Starting phenix.real_space_refine on Mon May 12 23:24:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzr_41767/05_2025/8tzr_41767.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzr_41767/05_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_41767/05_2025/8tzr_41767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzr_41767/05_2025/8tzr_41767.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzr_41767/05_2025/8tzr_41767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzr_41767/05_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-5687/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: 5.24, per 1000 atoms: 0.59 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: 2.29 Conformation dependent library (CDL) restraints added in 929.2 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: 0.87 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: 2.31 Time building geometry restraints manager: 2.65 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: 1.190 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.130 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.550 ------------------------------------------------------------------------------- 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 : 1.021 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: 0.2087 time to fit residues: 33.5100 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 : 0.923 ------------------------------------------------------------------------------- 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 = 0.197702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115985 restraints weight = 11779.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114251 restraints weight = 6426.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115394 restraints weight = 4736.297| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 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 4.21609 ( 3) link_BETA1-4 : bond 0.01084 ( 2) link_BETA1-4 : angle 3.51654 ( 6) link_ALPHA1-2 : bond 0.00864 ( 2) link_ALPHA1-2 : angle 1.52612 ( 6) link_ALPHA1-3 : bond 0.00273 ( 2) link_ALPHA1-3 : angle 1.55497 ( 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 : 0.993 Fit side-chains REVERT: A 42 CYS cc_start: 0.5095 (OUTLIER) cc_final: 0.4881 (m) REVERT: B 128 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8535 (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: 0.1990 time to fit residues: 35.2207 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: 0.1980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.192715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.108396 restraints weight = 11666.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112770 restraints weight = 5322.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115566 restraints weight = 3509.271| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9078 Z= 0.219 Angle : 0.670 12.597 12279 Z= 0.339 Chirality : 0.045 0.256 1302 Planarity : 0.004 0.046 1550 Dihedral : 11.589 102.142 1345 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.09 % Allowed : 13.77 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.25), residues: 406 sheet: -0.70 (0.36), residues: 189 loop : -1.10 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 200 HIS 0.005 0.001 HIS A 332 PHE 0.022 0.002 PHE C 46 TYR 0.016 0.002 TYR B 484 ARG 0.009 0.001 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 1) link_NAG-ASN : angle 2.83459 ( 3) link_BETA1-4 : bond 0.01223 ( 2) link_BETA1-4 : angle 3.66909 ( 6) link_ALPHA1-2 : bond 0.00715 ( 2) link_ALPHA1-2 : angle 1.47856 ( 6) link_ALPHA1-3 : bond 0.00323 ( 2) link_ALPHA1-3 : angle 1.58192 ( 6) hydrogen bonds : bond 0.04240 ( 436) hydrogen bonds : angle 5.06843 ( 1275) SS BOND : bond 0.00329 ( 15) SS BOND : angle 0.83550 ( 30) covalent geometry : bond 0.00514 ( 9055) covalent geometry : angle 0.66182 (12228) Misc. bond : bond 0.00123 ( 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 145 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.924 Fit side-chains REVERT: A 319 ARG cc_start: 0.7397 (mpt180) cc_final: 0.7176 (mpt-90) REVERT: B 140 TYR cc_start: 0.8497 (p90) cc_final: 0.8184 (p90) REVERT: B 161 LYS cc_start: 0.7616 (tptt) cc_final: 0.7354 (tptt) REVERT: B 265 LEU cc_start: 0.8286 (tp) cc_final: 0.8085 (tt) REVERT: B 379 MET cc_start: 0.8289 (tpp) cc_final: 0.8056 (tpt) outliers start: 29 outliers final: 21 residues processed: 132 average time/residue: 0.1910 time to fit residues: 35.8805 Evaluate side-chains 130 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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: 30.0000 chunk 83 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 30.0000 chunk 102 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 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 = 0.4334 r_free = 0.4334 target = 0.193245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109009 restraints weight = 11590.