Starting phenix.real_space_refine on Thu Jul 24 17:21:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e4c_27888/07_2025/8e4c_27888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e4c_27888/07_2025/8e4c_27888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e4c_27888/07_2025/8e4c_27888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e4c_27888/07_2025/8e4c_27888.map" model { file = "/net/cci-nas-00/data/ceres_data/8e4c_27888/07_2025/8e4c_27888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e4c_27888/07_2025/8e4c_27888.cif" } resolution = 4.0 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= 0.001 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 4094 2.51 5 N 1070 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6398 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1988 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 18, 'TRANS': 234} Chain: "A" Number of atoms: 1988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1988 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 18, 'TRANS': 234} Chain: "C" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1130 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 12, 'TRANS': 129} Chain: "D" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1222 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.48, per 1000 atoms: 0.70 Number of scatterers: 6398 At special positions: 0 Unit cell: (73.04, 107.9, 156.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1209 8.00 N 1070 7.00 C 4094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 415 " distance=2.04 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 124 " distance=2.06 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 120 " 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=0, symmetry=0 Links applied NAG-ASN " NAG C 401 " - " ASN C 58 " " NAG C 402 " - " ASN C 68 " " NAG D 301 " - " ASN D 68 " " NAG D 302 " - " ASN D 99 " " NAG D 303 " - " ASN D 130 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 840.9 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1518 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 15 sheets defined 27.5% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'B' and resid 232 through 240 removed outlier: 3.919A pdb=" N ILE B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.651A pdb=" N TRP B 297 " --> pdb=" O CYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 444 through 476 Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 339 through 345 removed outlier: 3.715A pdb=" N LEU A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.646A pdb=" N SER A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 476 removed outlier: 4.176A pdb=" N TRP A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.631A pdb=" N ARG C 96 " --> pdb=" O LYS C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 169 Proline residue: C 153 - end of helix Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 148 through 184 removed outlier: 3.760A pdb=" N ARG D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 3.639A pdb=" N ASP D 181 " --> pdb=" O PHE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 208 through 213 Processing sheet with id=AA1, first strand: chain 'B' and resid 225 through 229 removed outlier: 3.532A pdb=" N THR B 245 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASN B 243 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL B 292 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR B 245 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALA B 290 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 247 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLY B 288 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER B 249 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 286 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 274 " --> pdb=" O LYS B 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 258 through 263 removed outlier: 3.647A pdb=" N ILE B 320 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS B 305 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS B 318 " --> pdb=" O CYS B 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 332 through 336 removed outlier: 3.791A pdb=" N LYS B 356 