb=" OE2 GLU B 205 " model vdw 2.298 3.120 nonbonded pdb=" NZ LYS B 49 " pdb=" OD1 ASP B 218 " model vdw 2.326 3.120 nonbonded pdb=" O GLN C 70 " pdb=" OH TYR C 75 " model vdw 2.329 3.040 ... (remaining 70384 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.410 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 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 : 0.006 0.089 9078 Z= 0.254 Angle : 0.846 13.314 12279 Z= 0.427 Chirality : 0.047 0.219 1302 Planarity : 0.005 0.091 1550 Dihedral : 16.976 118.313 3418 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.53 % Allowed : 13.13 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1071 helix: 1.16 (0.25), residues: 392 sheet: -0.55 (0.36), residues: 205 loop : -0.96 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 252 HIS 0.006 0.001 HIS A 113 PHE 0.026 0.002 PHE C 148 TYR 0.018 0.002 TYR B 140 ARG 0.009 0.001 ARG B 431 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 1) link_NAG-ASN : angle 4.66901 ( 3) link_BETA1-4 : bond 0.01150 ( 2) link_BETA1-4 : angle 2.63475 ( 6) link_ALPHA1-2 : bond 0.00521 ( 2) link_ALPHA1-2 : angle 1.65276 ( 6) link_ALPHA1-3 : bond 0.00083 ( 2) link_ALPHA1-3 : angle 2.22397 ( 6) hydrogen bonds : bond 0.15344 ( 436) hydrogen bonds : angle 7.28379 ( 1275) SS BOND : bond 0.00306 ( 15) SS BOND : angle 0.93532 ( 30) covalent geometry : bond 0.00561 ( 9055) covalent geometry : angle 0.83857 (12228) Misc. bond : bond 0.00166 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8496 (mm-30) outliers start: 5 outliers final: 2 residues processed: 115 average time/residue: 0.2342 time to fit residues: 37.7480 Evaluate side-chains 106 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 438 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.0770 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 97 optimal weight: 30.0000 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS C 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.197697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115989 restraints weight = 11779.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114234 restraints weight = 6423.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115393 restraints weight = 4735.399| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9078 Z= 0.139 Angle : 0.660 9.903 12279 Z= 0.330 Chirality : 0.044 0.274 1302 Planarity : 0.004 0.042 1550 Dihedral : 12.136 104.009 1348 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.92 % Allowed : 13.45 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1071 helix: 1.29 (0.25), residues: 409 sheet: -0.43 (0.37), residues: 184 loop : -1.07 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 200 HIS 0.004 0.001 HIS A 332 PHE 0.022 0.001 PHE C 113 TYR 0.011 0.001 TYR B 484 ARG 0.008 0.001 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00812 ( 1) link_NAG-ASN : angle 4.21610 ( 3) link_BETA1-4 : bond 0.01084 ( 2) link_BETA1-4 : angle 3.51653 ( 6) link_ALPHA1-2 : bond 0.00864 ( 2) link_ALPHA1-2 : angle 1.52613 ( 6) link_ALPHA1-3 : bond 0.00273 ( 2) link_ALPHA1-3 : angle 1.55498 ( 6) hydrogen bonds : bond 0.04310 ( 436) hydrogen bonds : angle 5.22410 ( 1275) SS BOND : bond 0.00244 ( 15) SS BOND : angle 0.82358 ( 30) covalent geometry : bond 0.00307 ( 9055) covalent geometry : angle 0.65063 (12228) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.109 Fit side-chains REVERT: A 42 CYS cc_start: 0.5095 (OUTLIER) cc_final: 0.4883 (m) REVERT: B 128 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8534 (mm-30) REVERT: B 379 MET cc_start: 0.8168 (tpp) cc_final: 0.7919 (tpt) outliers start: 18 outliers final: 9 residues processed: 126 average time/residue: 0.2133 time to fit residues: 37.9589 Evaluate side-chains 109 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN C 99 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.192346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108037 restraints weight = 11681.