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113425 restraints weight = 5253.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.116230 restraints weight = 3456.298| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9078 Z= 0.186 Angle : 0.642 13.625 12279 Z= 0.321 Chirality : 0.044 0.238 1302 Planarity : 0.004 0.041 1550 Dihedral : 11.049 98.742 1345 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.84 % Allowed : 14.83 % Favored : 81.32 % 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: -0.17 (0.25), residues: 1071 helix: 1.30 (0.25), residues: 410 sheet: -0.75 (0.37), residues: 189 loop : -1.07 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 200 HIS 0.006 0.001 HIS C 99 PHE 0.018 0.001 PHE A 169 TYR 0.013 0.001 TYR B 484 ARG 0.008 0.000 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 1) link_NAG-ASN : angle 1.84965 ( 3) link_BETA1-4 : bond 0.01180 ( 2) link_BETA1-4 : angle 3.61263 ( 6) link_ALPHA1-2 : bond 0.00792 ( 2) link_ALPHA1-2 : angle 1.50384 ( 6) link_ALPHA1-3 : bond 0.00323 ( 2) link_ALPHA1-3 : angle 1.54269 ( 6) hydrogen bonds : bond 0.03869 ( 436) hydrogen bonds : angle 4.91524 ( 1275) SS BOND : bond 0.00296 ( 15) SS BOND : angle 0.85377 ( 30) covalent geometry : bond 0.00435 ( 9055) covalent geometry : angle 0.63446 (12228) Misc. bond : bond 0.00105 ( 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 145 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.971 Fit side-chains REVERT: A 268 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6222 (pp20) REVERT: A 319 ARG cc_start: 0.7394 (mpt180) cc_final: 0.7149 (mpt-90) REVERT: B 140 TYR cc_start: 0.8549 (p90) cc_final: 0.8113 (p90) REVERT: B 161 LYS cc_start: 0.7736 (tptt) cc_final: 0.7473 (tptt) REVERT: B 205 GLU cc_start: 0.7924 (mp0) cc_final: 0.7679 (mp0) outliers start: 36 outliers final: 26 residues processed: 128 average time/residue: 0.1901 time to fit residues: 34.8901 Evaluate side-chains 131 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 164 MET Chi-restraints excluded: chain A residue 256 LEU 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 111 LEU 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 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 275 ILE 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 122 MET Chi-restraints excluded: chain C residue 146 VAL 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: 2.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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** ** 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 = 0.4368 r_free = 0.4368 target = 0.196795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.116047 restraints weight = 11928.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117097 restraints weight = 6048.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117610 restraints weight = 4444.359| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9078 Z= 0.124 Angle : 0.601 14.544 12279 Z= 0.295 Chirality : 0.042 0.232 1302 Planarity : 0.004 0.035 1550 Dihedral : 10.507 94.297 1345 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: 0.08 (0.25), residues: 1071 helix: 1.61 (0.25), residues: 410 sheet: -0.53 (0.38), residues: 184 loop : -1.08 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 200 HIS 0.005 0.001 HIS A 332 PHE 0.017 0.001 PHE C 113 TYR 0.009 0.001 TYR B 492 ARG 0.006 0.000 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00006 ( 1) link_NAG-ASN : angle 1.34328 ( 3) link_BETA1-4 : bond 0.01254 ( 2) link_BETA1-4 : angle 3.55709 ( 6) link_ALPHA1-2 : bond 0.00704 ( 2) link_ALPHA1-2 : angle 1.51929 ( 6) link_ALPHA1-3 : bond 0.00291 ( 2) link_ALPHA1-3 : angle 1.49149 ( 6) hydrogen bonds : bond 0.03521 ( 436) hydrogen bonds : angle 4.69372 ( 1275) SS BOND : bond 0.00223 ( 15) SS BOND : angle 0.75652 ( 30) covalent geometry : bond 0.00279 ( 9055) covalent geometry : angle 0.59341 (12228) Misc. bond : bond 0.00056 ( 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: 31 poor density : 113 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7061 (ptm) REVERT: A 319 ARG cc_start: 0.7456 (mpt180) cc_final: 0.7198 (mpt-90) REVERT: A 331 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: B 140 TYR cc_start: 0.8536 (p90) cc_final: 0.8146 (p90) REVERT: B 154 GLU cc_start: 0.7230 (mt-10) cc_final: 0.7029 (mt-10) REVERT: B 161 LYS cc_start: 0.7756 (tptt) cc_final: 0.7487 (tptt) REVERT: C 77 LEU cc_start: 0.3050 (OUTLIER) cc_final: 0.2652 (mm) outliers start: 31 outliers final: 18 residues processed: 132 average time/residue: 0.2110 time to fit residues: 39.7124 Evaluate side-chains 126 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 330 VAL Chi-restraints excluded: chain A residue 331 PHE 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 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 394 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 LEU 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: 8.