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 354 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 352 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 355 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR B 394 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 332 through 336 removed outlier: 3.791A pdb=" N LYS B 356 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 354 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 352 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 372 through 373 removed outlier: 3.533A pdb=" N THR B 414 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS B 415 " --> pdb=" O ARG B 429 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 429 " --> pdb=" O CYS B 415 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 226 through 228 removed outlier: 5.807A pdb=" N PHE A 284 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 290 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 228 removed outlier: 5.807A pdb=" N PHE A 284 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 274 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 263 removed outlier: 3.775A pdb=" N CYS A 305 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS A 318 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 307 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 316 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 332 through 336 removed outlier: 3.508A pdb=" N SER A 398 " --> pdb=" O CYS A 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 332 through 336 removed outlier: 5.959A pdb=" N TYR A 394 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.745A pdb=" N THR A 414 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 74 through 75 removed outlier: 3.545A pdb=" N TRP C 100 " --> pdb=" O TRP C 62 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 103 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 110 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 74 through 75 removed outlier: 3.545A pdb=" N TRP C 100 " --> pdb=" O TRP C 62 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 97 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AB6, first strand: chain 'D' and resid 62 through 63 281 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1415 1.33 - 1.45: 1448 1.45 - 1.57: 3663 1.57 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 6557 Sorted by residual: bond pdb=" CE1 HIS A 424 " pdb=" NE2 HIS A 424 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.77e+01 bond pdb=" CE1 HIS B 419 " pdb=" NE2 HIS B 419 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" CE1 HIS C 95 " pdb=" NE2 HIS C 95 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.65e+01 bond pdb=" CE1 HIS B 397 " pdb=" NE2 HIS B 397 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.55e+01 bond pdb=" N ILE C 59 " pdb=" CA ILE C 59 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.18e-02 7.18e+03 1.06e+01 ... (remaining 6552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 8800 2.90 - 5.80: 121 5.80 - 8.69: 8 8.69 - 11.59: 3 11.59 - 14.49: 1 Bond angle restraints: 8933 Sorted by residual: angle pdb=" N GLU B 443 " pdb=" CA GLU B 443 " pdb=" CB GLU B 443 " ideal model delta sigma weight residual 110.49 124.98 -14.49 1.69e+00 3.50e-01 7.35e+01 angle pdb=" C PRO C 57 " pdb=" CA PRO C 57 " pdb=" CB PRO C 57 " ideal model delta sigma weight residual 111.56 101.97 9.59 1.65e+00 3.67e-01 3.38e+01 angle pdb=" N ASN D 130 " pdb=" CA ASN D 130 " pdb=" C ASN D 130 " ideal model delta sigma weight residual 108.63 101.14 7.49 1.60e+00 3.91e-01 2.19e+01 angle pdb=" CA PRO D 42 " pdb=" N PRO D 42 " pdb=" CD PRO D 42 " ideal model delta sigma weight residual 112.00 105.45 6.55 1.40e+00 5.10e-01 2.19e+01 angle pdb=" C ASN C 58 " pdb=" CA ASN C 58 " pdb=" CB ASN C 58 " ideal model delta sigma weight residual 109.90 116.92 -7.02 1.56e+00 4.11e-01 2.03e+01 ... (remaining 8928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3481 17.92 - 35.85: 379 35.85 - 53.77: 107 53.77 - 71.70: 22 71.70 - 89.62: 7 Dihedral angle restraints: 3996 sinusoidal: 1661 harmonic: 2335 Sorted by residual: dihedral pdb=" N GLU B 443 " pdb=" C GLU B 443 " pdb=" CA GLU B 443 " pdb=" CB GLU B 443 " ideal