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112356 restraints weight = 5339.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115139 restraints weight = 3526.141| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9078 Z= 0.232 Angle : 0.676 12.599 12279 Z= 0.342 Chirality : 0.045 0.256 1302 Planarity : 0.004 0.045 1550 Dihedral : 11.645 102.377 1345 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.09 % Allowed : 13.87 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1071 helix: 1.21 (0.25), residues: 406 sheet: -0.71 (0.36), residues: 189 loop : -1.11 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 200 HIS 0.006 0.001 HIS A 332 PHE 0.028 0.002 PHE C 46 TYR 0.017 0.002 TYR B 484 ARG 0.009 0.001 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 1) link_NAG-ASN : angle 2.92402 ( 3) link_BETA1-4 : bond 0.01248 ( 2) link_BETA1-4 : angle 3.66380 ( 6) link_ALPHA1-2 : bond 0.00701 ( 2) link_ALPHA1-2 : angle 1.47026 ( 6) link_ALPHA1-3 : bond 0.00319 ( 2) link_ALPHA1-3 : angle 1.58976 ( 6) hydrogen bonds : bond 0.04277 ( 436) hydrogen bonds : angle 5.09669 ( 1275) SS BOND : bond 0.00328 ( 15) SS BOND : angle 0.84776 ( 30) covalent geometry : bond 0.00544 ( 9055) covalent geometry : angle 0.66821 (12228) Misc. bond : bond 0.00122 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.965 Fit side-chains REVERT: A 319 ARG cc_start: 0.7399 (mpt180) cc_final: 0.7178 (mpt-90) REVERT: B 140 TYR cc_start: 0.8503 (p90) cc_final: 0.8200 (p90) REVERT: B 161 LYS cc_start: 0.7633 (tptt) cc_final: 0.7372 (tptt) REVERT: B 265 LEU cc_start: 0.8310 (tp) cc_final: 0.8105 (tt) REVERT: B 379 MET cc_start: 0.8302 (tpp) cc_final: 0.8062 (tpt) outliers start: 29 outliers final: 21 residues processed: 131 average time/residue: 0.1934 time to fit residues: 36.1575 Evaluate side-chains 131 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 53 optimal weight: 0.8980 chunk 99 optimal weight: 40.0000 chunk 83 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 2 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN ** B 281 ASN ** 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 = 0.4366 r_free = 0.4366 target = 0.196702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112557 restraints weight = 11502.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117154 restraints weight = 5136.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120134 restraints weight = 3342.329| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9078 Z= 0.120 Angle : 0.603 13.865 12279 Z= 0.299 Chirality : 0.042 0.241 1302 Planarity : 0.004 0.035 1550 Dihedral : 10.870 98.054 1345 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.35 % Allowed : 15.80 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1071 helix: 1.58 (0.25), residues: 410 sheet: -0.64 (0.35), residues: 207 loop : -1.09 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 200 HIS 0.008 0.001 HIS C 99 PHE 0.019 0.001 PHE A 169 TYR 0.010 0.001 TYR B 492 ARG 0.007 0.000 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00005 ( 1) link_NAG-ASN : angle 1.70438 ( 3) link_BETA1-4 : bond 0.01212 ( 2) link_BETA1-4 : angle 3.64257 ( 6) link_ALPHA1-2 : bond 0.00762 ( 2) link_ALPHA1-2 : angle 1.56004 ( 6) link_ALPHA1-3 : bond 0.00338 ( 2) link_ALPHA1-3 : angle 1.46362 ( 6) hydrogen bonds : bond 0.03571 ( 436) hydrogen bonds : angle 4.76062 ( 1275) SS BOND : bond 0.00455 ( 15) SS BOND : angle 0.80369 ( 30) covalent geometry : bond 0.00265 ( 9055) covalent geometry : angle 0.59514 (12228) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.056 Fit side-chains REVERT: A 268 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6920 (mp0) REVERT: A 319 ARG cc_start: 0.7388 (mpt180) cc_final: 0.7138 (mpt-90) REVERT: B 140 TYR cc_start: 0.8442 (p90) cc_final: 0.8061 (p90) REVERT: B 161 LYS cc_start: 0.7562 (tptt) cc_final: 0.7329 (tptt) outliers start: 22 outliers final: 15 residues processed: 121 average time/residue: 0.2101 time to fit residues: 36.3265 Evaluate side-chains 118 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.0670 chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** 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 = 0.4376 r_free = 0.4376 target = 0.197865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.117688 restraints weight = 11876.