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.198072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118370 restraints weight = 11873.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117490 restraints weight = 6097.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119095 restraints weight = 4354.570| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9078 Z= 0.119 Angle : 0.602 15.142 12279 Z= 0.295 Chirality : 0.042 0.233 1302 Planarity : 0.004 0.034 1550 Dihedral : 9.964 88.849 1345 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.63 % Allowed : 16.97 % 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: 0.15 (0.25), residues: 1071 helix: 1.65 (0.25), residues: 411 sheet: -0.36 (0.39), residues: 184 loop : -1.09 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 200 HIS 0.004 0.001 HIS C 170 PHE 0.030 0.001 PHE B 318 TYR 0.014 0.001 TYR B 492 ARG 0.004 0.000 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00022 ( 1) link_NAG-ASN : angle 1.06558 ( 3) link_BETA1-4 : bond 0.01283 ( 2) link_BETA1-4 : angle 3.52552 ( 6) link_ALPHA1-2 : bond 0.00678 ( 2) link_ALPHA1-2 : angle 1.52610 ( 6) link_ALPHA1-3 : bond 0.00320 ( 2) link_ALPHA1-3 : angle 1.49836 ( 6) hydrogen bonds : bond 0.03421 ( 436) hydrogen bonds : angle 4.58210 ( 1275) SS BOND : bond 0.00208 ( 15) SS BOND : angle 0.75693 ( 30) covalent geometry : bond 0.00266 ( 9055) covalent geometry : angle 0.59440 (12228) Misc. bond : bond 0.00059 ( 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 145 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.048 Fit side-chains REVERT: A 241 MET cc_start: 0.6974 (ptm) cc_final: 0.6306 (ppp) REVERT: A 268 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6676 (pm20) REVERT: A 319 ARG cc_start: 0.7403 (mpt180) cc_final: 0.7158 (mpt-90) REVERT: A 331 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8183 (m-10) REVERT: B 140 TYR cc_start: 0.8500 (p90) cc_final: 0.8037 (p90) REVERT: B 141 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7321 (ttp-170) REVERT: B 426 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8088 (tm-30) REVERT: C 77 LEU cc_start: 0.3046 (OUTLIER) cc_final: 0.2638 (mm) outliers start: 34 outliers final: 22 residues processed: 134 average time/residue: 0.1946 time to fit residues: 37.0811 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 : 1.049 ------------------------------------------------------------------------------- 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 63 MET 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 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: 1.9990 chunk 101 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** 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 = 0.4317 r_free = 0.4317 target = 0.191375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109305 restraints weight = 12085.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106550 restraints weight = 6712.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109279 restraints weight = 5145.863| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9078 Z= 0.291 Angle : 0.716 14.331 12279 Z= 0.357 Chirality : 0.046 0.244 1302 Planarity : 0.004 0.046 1550 Dihedral : 10.024 88.307 1345 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.16 % Allowed : 16.65 % Favored : 79.19 % 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: -0.28 (0.25), residues: 1071 helix: 1.21 (0.24), residues: 410 sheet: -0.65 (0.39), residues: 186 loop : -1.22 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 336 HIS 0.006 0.001 HIS B 70 PHE 0.033 0.002 PHE B 318 TYR 0.019 0.002 TYR B 484 ARG 0.005 0.001 ARG B 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 1) link_NAG-ASN : angle 1.63285 ( 3) link_BETA1-4 : bond 0.01368 ( 2) link_BETA1-4 : angle 3.43056 ( 6) link_ALPHA1-2 : bond 0.00594 ( 2) link_ALPHA1-2 : angle 1.49905 ( 6) link_ALPHA1-3 : bond 0.00281 ( 2) link_ALPHA1-3 : angle 1.56851 ( 6) hydrogen bonds : bond 0.04071 ( 436) hydrogen bonds : angle 4.85094 ( 1275) SS BOND : bond 0.00367 ( 15) SS BOND : angle 0.89445 ( 30) covalent geometry : bond 0.00693 ( 9055) covalent geometry : angle 0.70953 (12228) Misc. bond : bond 0.00178 ( 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 150 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 1.053 Fit side-chains REVERT: A 241 MET cc_start: 0.7357 (ptm) cc_final: 0.6296 (ppp) REVERT: A 268 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6558 (pp20) REVERT: A 319 ARG cc_start: 0.7440 (mpt180) cc_final: 0.7220 (mpt-90) REVERT: A 331 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8228 (m-10) REVERT: B 140 TYR cc_start: 0.8689 (p90) cc_final: 0.8163 (p90) REVERT: B 195 TYR cc_start: 0.8713 (m-80) cc_final: 0.7925 (m-10) REVERT: B 330 ASN cc_start: 0.6344 (p0) cc_final: 0.6075 (p0) REVERT: B 480 MET cc_start: 0.8528 (tpp) cc_final: 0.8327 (ttm) REVERT: C 77 LEU cc_start: 0.3147 (OUTLIER) cc_final: 0.2717 (mm) outliers start: 39 outliers final: 27 residues processed: 136 average time/residue: 0.2093 time to fit residues: 39.9768 Evaluate side-chains 139 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 164 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 31 VAL 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 289 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 384 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 50.0000 chunk 72 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.196370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115403 restraints weight = 12098.