model delta harmonic sigma weight residual 122.80 158.13 -35.33 0 2.50e+00 1.60e-01 2.00e+02 dihedral pdb=" C GLU B 443 " pdb=" N GLU B 443 " pdb=" CA GLU B 443 " pdb=" CB GLU B 443 " ideal model delta harmonic sigma weight residual -122.60 -155.37 32.77 0 2.50e+00 1.60e-01 1.72e+02 dihedral pdb=" C PRO C 57 " pdb=" N PRO C 57 " pdb=" CA PRO C 57 " pdb=" CB PRO C 57 " ideal model delta harmonic sigma weight residual -120.70 -108.74 -11.96 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 3993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.291: 1034 0.291 - 0.581: 2 0.581 - 0.872: 0 0.872 - 1.162: 0 1.162 - 1.453: 1 Chirality restraints: 1037 Sorted by residual: chirality pdb=" CA GLU B 443 " pdb=" N GLU B 443 " pdb=" C GLU B 443 " pdb=" CB GLU B 443 " both_signs ideal model delta sigma weight residual False 2.51 1.06 1.45 2.00e-01 2.50e+01 5.27e+01 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 58 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA ILE C 69 " pdb=" N ILE C 69 " pdb=" C ILE C 69 " pdb=" CB ILE C 69 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1034 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.277 2.00e-02 2.50e+03 2.37e-01 7.00e+02 pdb=" C7 NAG C 402 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.412 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.205 2.00e-02 2.50e+03 1.74e-01 3.80e+02 pdb=" C7 NAG C 401 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.287 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 302 " -0.170 2.00e-02 2.50e+03 1.45e-01 2.63e+02 pdb=" C7 NAG D 302 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG D 302 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG D 302 " 0.238 2.00e-02 2.50e+03 pdb=" O7 NAG D 302 " -0.132 2.00e-02 2.50e+03 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1222 2.78 - 3.31: 6087 3.31 - 3.84: 10132 3.84 - 4.37: 11183 4.37 - 4.90: 19265 Nonbonded interactions: 47889 Sorted by model distance: nonbonded pdb=" O GLY C 131 " pdb=" OG1 THR C 134 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR A 414 " pdb=" O ARG A 429 " model vdw 2.258 3.040 nonbonded pdb=" O SER A 382 " pdb=" OG1 THR A 396 " model vdw 2.294 3.040 nonbonded pdb=" O VAL C 152 " pdb=" OG1 THR C 155 " model vdw 2.353 3.040 nonbonded pdb=" O CYS D 43 " pdb=" OG1 THR D 132 " model vdw 2.357 3.040 ... (remaining 47884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.940 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.690 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:3.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4891 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 : 0.005 0.048 6570 Z= 0.339 Angle : 0.848 14.491 8964 Z= 0.515 Chirality : 0.073 1.453 1037 Planarity : 0.011 0.237 1133 Dihedral : 16.284 89.622 2454 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.84 % Allowed : 22.46 % Favored : 75.71 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.31), residues: 793 helix: 1.29 (0.38), residues: 196 sheet: -0.42 (0.36), residues: 240 loop : -0.69 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 450 HIS 0.008 0.001 HIS D 49 PHE 0.022 0.001 PHE D 119 TYR 0.014 0.001 TYR C 116 ARG 0.003 0.001 ARG C 118 Details of bonding type rmsd link_NAG-ASN : bond 0.01638 ( 5) link_NAG-ASN : angle 3.00486 ( 15) hydrogen bonds : bond 0.20036 ( 258) hydrogen bonds : angle 9.50777 ( 750) SS BOND : bond 0.01155 ( 8) SS BOND : angle 1.47526 ( 16) covalent geometry : bond 0.00502 ( 6557) covalent geometry : angle 0.83843 ( 8933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.2872 (t-100) cc_final: 0.0896 (t-100) REVERT: B 351 VAL cc_start: 0.7019 (t) cc_final: 0.6665 (m) REVERT: B 408 ASN cc_start: 0.6788 (m-40) cc_final: 0.6554 (m110) REVERT: B 409 SER cc_start: 0.7094 (p) cc_final: 0.6880 (m) REVERT: B 462 LEU cc_start: 0.6787 (mp) cc_final: 0.6307 (tp) REVERT: C 55 ARG cc_start: 0.1671 (mtt180) cc_final: 0.1106 (mmt180) REVERT: C 71 TRP cc_start: 0.4693 (m100) cc_final: 0.4420 (m100) REVERT: C 162 ARG cc_start: 0.2063 (ttp-110) cc_final: 0.0977 (mmt180) REVERT: D 103 TYR cc_start: 0.5257 (m-80) cc_final: 0.4897 (m-80) REVERT: D 144 PHE cc_start: 0.6547 (p90) cc_final: 0.6092 (p90) outliers start: 13 outliers final: 5 residues processed: 163 average time/residue: 0.2234 time to fit residues: 45.8679 Evaluate side-chains 95 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 164 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 HIS A 372 GLN A 408 ASN C 52 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.189782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.184953 restraints weight = 18786.