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116946 restraints weight = 6051.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.118534 restraints weight = 4358.464| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9078 Z= 0.122 Angle : 0.594 14.328 12279 Z= 0.291 Chirality : 0.042 0.234 1302 Planarity : 0.004 0.035 1550 Dihedral : 10.313 92.891 1345 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.42 % Allowed : 15.47 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1071 helix: 1.64 (0.25), residues: 410 sheet: -0.54 (0.38), residues: 187 loop : -1.09 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 200 HIS 0.004 0.001 HIS C 170 PHE 0.016 0.001 PHE C 113 TYR 0.009 0.001 TYR B 484 ARG 0.005 0.000 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00044 ( 1) link_NAG-ASN : angle 1.24420 ( 3) link_BETA1-4 : bond 0.01189 ( 2) link_BETA1-4 : angle 3.57362 ( 6) link_ALPHA1-2 : bond 0.00704 ( 2) link_ALPHA1-2 : angle 1.53367 ( 6) link_ALPHA1-3 : bond 0.00297 ( 2) link_ALPHA1-3 : angle 1.44239 ( 6) hydrogen bonds : bond 0.03456 ( 436) hydrogen bonds : angle 4.62480 ( 1275) SS BOND : bond 0.00232 ( 15) SS BOND : angle 0.73353 ( 30) covalent geometry : bond 0.00272 ( 9055) covalent geometry : angle 0.58630 (12228) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7320 (ptm) REVERT: A 319 ARG cc_start: 0.7460 (mpt180) cc_final: 0.7192 (mpt-90) REVERT: A 331 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: B 140 TYR cc_start: 0.8501 (p90) cc_final: 0.8120 (p90) REVERT: B 154 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6540 (mt-10) REVERT: B 161 LYS cc_start: 0.7726 (tptt) cc_final: 0.7502 (tptt) REVERT: C 77 LEU cc_start: 0.3031 (OUTLIER) cc_final: 0.2627 (mm) outliers start: 32 outliers final: 21 residues processed: 132 average time/residue: 0.1912 time to fit residues: 36.4580 Evaluate side-chains 129 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 92 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** 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 = 0.4384 r_free = 0.4384 target = 0.198693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.118703 restraints weight = 11863.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117683 restraints weight = 6089.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119356 restraints weight = 4367.600| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9078 Z= 0.116 Angle : 0.589 14.868 12279 Z= 0.288 Chirality : 0.042 0.235 1302 Planarity : 0.004 0.035 1550 Dihedral : 9.805 87.686 1345 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.31 % Allowed : 16.22 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1071 helix: 1.73 (0.25), residues: 411 sheet: -0.39 (0.38), residues: 186 loop : -1.10 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 200 HIS 0.004 0.001 HIS C 170 PHE 0.029 0.001 PHE B 318 TYR 0.013 0.001 TYR B 492 ARG 0.004 0.000 ARG C 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 1.03208 ( 3) link_BETA1-4 : bond 0.01259 ( 2) link_BETA1-4 : angle 3.51851 ( 6) link_ALPHA1-2 : bond 0.00662 ( 2) link_ALPHA1-2 : angle 1.52626 ( 6) link_ALPHA1-3 : bond 0.00316 ( 2) link_ALPHA1-3 : angle 1.46057 ( 6) hydrogen bonds : bond 0.03305 ( 436) hydrogen bonds : angle 4.52539 ( 1275) SS BOND : bond 0.00206 ( 15) SS BOND : angle 0.73147 ( 30) covalent geometry : bond 0.00260 ( 9055) covalent geometry : angle 0.58169 (12228) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.834 Fit side-chains REVERT: A 268 