Starting phenix.real_space_refine on Tue Feb 11 18:43:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e4c_27888/02_2025/8e4c_27888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e4c_27888/02_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_27888/02_2025/8e4c_27888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e4c_27888/02_2025/8e4c_27888.map" model { file = "/net/cci-nas-00/data/ceres_data/8e4c_27888/02_2025/8e4c_27888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e4c_27888/02_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-5592/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: 4.43, per 1000 atoms: 0.69 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: 1.72 Conformation dependent library (CDL) restraints added in 944.3 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: 0.72 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: 1.91 Time building geometry restraints manager: 1.97 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: 1.540 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.810 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.690 ------------------------------------------------------------------------------- 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 6557 Z= 0.328 Angle : 0.838 14.491 8933 Z= 0.513 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 *********************** 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 : 0.656 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: 0.2248 time to fit residues: 46.0916 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 : 0.679 ------------------------------------------------------------------------------- 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: 4.9990 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 = 60)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.184891 restraints weight = 18786.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.184057 restraints weight = 27671.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.183725 restraints weight = 28943.824| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4392 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 6557 Z= 0.205 Angle : 0.695 9.097 8933 Z= 0.346 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 *********************** 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 : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3202 (t-100) cc_final: 0.1342 (t-100) REVERT: B 351 VAL cc_start: 0.6825 (t) cc_final: 0.6605 (m) REVERT: B 409 SER cc_start: 0.6139 (p) cc_final: 0.5781 (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: 0.4404 (m100) REVERT: C 147 LEU cc_start: 0.7018 (tp) cc_final: 0.6597 (tp) REVERT: C 162 ARG cc_start: 0.1526 (ttp-110) cc_final: 0.0938 (mmt180) REVERT: D 144 PHE cc_start: 0.5695 (p90) cc_final: 0.5379 (p90) outliers start: 30 outliers final: 16 residues processed: 117 average time/residue: 0.2096 time to fit residues: 31.4993 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 : 0.788 ------------------------------------------------------------------------------- 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: 0.2980 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4587 r_free = 0.4587 target = 0.188064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.182471 restraints weight = 19346.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.181115 restraints weight = 26584.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.181128 restraints weight = 25169.423| |-----------------------------------------------------------------------------| r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4563 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6557 Z= 0.271 Angle : 0.724 12.348 8933 Z= 0.361 Chirality : 0.048 0.240 1037 Planarity : 0.006 0.062 1133 Dihedral : 6.432 53.664 961 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.50 % Allowed : 20.90 % Favored : 72.60 % 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: -0.60 (0.30), residues: 793 helix: 0.92 (0.35), residues: 199 sheet: -0.72 (0.33), residues: 254 loop : -0.81 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 100 HIS 0.010 0.002 HIS D 49 PHE 0.026 0.002 PHE A 456 TYR 0.020 0.002 TYR B 254 ARG 0.005 0.000 ARG C 55 *********************** 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 147 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.0392 (OUTLIER) cc_final: 0.0062 (pt) REVERT: B 297 TRP cc_start: 0.3236 (t-100) cc_final: 0.2184 (t60) REVERT: B 351 VAL cc_start: 0.6960 (t) cc_final: 0.6742 (m) REVERT: B 364 SER cc_start: 0.6470 (OUTLIER) cc_final: 0.6176 (t) REVERT: B 409 SER cc_start: 0.5890 (p) cc_final: 0.5627 (m) REVERT: A 276 MET cc_start: 0.4834 (mmp) cc_final: 0.4409 (mmp) REVERT: C 55 ARG cc_start: 0.1798 (mtt180) cc_final: 0.0713 (mmt-90) REVERT: C 147 LEU cc_start: 0.7197 (tp) cc_final: 0.6847 (tp) REVERT: D 144 PHE cc_start: 0.5797 (p90) cc_final: 0.5528 (p90) outliers start: 46 outliers final: 27 residues processed: 131 average time/residue: 0.1932 time to fit residues: 33.0906 Evaluate side-chains 119 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 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 49 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 102 VAL 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: 6.9990 chunk 14 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.9202 ------------------------------------------------------------------------------- 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 ** D 108 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 = 0.188450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.183774 restraints weight = 19398.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.182570 restraints weight = 23901.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.182329 restraints weight = 25172.689| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4517 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6557 Z= 0.212 Angle : 0.692 10.977 8933 Z= 0.343 Chirality : 0.046 0.251 1037 Planarity : 0.005 0.064 1133 Dihedral : 6.519 57.533 958 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.55 % Favored : 94.33 % Rotamer: Outliers : 5.79 % Allowed : 22.60 % Favored : 71.61 % 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: -0.50 (0.30), residues: 793 helix: 0.94 (0.36), residues: 198 sheet: -0.70 (0.33), residues: 256 loop : -0.66 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 450 HIS 0.009 0.001 HIS D 49 PHE 0.024 0.002 PHE B 460 TYR 0.021 0.001 TYR B 254 ARG 0.003 0.000 ARG C 55 *********************** 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 139 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3234 (t-100) cc_final: 0.2147 (t60) REVERT: B 351 VAL cc_start: 0.6989 (t) cc_final: 0.6770 (m) REVERT: B 364 SER cc_start: 0.6432 (OUTLIER) cc_final: 0.6196 (t) REVERT: B 409 SER cc_start: 0.5894 (p) cc_final: 0.5603 (m) REVERT: B 443 GLU cc_start: 0.6006 (pp20) cc_final: 0.5758 (pp20) REVERT: A 276 MET cc_start: 0.4823 (mmp) cc_final: 0.4436 (mmp) REVERT: A 356 LYS cc_start: 0.7503 (tmtt) cc_final: 0.7259 (tptt) REVERT: A 456 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.7084 (t80) REVERT: C 55 ARG cc_start: 0.1695 (mtt180) cc_final: 0.0703 (mmt180) REVERT: C 147 LEU cc_start: 0.7147 (tp) cc_final: 0.6940 (tp) REVERT: D 144 PHE cc_start: 0.5872 (p90) cc_final: 0.5644 (p90) outliers start: 41 outliers final: 28 residues processed: 124 average time/residue: 0.1920 time to fit residues: 31.2548 Evaluate side-chains 120 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 380 VAL 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 37 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 69 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: 3.9990 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.186598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.179952 restraints weight = 18579.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.179366 restraints weight = 25718.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.179282 restraints weight = 27522.402| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4689 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6557 Z= 0.299 Angle : 0.770 15.131 8933 Z= 0.383 Chirality : 0.048 0.285 1037 Planarity : 0.006 0.066 1133 Dihedral : 6.624 56.858 958 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 6.36 % Allowed : 23.45 % Favored : 70.20 % 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: 0.35 (0.35), residues: 199 sheet: -1.04 (0.33), residues: 253 loop : -0.64 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 100 HIS 0.032 0.003 HIS D 129 PHE 0.018 0.002 PHE A 456 TYR 0.018 0.002 TYR B 254 ARG 0.005 0.001 ARG C 55 *********************** 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 135 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 90 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 273 ILE cc_start: 0.0516 (OUTLIER) cc_final: 0.0213 (pt) REVERT: B 297 TRP cc_start: 0.3276 (t-100) cc_final: 0.2042 (t60) REVERT: B 351 VAL cc_start: 0.6986 (t) cc_final: 0.6735 (m) REVERT: B 364 SER cc_start: 0.6622 (OUTLIER) cc_final: 0.6402 (t) REVERT: B 409 SER cc_start: 0.6096 (p) cc_final: 0.5867 (m) REVERT: A 356 LYS cc_start: 0.7581 (tmtt) cc_final: 0.7358 (tptp) REVERT: A 456 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7169 (t80) REVERT: C 55 ARG cc_start: 0.1739 (mtt180) cc_final: 0.0872 (mmt180) REVERT: D 138 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7049 (tm-30) REVERT: D 144 PHE cc_start: 0.6143 (p90) cc_final: 0.5709 (p90) outliers start: 45 outliers final: 31 residues processed: 119 average time/residue: 0.2127 