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.184135 restraints weight = 27709.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.183905 restraints weight = 28783.700| |-----------------------------------------------------------------------------| r_work (final): 0.4520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4385 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6570 Z= 0.145 Angle : 0.706 9.097 8964 Z= 0.348 Chirality : 0.048 0.278 1037 Planarity : 0.006 0.074 1133 Dihedral : 6.355 60.783 962 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.24 % Allowed : 21.33 % Favored : 74.44 % 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: -0.29 (0.30), residues: 793 helix: 1.28 (0.36), residues: 197 sheet: -0.54 (0.34), residues: 252 loop : -0.67 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 450 HIS 0.013 0.001 HIS D 49 PHE 0.019 0.002 PHE D 119 TYR 0.021 0.002 TYR B 254 ARG 0.004 0.001 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.01431 ( 5) link_NAG-ASN : angle 3.01413 ( 15) hydrogen bonds : bond 0.04412 ( 258) hydrogen bonds : angle 6.57209 ( 750) SS BOND : bond 0.00570 ( 8) SS BOND : angle 0.97594 ( 16) covalent geometry : bond 0.00320 ( 6557) covalent geometry : angle 0.69501 ( 8933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3200 (t-100) cc_final: 0.1346 (t-100) REVERT: B 351 VAL cc_start: 0.6822 (t) cc_final: 0.6602 (m) REVERT: B 409 SER cc_start: 0.6139 (p) cc_final: 0.5780 (m) REVERT: C 55 ARG cc_start: 0.2087 (mtt180) cc_final: 0.1401 (mmt180) REVERT: C 71 TRP cc_start: 0.4653 (m100) cc_final: 0.4403 (m100) REVERT: C 147 LEU cc_start: 0.7017 (tp) cc_final: 0.6596 (tp) REVERT: C 162 ARG cc_start: 0.1522 (ttp-110) cc_final: 0.0936 (mmt180) REVERT: D 144 PHE cc_start: 0.5694 (p90) cc_final: 0.5380 (p90) outliers start: 30 outliers final: 16 residues processed: 117 average time/residue: 0.2122 time to fit residues: 32.0070 Evaluate side-chains 103 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain D residue 164 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN D 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.186580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.180622 restraints weight = 19254.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.180478 restraints weight = 27319.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.180258 restraints weight = 27455.097| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4579 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 6570 Z= 0.220 Angle : 0.825 19.348 8964 Z= 0.400 Chirality : 0.050 0.293 1037 Planarity : 0.006 0.064 1133 Dihedral : 6.781 55.028 961 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.92 % Allowed : 21.19 % Favored : 71.89 % 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: -0.89 (0.29), residues: 793 helix: 0.53 (0.35), residues: 200 sheet: -0.94 (0.33), residues: 250 loop : -0.84 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 100 HIS 0.012 0.002 HIS D 49 PHE 0.031 0.003 PHE B 303 TYR 0.018 0.002 TYR B 254 ARG 0.006 0.001 ARG C 55 Details of bonding type rmsd link_NAG-ASN : bond 0.02596 ( 5) link_NAG-ASN : angle 6.40896 ( 15) hydrogen bonds : bond 0.04369 ( 258) hydrogen bonds : angle 6.34837 ( 750) SS BOND : bond 0.00715 ( 8) SS BOND : angle 1.17010 ( 16) covalent geometry : bond 0.00494 ( 6557) covalent geometry : angle 0.78239 ( 8933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.0639 (OUTLIER) cc_final: 0.0305 (pt) REVERT: B 297 TRP cc_start: 0.3400 (t-100) cc_final: 0.2308 (t60) REVERT: B 351 VAL cc_start: 0.6898 (t) cc_final: 0.6678 (m) REVERT: B 364 SER cc_start: 0.6546 (OUTLIER) cc_final: 0.6300 (t) REVERT: A 276 MET cc_start: 0.4793 (mmp) cc_final: 0.4314 (mmp) REVERT: A 476 LYS cc_start: 0.4110 (tptp) cc_final: 0.2400 (ptmm) REVERT: C 55 ARG cc_start: 0.1890 (mtt180) cc_final: 0.1689 (mtt90) REVERT: C 147 LEU cc_start: 0.7343 (tp) cc_final: 0.7127 (tp) REVERT: D 144 PHE cc_start: 0.5711 (p90) cc_final: 0.5504 (p90) outliers start: 49 outliers final: 28 residues processed: 134 average time/residue: 0.1977 time to fit residues: 34.6197 Evaluate side-chains 116 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 174 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 440 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.185184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.4384 r_free = 0.4384 target = 0.171347 restraints weight = 17760.