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6750 (pm20) REVERT: A 319 ARG cc_start: 0.7444 (mpt180) cc_final: 0.7192 (mpt-90) REVERT: A 331 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8166 (m-10) REVERT: B 140 TYR cc_start: 0.8482 (p90) cc_final: 0.8044 (p90) REVERT: B 141 ARG cc_start: 0.7792 (ttp-170) cc_final: 0.7305 (ttp-170) REVERT: B 154 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6496 (mt-10) REVERT: B 161 LYS cc_start: 0.7699 (tptt) cc_final: 0.7479 (tptt) REVERT: B 426 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8125 (tm-30) REVERT: C 77 LEU cc_start: 0.3046 (OUTLIER) cc_final: 0.2638 (mm) outliers start: 31 outliers final: 21 residues processed: 133 average time/residue: 0.2387 time to fit residues: 45.8719 Evaluate side-chains 128 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 281 ASN ** 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 = 0.4322 r_free = 0.4322 target = 0.191943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109935 restraints weight = 12093.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106816 restraints weight = 6821.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109641 restraints weight = 5158.458| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 9078 Z= 0.282 Angle : 0.708 13.367 12279 Z= 0.354 Chirality : 0.046 0.246 1302 Planarity : 0.004 0.048 1550 Dihedral : 9.855 84.648 1345 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.74 % Allowed : 16.65 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1071 helix: 1.22 (0.24), residues: 409 sheet: -0.61 (0.39), residues: 186 loop : -1.22 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 336 HIS 0.006 0.001 HIS B 70 PHE 0.027 0.002 PHE B 318 TYR 0.020 0.002 TYR B 484 ARG 0.004 0.001 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 1) link_NAG-ASN : angle 1.63286 ( 3) link_BETA1-4 : bond 0.01209 ( 2) link_BETA1-4 : angle 3.41180 ( 6) link_ALPHA1-2 : bond 0.00557 ( 2) link_ALPHA1-2 : angle 1.48206 ( 6) link_ALPHA1-3 : bond 0.00263 ( 2) link_ALPHA1-3 : angle 1.56851 ( 6) hydrogen bonds : bond 0.04104 ( 436) hydrogen bonds : angle 4.85830 ( 1275) SS BOND : bond 0.00380 ( 15) SS BOND : angle 0.87248 ( 30) covalent geometry : bond 0.00660 ( 9055) covalent geometry : angle 0.70214 (12228) Misc. bond : bond 0.00217 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.977 Fit side-chains REVERT: A 268 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6633 (pp20) REVERT: A 319 ARG cc_start: 0.7424 (mpt180) cc_final: 0.7197 (mpt-90) REVERT: A 331 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8235 (m-10) REVERT: B 140 TYR cc_start: 0.8622 (p90) cc_final: 0.8101 (p90) REVERT: B 161 LYS cc_start: 0.7786 (tptt) cc_final: 0.7564 (tptt) REVERT: B 195 TYR cc_start: 0.8739 (m-80) cc_final: 0.7996 (m-10) REVERT: B 265 LEU cc_start: 0.8367 (tp) cc_final: 0.8162 (tp) REVERT: C 77 LEU cc_start: 0.3292 (OUTLIER) cc_final: 0.2887 (mm) outliers start: 35 outliers final: 24 residues processed: 131 average time/residue: 0.2121 time to fit residues: 39.2339 Evaluate side-chains 135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 71 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 96 optimal weight: 40.0000 chunk 72 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 HIS ** C 115 ASN ** 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 = 0.4371 r_free = 0.4371 target = 0.197221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110061 restraints weight = 12082.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114898 restraints weight = 5392.