time to fit residues: 32.4551 Evaluate side-chains 115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 364 SER Chi-restraints excluded: chain B residue 368 LEU 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 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 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 37 SER 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 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 D residue 49 HIS Chi-restraints excluded: chain D residue 104 THR 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: 0.7980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 13 optimal weight: 0.0670 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 108 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 = 0.4581 r_free = 0.4581 target = 0.188424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.183468 restraints weight = 18346.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.182962 restraints weight = 28904.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.182887 restraints weight = 29636.802| |-----------------------------------------------------------------------------| r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4526 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6557 Z= 0.186 Angle : 0.667 11.786 8933 Z= 0.326 Chirality : 0.045 0.257 1037 Planarity : 0.005 0.070 1133 Dihedral : 6.191 59.993 958 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.93 % Allowed : 25.14 % Favored : 68.93 % 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: -0.54 (0.30), residues: 793 helix: 0.79 (0.36), residues: 198 sheet: -0.92 (0.33), residues: 255 loop : -0.42 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 450 HIS 0.011 0.001 HIS D 49 PHE 0.016 0.001 PHE A 456 TYR 0.020 0.001 TYR B 254 ARG 0.005 0.000 ARG C 111 *********************** 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 125 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3286 (t-100) cc_final: 0.2027 (t60) REVERT: B 351 VAL cc_start: 0.7116 (t) cc_final: 0.6910 (m) REVERT: B 364 SER cc_start: 0.6565 (OUTLIER) cc_final: 0.6337 (t) REVERT: A 276 MET cc_start: 0.4797 (OUTLIER) cc_final: 0.4294 (mmp) REVERT: A 356 LYS cc_start: 0.7484 (tmtt) cc_final: 0.7257 (tptp) REVERT: A 456 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.7079 (t80) REVERT: A 476 LYS cc_start: 0.4185 (tptp) cc_final: 0.2273 (ptmm) REVERT: C 55 ARG cc_start: 0.1765 (mtt180) cc_final: 0.0744 (mmt180) REVERT: C 128 LEU cc_start: 0.4412 (OUTLIER) cc_final: 0.4151 (pt) REVERT: D 144 PHE cc_start: 0.6048 (p90) cc_final: 0.5677 (p90) outliers start: 42 outliers final: 25 residues processed: 117 average time/residue: 0.2104 time to fit residues: 31.8339 Evaluate side-chains 104 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 364 SER 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 416 VAL 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 353 CYS 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 A residue 439 VAL Chi-restraints excluded: chain A residue 456 PHE 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 91 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 102 VAL 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: 0.9980 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.0060 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 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 = 0.4563 r_free = 0.4563 target = 0.186653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.173291 restraints weight = 18336.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.171089 restraints weight = 19370.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.171748 restraints weight = 16506.685| |-----------------------------------------------------------------------------| r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5042 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6557 Z= 0.210 Angle : 0.696 12.831 8933 Z= 0.341 Chirality : 0.047 0.268 1037 Planarity : 0.005 0.072 1133 Dihedral : 5.916 54.942 956 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.79 % Allowed : 24.86 % 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: -0.63 (0.30), residues: 793 helix: 0.66 (0.35), residues: 198 sheet: -0.91 (0.32), residues: 258 loop : -0.48 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 450 HIS 0.013 0.002 HIS D 49 PHE 0.017 0.002 PHE A 456 TYR 0.018 0.001 TYR B 254 ARG 0.012 0.001 ARG D 153 *********************** 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 123 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3162 (t-100) cc_final: 0.2855 (t-100) REVERT: B 351 VAL cc_start: 0.7064 (t) cc_final: 0.6835 (m) REVERT: B 364 SER cc_start: 0.6717 (OUTLIER) cc_final: 0.6450 (t) REVERT: A 456 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7111 (t80) REVERT: C 55 ARG cc_start: 0.1903 (mtt180) cc_final: 0.1261 (mmt180) REVERT: C 128 LEU cc_start: 0.4540 (OUTLIER) cc_final: 0.4252 (pt) REVERT: C 162 ARG cc_start: 0.1998 (ttp-110) cc_final: 0.0624 (mmt180) REVERT: D 118 TYR cc_start: 0.6487 (m-80) cc_final: 0.6205 (m-10) REVERT: D 144 PHE cc_start: 0.6298 (p90) cc_final: 0.5806 (p90) outliers start: 41 outliers final: 30 residues processed: 113 average time/residue: 0.2084 time to fit residues: 30.5005 Evaluate side-chains 110 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 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 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 37 SER Chi-restraints excluded: chain C residue 42 LEU 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 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 113 GLU Chi-restraints excluded: chain D residue 141 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.187377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.181008 restraints weight = 18530.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.180204 restraints weight = 28976.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.180275 restraints weight = 27667.364| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4752 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6557 Z= 0.266 Angle : 0.757 15.469 8933 Z= 0.371 Chirality : 0.048 0.296 1037 Planarity : 0.006 0.073 1133 Dihedral : 6.299 56.255 956 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.21 % Allowed : 24.29 % 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: -0.84 (0.30), residues: 793 helix: 0.39 (0.35), residues: 198 sheet: -0.83 (0.31), residues: 267 loop : -0.73 (0.36), residues: 328 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 0.022 0.002 PHE B 303 TYR 0.017 0.002 TYR B 254 ARG 0.016 0.001 ARG D 153 *********************** 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 123 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 79 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: 0.0453 (OUTLIER) cc_final: 0.0166 (pt) REVERT: B 297 TRP cc_start: 0.3227 (t-100) cc_final: 0.1890 (t60) REVERT: B 351 VAL cc_start: 0.7130 (t) cc_final: 0.6860 (m) REVERT: B 364 SER cc_start: 0.6710 (OUTLIER) cc_final: 0.6422 (t) REVERT: A 456 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.7146 (t80) REVERT: A 473 PHE cc_start: 0.3370 (OUTLIER) cc_final: 0.3090 (t80) REVERT: C 55 ARG cc_start: 0.1634 (OUTLIER) cc_final: 0.1269 (mtt90) REVERT: C 128 LEU cc_start: 0.4571 (OUTLIER) cc_final: 0.4280 (pt) REVERT: C 162 ARG cc_start: 0.1612 (ttp-110) cc_final: 0.0430 (mmt180) REVERT: D 118 TYR cc_start: 0.6566 (m-80) cc_final: 0.6226 (m-10) REVERT: D 144 PHE cc_start: 0.6403 (p90) cc_final: 0.5878 (p90) outliers start: 44 outliers final: 34 residues processed: 112 average time/residue: 0.2077 time to fit residues: 29.9018 Evaluate side-chains 112 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 72 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 278 SER 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 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 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 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 A residue 473 PHE Chi-restraints excluded: chain C residue 31 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 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 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 113 GLU Chi-restraints excluded: chain D residue 141 VAL 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: 1.9990 chunk 29 optimal weight: 7.9990 chunk 62 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 16 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 A 440 ASN ** 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 = 0.4576 r_free = 0.4576 target = 0.188536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.181922 restraints weight = 18618.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.180580 restraints weight = 25039.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 84)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.179882 restraints weight = 25425.450| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4788 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6557 Z= 0.208 Angle : 0.715 13.790 8933 Z= 0.349 Chirality : 0.046 0.275 1037 Planarity : 0.005 0.073 1133 Dihedral : 6.026 57.770 956 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.79 % Allowed : 25.28 % Favored : 68.93 % 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: -0.71 (0.30), residues: 793 helix: 0.59 (0.35), residues: 198 sheet: -0.76 (0.32), residues: 266 loop : -0.72 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 450 HIS 0.014 0.002 HIS D 49 PHE 0.018 0.002 PHE B 319 TYR 0.018 0.001 TYR B 254 ARG 0.011 0.001 ARG A 346 *********************** 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 