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.169670 restraints weight = 19504.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.170053 restraints weight = 16346.447| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5059 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6570 Z= 0.172 Angle : 0.809 18.599 8964 Z= 0.381 Chirality : 0.047 0.279 1037 Planarity : 0.006 0.066 1133 Dihedral : 6.667 48.785 958 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.80 % Favored : 94.07 % Rotamer: Outliers : 6.07 % Allowed : 22.88 % Favored : 71.05 % 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: -0.84 (0.30), residues: 793 helix: 0.55 (0.35), residues: 199 sheet: -0.95 (0.32), residues: 260 loop : -0.75 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 450 HIS 0.010 0.002 HIS D 49 PHE 0.025 0.002 PHE B 460 TYR 0.019 0.002 TYR B 254 ARG 0.004 0.000 ARG C 55 Details of bonding type rmsd link_NAG-ASN : bond 0.01670 ( 5) link_NAG-ASN : angle 8.51466 ( 15) hydrogen bonds : bond 0.03958 ( 258) hydrogen bonds : angle 5.93436 ( 750) SS BOND : bond 0.00494 ( 8) SS BOND : angle 1.42139 ( 16) covalent geometry : bond 0.00387 ( 6557) covalent geometry : angle 0.72911 ( 8933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3225 (t-100) cc_final: 0.2022 (t60) REVERT: B 364 SER cc_start: 0.6449 (OUTLIER) cc_final: 0.6221 (t) REVERT: B 443 GLU cc_start: 0.6053 (pp20) cc_final: 0.5723 (pp20) REVERT: A 276 MET cc_start: 0.4458 (mmp) cc_final: 0.4219 (mmp) REVERT: A 356 LYS cc_start: 0.7527 (tmtt) cc_final: 0.7292 (tptt) REVERT: A 456 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7136 (t80) REVERT: A 476 LYS cc_start: 0.4188 (tptp) cc_final: 0.2403 (ptmm) REVERT: C 55 ARG cc_start: 0.1848 (mtt180) cc_final: 0.0816 (mmt-90) REVERT: D 118 TYR cc_start: 0.6680 (m-80) cc_final: 0.6231 (m-10) REVERT: D 144 PHE cc_start: 0.6254 (p90) cc_final: 0.5794 (p90) REVERT: D 177 PHE cc_start: 0.3475 (m-10) cc_final: 0.3205 (t80) outliers start: 43 outliers final: 32 residues processed: 118 average time/residue: 0.1887 time to fit residues: 29.0292 Evaluate side-chains 116 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 174 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 440 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.185069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.4402 r_free = 0.4402 target = 0.172926 restraints weight = 18054.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 117)---------------| | r_work = 0.4368 r_free = 0.4368 target = 0.170412 restraints weight = 24353.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.169638 restraints weight = 26361.894| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5040 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6570 Z= 0.180 Angle : 0.792 18.709 8964 Z= 0.373 Chirality : 0.047 0.276 1037 Planarity : 0.006 0.071 1133 Dihedral : 6.587 55.829 958 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 7.34 % Allowed : 23.16 % Favored : 69.49 % 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: -0.91 (0.30), residues: 793 helix: 0.37 (0.35), residues: 198 sheet: -1.15 (0.32), residues: 259 loop : -0.54 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 450 HIS 0.013 0.002 HIS D 49 PHE 0.020 0.002 PHE D 119 TYR 0.019 0.002 TYR B 254 ARG 0.014 0.001 ARG D 153 Details of bonding type rmsd link_NAG-ASN : bond 0.01903 ( 5) link_NAG-ASN : angle 7.53735 ( 15) hydrogen bonds : bond 0.03967 ( 258) hydrogen bonds : angle 5.87644 ( 750) SS BOND : bond 0.00540 ( 8) SS BOND : angle 1.35277 ( 16) covalent geometry : bond 0.00408 ( 6557) covalent geometry : angle 