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117824 restraints weight = 3545.996| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9078 Z= 0.116 Angle : 0.596 12.731 12279 Z= 0.292 Chirality : 0.042 0.245 1302 Planarity : 0.004 0.036 1550 Dihedral : 9.237 77.579 1345 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.31 % Allowed : 17.08 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1071 helix: 1.78 (0.25), residues: 403 sheet: -0.36 (0.39), residues: 185 loop : -1.06 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 336 HIS 0.004 0.001 HIS C 170 PHE 0.028 0.001 PHE A 169 TYR 0.013 0.001 TYR B 492 ARG 0.004 0.000 ARG C 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 1) link_NAG-ASN : angle 1.05233 ( 3) link_BETA1-4 : bond 0.01365 ( 2) link_BETA1-4 : angle 3.57608 ( 6) link_ALPHA1-2 : bond 0.00665 ( 2) link_ALPHA1-2 : angle 1.53598 ( 6) link_ALPHA1-3 : bond 0.00367 ( 2) link_ALPHA1-3 : angle 1.48637 ( 6) hydrogen bonds : bond 0.03433 ( 436) hydrogen bonds : angle 4.55654 ( 1275) SS BOND : bond 0.00222 ( 15) SS BOND : angle 0.74151 ( 30) covalent geometry : bond 0.00254 ( 9055) covalent geometry : angle 0.58843 (12228) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 1.639 Fit side-chains REVERT: A 268 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6747 (pm20) REVERT: A 319 ARG cc_start: 0.7411 (mpt180) cc_final: 0.7177 (mpt-90) REVERT: A 331 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8114 (m-10) REVERT: B 140 TYR cc_start: 0.8554 (p90) cc_final: 0.7978 (p90) REVERT: B 141 ARG cc_start: 0.7890 (ttp-170) cc_final: 0.7438 (ttp-170) REVERT: B 154 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6462 (mt-10) REVERT: B 436 MET cc_start: 0.6752 (mmt) cc_final: 0.6504 (mmt) REVERT: C 77 LEU cc_start: 0.3419 (OUTLIER) cc_final: 0.3017 (mm) outliers start: 31 outliers final: 21 residues processed: 133 average time/residue: 0.2366 time to fit residues: 43.9372 Evaluate side-chains 132 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 11 optimal weight: 0.0370 chunk 91 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** C 115 ASN ** 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 = 0.4373 r_free = 0.4373 target = 0.197428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112822 restraints weight = 11724.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117455 restraints weight = 5282.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120420 restraints weight = 3454.270| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9078 Z= 0.117 Angle : 0.597 12.343 12279 Z= 0.290 Chirality : 0.042 0.242 1302 Planarity : 0.004 0.037 1550 Dihedral : 8.711 70.399 1345 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.88 % Allowed : 17.72 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1071 helix: 2.05 (0.25), residues: 395 sheet: -0.25 (0.40), residues: 184 loop : -0.99 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 336 HIS 0.005 0.001 HIS C 170 PHE 0.031 0.001 PHE B 318 TYR 0.011 0.001 TYR B 492 ARG 0.006 0.000 ARG C 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 1) link_NAG-ASN : angle 0.99989 ( 3) link_BETA1-4 : bond 0.01433 ( 2) link_BETA1-4 : angle 3.73118 ( 6) link_ALPHA1-2 : bond 0.00556 ( 2) link_ALPHA1-2 : angle 1.56394 ( 6) link_ALPHA1-3 : bond 0.00329 ( 2) link_ALPHA1-3 : angle 1.47292 ( 6) hydrogen bonds : bond 0.03398 ( 436) hydrogen bonds : angle 4.44508 ( 1275) SS BOND : bond 0.00212 ( 15) SS BOND : angle 0.70886 ( 30) covalent geometry : bond 0.00263 ( 9055) covalent geometry : angle 0.58910 (12228) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 HIS cc_start: 0.5770 (t70) cc_final: 0.5542 (t70) REVERT: A 331 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: B 140 TYR cc_start: 0.8509 (p90) cc_final: 0.7934 (p90) REVERT: B 141 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7274 (ttp-170) REVERT: B 154 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6468 (mt-10) REVERT: B 436 MET cc_start: 0.6830 (mmt) cc_final: 0.6602 (mmt) REVERT: B 480 MET cc_start: 0.8226 (tpp) cc_final: 0.7697 (tpp) REVERT: C 77 LEU cc_start: 0.3349 (OUTLIER) cc_final: 0.2943 (mm) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.2235 time to fit residues: 40.6099 Evaluate side-chains 131 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 56 optimal weight: 0.1980 chunk 5 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 25 optimal weight: 20.