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115223 restraints weight = 6007.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116669 restraints weight = 4377.419| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9078 Z= 0.125 Angle : 0.607 14.299 12279 Z= 0.298 Chirality : 0.042 0.243 1302 Planarity : 0.004 0.035 1550 Dihedral : 9.411 79.840 1345 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.63 % Allowed : 17.61 % Favored : 78.76 % 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: 0.13 (0.25), residues: 1071 helix: 1.63 (0.25), residues: 409 sheet: -0.42 (0.39), residues: 185 loop : -1.06 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 336 HIS 0.004 0.001 HIS C 170 PHE 0.028 0.001 PHE B 318 TYR 0.012 0.001 TYR B 492 ARG 0.007 0.000 ARG C 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 1.11710 ( 3) link_BETA1-4 : bond 0.01311 ( 2) link_BETA1-4 : angle 3.53924 ( 6) link_ALPHA1-2 : bond 0.00673 ( 2) link_ALPHA1-2 : angle 1.52934 ( 6) link_ALPHA1-3 : bond 0.00336 ( 2) link_ALPHA1-3 : angle 1.48930 ( 6) hydrogen bonds : bond 0.03459 ( 436) hydrogen bonds : angle 4.56950 ( 1275) SS BOND : bond 0.00224 ( 15) SS BOND : angle 0.75568 ( 30) covalent geometry : bond 0.00280 ( 9055) covalent geometry : angle 0.60034 (12228) Misc. bond : bond 0.00059 ( 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 147 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.074 Fit side-chains REVERT: A 241 MET cc_start: 0.7024 (ptm) cc_final: 0.6139 (ppp) REVERT: A 268 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: A 319 ARG cc_start: 0.7417 (mpt180) cc_final: 0.7207 (mpt-90) REVERT: A 331 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8133 (m-10) REVERT: B 140 TYR cc_start: 0.8577 (p90) cc_final: 0.8053 (p90) REVERT: B 154 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6440 (mt-10) REVERT: B 480 MET cc_start: 0.8468 (tpp) cc_final: 0.7934 (tpp) REVERT: B 489 MET cc_start: 0.7010 (mtt) cc_final: 0.6773 (mtt) REVERT: C 77 LEU cc_start: 0.3280 (OUTLIER) cc_final: 0.2849 (mm) outliers start: 34 outliers final: 25 residues processed: 134 average time/residue: 0.2114 time to fit residues: 39.3003 Evaluate side-chains 136 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 159 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 GLU 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 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 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 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: 7.9990 chunk 5 optimal weight: 0.1980 chunk 83 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS ** 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 = 0.4353 r_free = 0.4353 target = 0.195429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113900 restraints weight = 12118.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113132 restraints weight = 6093.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114505 restraints weight = 4462.084| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9078 Z= 0.149 Angle : 0.618 14.442 12279 Z= 0.301 Chirality : 0.043 0.242 1302 Planarity : 0.004 0.035 1550 Dihedral : 9.030 77.337 1345 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.52 % Allowed : 17.50 % Favored : 78.98 % 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: 1.77 (0.25), residues: 403 sheet: -0.43 (0.40), residues: 185 loop : -1.03 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 336 HIS 0.004 0.001 HIS C 170 PHE 0.026 0.001 PHE B 318 TYR 0.012 0.001 TYR A 346 ARG 0.006 0.000 ARG B 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 1.22764 ( 3) link_BETA1-4 : bond 0.01370 ( 2) link_BETA1-4 : angle 3.63698 ( 6) link_ALPHA1-2 : bond 0.00580 ( 2) link_ALPHA1-2 : angle 1.53906 ( 6) link_ALPHA1-3 : bond 0.00315 ( 2) link_ALPHA1-3 : angle 1.50779 ( 6) hydrogen bonds : bond 0.03506 ( 436) hydrogen bonds : angle 4.54095 ( 1275) SS BOND : bond 0.00249 ( 15) SS BOND : angle 0.75527 ( 30) covalent geometry : bond 0.00345 ( 9055) covalent geometry : angle 0.61031 (12228) Misc. bond : bond 0.00091 ( 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 144 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.7003 (ptm) cc_final: 0.6011 (ppp) REVERT: A 268 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: A 331 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: B 