0.72810 ( 8933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 86 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 273 ILE cc_start: -0.0147 (OUTLIER) cc_final: -0.0404 (pt) REVERT: B 297 TRP cc_start: 0.3358 (t-100) cc_final: 0.2035 (t60) REVERT: B 432 ASP cc_start: 0.1482 (p0) cc_final: 0.1279 (p0) REVERT: A 356 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7304 (tptp) REVERT: A 456 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7086 (t80) REVERT: C 55 ARG cc_start: 0.1715 (mtt180) cc_final: 0.1372 (mtt90) REVERT: D 144 PHE cc_start: 0.6454 (p90) cc_final: 0.5930 (p90) outliers start: 52 outliers final: 34 residues processed: 125 average time/residue: 0.1948 time to fit residues: 31.9307 Evaluate side-chains 115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 174 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 59 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN D 69 HIS ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.186319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.176608 restraints weight = 17838.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.175601 restraints weight = 23163.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.175919 restraints weight = 22647.510| |-----------------------------------------------------------------------------| r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4758 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6570 Z= 0.136 Angle : 0.751 17.884 8964 Z= 0.348 Chirality : 0.046 0.270 1037 Planarity : 0.005 0.071 1133 Dihedral : 6.548 59.967 958 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.78 % Allowed : 24.44 % Favored : 68.79 % 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: -0.75 (0.30), residues: 793 helix: 0.60 (0.35), residues: 198 sheet: -1.06 (0.31), residues: 269 loop : -0.48 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 450 HIS 0.013 0.001 HIS D 49 PHE 0.025 0.002 PHE B 319 TYR 0.020 0.001 TYR B 254 ARG 0.004 0.000 ARG D 153 Details of bonding type rmsd link_NAG-ASN : bond 0.01588 ( 5) link_NAG-ASN : angle 7.61662 ( 15) hydrogen bonds : bond 0.03750 ( 258) hydrogen bonds : angle 5.47917 ( 750) SS BOND : bond 0.00420 ( 8) SS BOND : angle 1.14476 ( 16) covalent geometry : bond 0.00307 ( 6557) covalent geometry : angle 0.68331 ( 8933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 ILE cc_start: 0.0349 (OUTLIER) cc_final: 0.0047 (pt) REVERT: B 297 TRP cc_start: 0.3357 (t-100) cc_final: 0.2069 (t60) REVERT: A 276 MET cc_start: 0.4657 (OUTLIER) cc_final: 0.4199 (mmp) REVERT: A 356 LYS cc_start: 0.7449 (tmtt) cc_final: 0.7233 (tptp) REVERT: A 456 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.7078 (t80) REVERT: C 55 ARG cc_start: 0.1773 (OUTLIER) cc_final: 0.0763 (mmt180) REVERT: C 128 LEU cc_start: 0.4466 (OUTLIER) cc_final: 0.4202 (pt) REVERT: C 162 ARG cc_start: 0.1918 (ttp-110) cc_final: 0.0719 (mmt180) REVERT: D 144 PHE cc_start: 0.6179 (p90) cc_final: 0.5702 (p90) outliers start: 48 outliers final: 32 residues processed: 117 average time/residue: 0.2066 time to fit residues: 31.5261 Evaluate side-chains 111 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.0570 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.187435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.182870 restraints weight = 18724.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.182151 restraints weight = 30108.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.182061 restraints weight = 30712.266| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4543 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6570 Z= 0.154 Angle : 0.768 17.767 8964 Z= 0.361 Chirality : 0.047 0.277 1037 Planarity : 0.005 0.072 1133 Dihedral : 6.439 54.708 958 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.07 % Allowed : 24.58 % Favored : 69.35 % 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: -0.74 (0.30), residues: 793 helix: 0.57 (0.35), residues: 198 sheet: -0.96 (0.32), residues: 257 loop : -0.56 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B 450 HIS 0.014 0.002 HIS D 49 PHE 0.021 0.002 PHE B 319 TYR 0.019 0.001 TYR B 254 ARG 0.008 0.001 ARG D 153 Details of bonding type rmsd link_NAG-ASN : bond 