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 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 = 0.4390 r_free = 0.4390 target = 0.199311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.119345 restraints weight = 11982.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118516 restraints weight = 5972.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120210 restraints weight = 4347.506| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9078 Z= 0.112 Angle : 0.605 12.138 12279 Z= 0.292 Chirality : 0.042 0.231 1302 Planarity : 0.004 0.038 1550 Dihedral : 8.144 61.633 1345 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.88 % Allowed : 18.36 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1071 helix: 2.28 (0.25), residues: 389 sheet: -0.21 (0.39), residues: 184 loop : -0.94 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 336 HIS 0.005 0.001 HIS C 170 PHE 0.032 0.001 PHE B 318 TYR 0.014 0.001 TYR A 346 ARG 0.005 0.000 ARG B 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 1) link_NAG-ASN : angle 0.97252 ( 3) link_BETA1-4 : bond 0.01455 ( 2) link_BETA1-4 : angle 3.91454 ( 6) link_ALPHA1-2 : bond 0.00525 ( 2) link_ALPHA1-2 : angle 1.60183 ( 6) link_ALPHA1-3 : bond 0.00401 ( 2) link_ALPHA1-3 : angle 1.46539 ( 6) hydrogen bonds : bond 0.03259 ( 436) hydrogen bonds : angle 4.36472 ( 1275) SS BOND : bond 0.00212 ( 15) SS BOND : angle 0.70847 ( 30) covalent geometry : bond 0.00248 ( 9055) covalent geometry : angle 0.59719 (12228) Misc. bond : bond 0.00060 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 HIS cc_start: 0.5774 (t70) cc_final: 0.5566 (t70) REVERT: A 331 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8142 (m-10) REVERT: B 66 TRP cc_start: 0.8167 (p-90) cc_final: 0.7903 (p90) REVERT: B 140 TYR cc_start: 0.8476 (p90) cc_final: 0.7887 (p90) REVERT: B 154 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6444 (mt-10) REVERT: C 77 LEU cc_start: 0.3279 (OUTLIER) cc_final: 0.2863 (mm) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.2153 time to fit residues: 40.4860 Evaluate side-chains 133 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 0.0570 chunk 98 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN C 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.198318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110812 restraints weight = 12034.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115613 restraints weight = 5456.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.118705 restraints weight = 3600.126| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9078 Z= 0.143 Angle : 0.611 11.971 12279 Z= 0.296 Chirality : 0.042 0.222 1302 Planarity : 0.004 0.041 1550 Dihedral : 8.012 59.336 1345 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.56 % Allowed : 18.78 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1071 helix: 2.23 (0.25), residues: 389 sheet: -0.18 (0.40), residues: 184 loop : -0.97 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 336 HIS 0.007 0.001 HIS C 170 PHE 0.034 0.001 PHE B 318 TYR 0.008 0.001 TYR B 492 ARG 0.016 0.001 ARG C 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00031 ( 1) link_NAG-ASN : angle 1.04626 ( 3) link_BETA1-4 : bond 0.01452 ( 2) link_BETA1-4 : angle 3.98172 ( 6) link_ALPHA1-2 : bond 0.00467 ( 2) link_ALPHA1-2 : angle 1.57827 ( 6) link_ALPHA1-3 : bond 0.00377 ( 2) link_ALPHA1-3 : angle 1.49272 ( 6) hydrogen bonds : bond 0.03340 ( 436) hydrogen bonds : angle 4.37374 ( 1275) SS BOND : bond 0.00233 ( 15) SS BOND : angle 0.70484 ( 30) covalent geometry : bond 0.00330 ( 9055) covalent geometry : angle 0.60244 (12228) Misc. bond : bond 0.00082 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4085.19 seconds wall clock time: 74 minutes 22.94 seconds (4462.94 seconds total)