124 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3238 (t-100) cc_final: 0.2962 (t-100) REVERT: B 351 VAL cc_start: 0.7177 (t) cc_final: 0.6910 (m) REVERT: B 364 SER cc_start: 0.6803 (OUTLIER) cc_final: 0.6470 (t) REVERT: A 456 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7152 (t80) REVERT: C 55 ARG cc_start: 0.1671 (mtt180) cc_final: 0.1089 (mmt180) REVERT: C 105 GLU cc_start: 0.3619 (tp30) cc_final: 0.2145 (tt0) REVERT: C 162 ARG cc_start: 0.1664 (ttp-110) cc_final: 0.0352 (mmt180) REVERT: D 118 TYR cc_start: 0.6550 (m-80) cc_final: 0.6213 (m-10) REVERT: D 144 PHE cc_start: 0.6355 (p90) cc_final: 0.5743 (p90) outliers start: 41 outliers final: 33 residues processed: 111 average time/residue: 0.1993 time to fit residues: 28.8098 Evaluate side-chains 110 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 364 SER Chi-restraints excluded: chain B residue 368 LEU 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 415 CYS Chi-restraints excluded: chain B residue 416 VAL 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 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 37 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU 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 152 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 1 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- 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** D 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.189410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.180977 restraints weight = 19033.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.179662 restraints weight = 26272.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 161)---------------| | r_work = 0.4454 r_free = 0.4454 target = 0.179090 restraints weight = 23038.928| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4827 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6557 Z= 0.198 Angle : 0.713 13.264 8933 Z= 0.350 Chirality : 0.046 0.272 1037 Planarity : 0.005 0.073 1133 Dihedral : 5.907 58.556 956 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.23 % Allowed : 26.13 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.30), residues: 793 helix: 0.70 (0.36), residues: 198 sheet: -0.63 (0.32), residues: 266 loop : -0.64 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 450 HIS 0.014 0.001 HIS D 49 PHE 0.017 0.002 PHE B 460 TYR 0.017 0.001 TYR B 254 ARG 0.011 0.001 ARG A 346 ********************** 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 113 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3215 (t-100) cc_final: 0.2912 (t-100) REVERT: B 351 VAL cc_start: 0.7160 (t) cc_final: 0.6906 (m) REVERT: B 364 SER cc_start: 0.6754 (OUTLIER) cc_final: 0.6453 (t) REVERT: A 456 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.7078 (t80) REVERT: C 55 ARG cc_start: 0.1716 (OUTLIER) cc_final: 0.0844 (mmt180) REVERT: C 105 GLU cc_start: 0.3273 (tp30) cc_final: 0.1978 (tt0) REVERT: C 162 ARG cc_start: 0.1648 (ttp-110) cc_final: 0.0355 (mmt180) REVERT: D 118 TYR cc_start: 0.6382 (m-80) cc_final: 0.6070 (m-10) REVERT: D 144 PHE cc_start: 0.6193 (p90) cc_final: 0.5612 (p90) outliers start: 37 outliers final: 31 residues processed: 102 average time/residue: 0.2002 time to fit residues: 26.6739 Evaluate side-chains 108 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 380 VAL 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 444 GLU 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 355 VAL Chi-restraints excluded: chain A residue 363 ILE 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 37 SER 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 152 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 C 136 ASN D 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.187970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.179281 restraints weight = 19392.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.177721 restraints weight = 27209.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 93)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.177371 restraints weight = 24430.265| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4882 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6557 Z= 0.233 Angle : 0.740 15.023 8933 Z= 0.363 Chirality : 0.047 0.289 1037 Planarity : 0.006 0.074 1133 Dihedral : 6.196 58.513 956 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 6.07 % Allowed : 25.28 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.30), residues: 793 helix: 0.58 (0.36), residues: 198 sheet: -0.69 (0.32), residues: 268 loop : -0.77 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 450 HIS 0.015 0.002 HIS D 49 PHE 0.018 0.002 PHE A 456 TYR 0.017 0.001 TYR B 254 ARG 0.008 0.001 ARG D 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.43 seconds wall clock time: 41 minutes 34.06 seconds (2494.06 seconds total)