0.01682 ( 5) link_NAG-ASN : angle 7.37114 ( 15) hydrogen bonds : bond 0.03791 ( 258) hydrogen bonds : angle 5.45370 ( 750) SS BOND : bond 0.00453 ( 8) SS BOND : angle 1.15782 ( 16) covalent geometry : bond 0.00344 ( 6557) covalent geometry : angle 0.70633 ( 8933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 273 ILE cc_start: 0.0758 (OUTLIER) cc_final: 0.0507 (pt) REVERT: A 343 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6404 (mm) REVERT: C 55 ARG cc_start: 0.1745 (OUTLIER) cc_final: 0.0811 (mmt-90) REVERT: C 128 LEU cc_start: 0.4438 (OUTLIER) cc_final: 0.4213 (pt) REVERT: C 162 ARG cc_start: 0.1713 (ttp-110) cc_final: 0.0740 (mmt180) REVERT: D 144 PHE cc_start: 0.5895 (p90) cc_final: 0.5502 (p90) outliers start: 43 outliers final: 33 residues processed: 117 average time/residue: 0.2185 time to fit residues: 32.5196 Evaluate side-chains 113 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 397 HIS Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 0.0010 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN D 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.189552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.180006 restraints weight = 18466.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.179548 restraints weight = 23779.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.179547 restraints weight = 22141.829| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4750 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6570 Z= 0.137 Angle : 0.752 17.226 8964 Z= 0.356 Chirality : 0.046 0.278 1037 Planarity : 0.005 0.072 1133 Dihedral : 6.209 56.046 958 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.08 % Allowed : 26.98 % Favored : 67.94 % 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: -0.62 (0.30), residues: 793 helix: 0.70 (0.36), residues: 198 sheet: -0.85 (0.32), residues: 271 loop : -0.53 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 450 HIS 0.012 0.001 HIS D 49 PHE 0.031 0.002 PHE A 456 TYR 0.018 0.001 TYR B 254 ARG 0.016 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.01446 ( 5) link_NAG-ASN : angle 6.97816 ( 15) hydrogen bonds : bond 0.03635 ( 258) hydrogen bonds : angle 5.22929 ( 750) SS BOND : bond 0.00377 ( 8) SS BOND : angle 0.97742 ( 16) covalent geometry : bond 0.00305 ( 6557) covalent geometry : angle 0.69544 ( 8933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 343 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6625 (mm) REVERT: C 55 ARG cc_start: 0.1563 (OUTLIER) cc_final: 0.0656 (mmt180) REVERT: C 105 GLU cc_start: 0.3360 (tp30) cc_final: 0.2057 (tt0) REVERT: C 162 ARG cc_start: 0.1686 (ttp-110) cc_final: 0.0407 (mmt180) REVERT: D 144 PHE cc_start: 0.6268 (p90) cc_final: 0.5653 (p90) outliers start: 36 outliers final: 25 residues processed: 104 average time/residue: 0.2133 time to fit residues: 28.6251 Evaluate side-chains 103 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN ** D 164 GLN ** 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 = 0.4565 r_free = 0.4565 target = 0.187259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.178455 restraints weight = 19036.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.177639 restraints weight = 26998.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.177739 restraints weight = 26173.250| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4845 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6570 Z= 0.192 Angle : 0.828 17.696 8964 Z= 0.398 Chirality : 0.049 0.303 1037 Planarity : 0.006 0.073 1133 Dihedral : 6.326 58.846 956 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.23 % Allowed : 25.99 % Favored : 68.79 % 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: -0.80 (0.30), residues: 793 helix: 0.48 (0.36), residues: 198 sheet: -0.92 (0.31), residues: 277 loop : -0.60 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.003 TRP B 450 HIS 0.015 0.002 HIS D 49 PHE 0.032 0.002 PHE A 456 TYR 0.017 0.002 TYR B 254 ARG 0.011 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.01811 ( 5) link_NAG-ASN : angle 7.10299 ( 15) hydrogen bonds : bond 0.04029 ( 258) hydrogen bonds : angle 5.51958 ( 750) SS BOND : bond 0.00524 ( 8) SS BOND : angle 1.28630 ( 16) covalent geometry : bond 0.00435 ( 6557) covalent geometry : angle 0.77521 ( 8933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.0428 (OUTLIER) cc_final: 0.0169 (pt) REVERT: C 55 ARG cc_start: 0.1701 (OUTLIER) cc_final: 0.1331 (mtt90) REVERT: C 162 ARG cc_start: 0.1707 (ttp-110) cc_final: 0.0343 (mmt180) REVERT: D 118 TYR cc_start: 0.6347 (m-80) cc_final: 0.6098 (m-10) REVERT: D 144 PHE cc_start: 0.6287 (p90) cc_final: 0.5705 (p90) outliers start: 37 outliers final: 27 residues processed: 106 average time/residue: 0.2050 time to fit residues: 28.3247 Evaluate side-chains 101 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 0.0030 chunk 11 optimal weight: 0.1980 chunk 77 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 HIS A 440 ASN C 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.189426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.183505 restraints weight = 18399.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.182099 restraints weight = 23538.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 103)---------------| | r_work = 0.4497 r_free = 0.4497 target = 0.181405 restraints weight = 23397.140| |-----------------------------------------------------------------------------| r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6570 Z= 0.134 Angle : 0.761 17.139 8964 Z= 0.359 Chirality : 0.046 0.282 1037 Planarity : 0.005 0.073 1133 Dihedral : 5.899 59.727 956 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.81 % Allowed : 27.97 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.30), residues: 793 helix: 0.73 (0.36), residues: 198 sheet: -0.63 (0.31), residues: 280 loop : -0.60 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 450 HIS 0.013 0.001 HIS D 49 PHE 0.024 0.001 PHE A 456 TYR 0.018 0.001 TYR B 254 ARG 0.005 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.01389 ( 5) link_NAG-ASN : angle 6.81244 ( 15) hydrogen bonds : bond 0.03601 ( 258) hydrogen bonds : angle 5.21157 ( 750) SS BOND : bond 0.00340 ( 8) SS BOND : angle 1.05933 ( 16) covalent geometry : bond 0.00305 ( 6557) covalent geometry : angle 0.70788 ( 8933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: C 55 ARG cc_start: 0.1692 (OUTLIER) cc_final: 0.0827 (mmt180) REVERT: C 105 GLU cc_start: 0.3285 (tp30) cc_final: 0.2106 (tt0) REVERT: C 162 ARG cc_start: 0.1652 (ttp-110) cc_final: 0.0449 (mmt180) REVERT: D 144 PHE cc_start: 0.6091 (p90) cc_final: 0.5551 (p90) outliers start: 27 outliers final: 23 residues processed: 91 average time/residue: 0.2293 time to fit residues: 27.2185 Evaluate side-chains 94 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 7 optimal weight: 0.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN ** A 372 GLN ** 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 = 0.4590 r_free = 0.4590 target = 0.189070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.183007 restraints weight = 19013.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.182183 restraints weight = 28668.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.182273 restraints weight = 26655.196| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4588 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.152 6570 Z= 0.273 Angle : 1.162 59.188 8964 Z= 0.656 Chirality : 0.047 0.323 1037 Planarity : 0.006 0.073 1133 Dihedral : 5.939 59.742 956 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 3.81 % Allowed : 27.97 % Favored : 68.22 % Cbeta Deviations : 0.13 % 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: -0.51 (0.30), residues: 793 helix: 0.72 (0.36), residues: 198 sheet: -0.59 (0.31), residues: 280 loop : -0.60 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.004 TRP B 450 HIS 0.013 0.001 HIS D 49 PHE 0.021 0.002 PHE A 456 TYR 0.017 0.001 TYR B 254 ARG 0.038 0.001 ARG D 153 Details of bonding type rmsd link_NAG-ASN : bond 0.01405 ( 5) link_NAG-ASN : angle 6.81234 ( 15) hydrogen bonds : bond 0.03630 ( 258) hydrogen bonds : angle 5.21006 ( 750) SS BOND : bond 0.00359 ( 8) SS BOND : angle 1.02391 ( 16) covalent geometry : bond 0.00553 ( 6557) covalent geometry : angle 1.12947 ( 8933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.07 seconds wall clock time: 43 minutes 46.31 seconds (2626.31 seconds total)