140 TYR cc_start: 0.8543 (p90) cc_final: 0.7947 (p90) REVERT: B 154 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6536 (mt-10) REVERT: B 436 MET cc_start: 0.6804 (mmt) cc_final: 0.6539 (mmt) REVERT: B 480 MET cc_start: 0.8496 (tpp) cc_final: 0.7877 (ttm) REVERT: C 77 LEU cc_start: 0.3324 (OUTLIER) cc_final: 0.2902 (mm) outliers start: 33 outliers final: 26 residues processed: 131 average time/residue: 0.2485 time to fit residues: 45.8652 Evaluate side-chains 137 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 159 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 111 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 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL 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 61 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.196656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115428 restraints weight = 12017.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114964 restraints weight = 6038.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116359 restraints weight = 4443.504| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9078 Z= 0.128 Angle : 0.624 15.581 12279 Z= 0.301 Chirality : 0.043 0.242 1302 Planarity : 0.004 0.043 1550 Dihedral : 8.749 73.729 1345 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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 : 0.00 % 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: 0.31 (0.26), residues: 1071 helix: 1.93 (0.25), residues: 396 sheet: -0.38 (0.40), residues: 185 loop : -1.02 (0.27), residues: 490 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 0.025 0.001 PHE B 318 TYR 0.011 0.001 TYR B 492 ARG 0.008 0.000 ARG B 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 1.15150 ( 3) link_BETA1-4 : bond 0.01341 ( 2) link_BETA1-4 : angle 3.71861 ( 6) link_ALPHA1-2 : bond 0.00573 ( 2) link_ALPHA1-2 : angle 1.55361 ( 6) link_ALPHA1-3 : bond 0.00281 ( 2) link_ALPHA1-3 : angle 1.50021 ( 6) hydrogen bonds : bond 0.03404 ( 436) hydrogen bonds : angle 4.49370 ( 1275) SS BOND : bond 0.00232 ( 15) SS BOND : angle 0.73701 ( 30) covalent geometry : bond 0.00291 ( 9055) covalent geometry : angle 0.61633 (12228) Misc. bond : bond 0.00082 ( 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 138 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.6930 (ptm) cc_final: 0.6017 (ppp) REVERT: A 331 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8202 (m-10) REVERT: B 140 TYR cc_start: 0.8548 (p90) cc_final: 0.7963 (p90) REVERT: B 154 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6482 (mt-10) REVERT: B 261 ARG cc_start: 0.8145 (ptt90) cc_final: 0.7874 (ptt90) REVERT: B 436 MET cc_start: 0.6790 (mmt) cc_final: 0.6526 (mmt) REVERT: B 480 MET cc_start: 0.8485 (tpp) cc_final: 0.7856 (ttm) REVERT: C 77 LEU cc_start: 0.3281 (OUTLIER) cc_final: 0.2849 (mm) outliers start: 27 outliers final: 24 residues processed: 126 average time/residue: 0.2057 time to fit residues: 36.1620 Evaluate side-chains 134 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 159 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 GLU 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 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 239 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 394 LEU 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: 2.9990 chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 98 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.197114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116739 restraints weight = 11978.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115154 restraints weight = 6004.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116788 restraints weight = 4437.624| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9078 Z= 0.126 Angle : 0.615 15.552 12279 Z= 0.298 Chirality : 0.042 0.235 1302 Planarity : 0.004 0.043 1550 Dihedral : 8.492 70.425 1345 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.42 % Allowed : 18.14 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.26), residues: 1071 helix: 1.98 (0.25), residues: 396 sheet: -0.29 (0.40), residues: 184 loop : -1.01 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 336 HIS 0.003 0.001 HIS B 153 PHE 0.025 0.001 PHE B 318 TYR 0.012 0.001 TYR A 346 ARG 0.007 0.000 ARG B 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 1.10846 ( 3) link_BETA1-4 : bond 0.01394 ( 2) link_BETA1-4 : angle 3.82824 ( 6) link_ALPHA1-2 : bond 0.00550 ( 2) link_ALPHA1-2 : angle 1.56507 ( 6) link_ALPHA1-3 : bond 0.00369 ( 2) link_ALPHA1-3 : angle 1.49019 ( 6) hydrogen bonds : bond 0.03352 ( 436) hydrogen bonds : angle 4.45942 ( 1275) SS BOND : bond 0.00227 ( 15) SS BOND : angle 0.73363 ( 30) covalent geometry : bond 0.00288 ( 9055) covalent geometry : angle 0.60702 (12228) Misc. bond : bond 0.00079 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.80 seconds wall clock time: 60 minutes 15.94 seconds (3615.94 seconds total)