Starting phenix.real_space_refine on Tue Sep 24 01:21:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/09_2024/8e4c_27888.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/09_2024/8e4c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/09_2024/8e4c_27888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/09_2024/8e4c_27888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/09_2024/8e4c_27888.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/09_2024/8e4c_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-5461/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: 4.53, per 1000 atoms: 0.71 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: 1.56 Conformation dependent library (CDL) restraints added in 949.1 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: 0.80 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: 2.03 Time building geometry restraints manager: 1.84 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: 3.200 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.410 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.030 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 0.741 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: 0.2173 time to fit residues: 44.5112 Evaluate side-chains 95 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4994 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 fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3089 (t-100) cc_final: 0.1010 (t-100) REVERT: B 351 VAL cc_start: 0.7261 (t) cc_final: 0.6927 (m) REVERT: B 381 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7646 (m) REVERT: B 409 SER cc_start: 0.6658 (p) cc_final: 0.6437 (m) REVERT: B 450 TRP cc_start: 0.6931 (t60) cc_final: 0.6706 (t60) REVERT: B 462 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6265 (tp) REVERT: A 399 ILE cc_start: 0.8901 (mt) cc_final: 0.8641 (mm) REVERT: C 55 ARG cc_start: 0.1593 (mtt180) cc_final: 0.0919 (mmt180) REVERT: C 71 TRP cc_start: 0.4664 (m100) cc_final: 0.4329 (m100) REVERT: C 147 LEU cc_start: 0.6925 (tp) cc_final: 0.6514 (tp) REVERT: C 162 ARG cc_start: 0.1830 (ttp-110) cc_final: 0.0799 (mmt180) REVERT: D 64 HIS cc_start: 0.5371 (m90) cc_final: 0.5031 (m-70) REVERT: D 103 TYR cc_start: 0.5387 (m-80) cc_final: 0.4952 (m-80) REVERT: D 144 PHE cc_start: 0.6880 (p90) cc_final: 0.6170 (p90) outliers start: 30 outliers final: 16 residues processed: 117 average time/residue: 0.2109 time to fit residues: 31.8893 Evaluate side-chains 106 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 381 THR 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 B residue 462 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 39 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.0570 chunk 71 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5031 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6557 Z= 0.210 Angle : 0.664 9.653 8933 Z= 0.332 Chirality : 0.045 0.220 1037 Planarity : 0.005 0.062 1133 Dihedral : 6.199 54.436 961 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.37 % Allowed : 21.61 % Favored : 73.02 % 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: -0.30 (0.30), residues: 793 helix: 1.27 (0.35), residues: 199 sheet: -0.54 (0.33), residues: 250 loop : -0.71 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 100 HIS 0.007 0.001 HIS D 49 PHE 0.026 0.002 PHE A 456 TYR 0.021 0.001 TYR B 254 ARG 0.003 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 135 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 97 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3127 (t-100) cc_final: 0.2057 (t60) REVERT: B 351 VAL cc_start: 0.7311 (t) cc_final: 0.6956 (m) REVERT: B 364 SER cc_start: 0.6440 (OUTLIER) cc_final: 0.6161 (t) REVERT: B 381 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7631 (m) REVERT: B 406 GLU cc_start: 0.6000 (mm-30) cc_final: 0.5636 (mm-30) REVERT: B 450 TRP cc_start: 0.6945 (t60) cc_final: 0.6658 (t60) REVERT: B 462 LEU cc_start: 0.6665 (mp) cc_final: 0.6250 (tp) REVERT: B 472 LEU cc_start: 0.1994 (OUTLIER) cc_final: 0.1761 (mt) REVERT: A 356 LYS cc_start: 0.7886 (tttt) cc_final: 0.7658 (tmtt) REVERT: C 55 ARG cc_start: 0.1419 (mtt180) cc_final: 0.0848 (mmt180) REVERT: C 147 LEU cc_start: 0.6927 (tp) cc_final: 0.6605 (tp) REVERT: C 162 ARG cc_start: 0.1826 (ttp-110) cc_final: 0.0735 (mmt180) REVERT: D 144 PHE cc_start: 0.6979 (p90) cc_final: 0.6262 (p90) outliers start: 38 outliers final: 23 residues processed: 122 average time/residue: 0.1960 time to fit residues: 31.2356 Evaluate side-chains 112 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 381 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 335 LEU Chi-restraints excluded: chain A residue 352 THR 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 100 TRP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 164 GLN 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 37 optimal weight: 7.9990 chunk 7 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5018 moved from start: 0.3612 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= 0.193 Angle : 0.660 9.633 8933 Z= 0.327 Chirality : 0.045 0.227 1037 Planarity : 0.005 0.061 1133 Dihedral : 6.637 56.098 961 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.42 % Favored : 94.45 % Rotamer: Outliers : 5.93 % Allowed : 21.33 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.30), residues: 793 helix: 1.31 (0.36), residues: 198 sheet: -0.50 (0.33), residues: 254 loop : -0.56 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 100 HIS 0.008 0.001 HIS D 49 PHE 0.020 0.001 PHE D 119 TYR 0.022 0.001 TYR B 254 ARG 0.003 0.000 ARG A 340 *********************** 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 135 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 93 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.2994 (t-100) cc_final: 0.1911 (t60) REVERT: B 351 VAL cc_start: 0.7442 (t) cc_final: 0.7095 (m) REVERT: B 364 SER cc_start: 0.6421 (OUTLIER) cc_final: 0.6178 (t) REVERT: B 381 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7639 (m) REVERT: B 443 GLU cc_start: 0.6310 (pp20) cc_final: 0.5907 (pp20) REVERT: B 450 TRP cc_start: 0.7007 (t60) cc_final: 0.6703 (t60) REVERT: B 462 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6190 (tp) REVERT: B 472 LEU cc_start: 0.2075 (OUTLIER) cc_final: 0.1866 (mt) REVERT: A 356 LYS cc_start: 0.7863 (tttt) cc_final: 0.7608 (tmtt) REVERT: A 456 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6781 (t80) REVERT: C 55 ARG cc_start: 0.1197 (mtt180) cc_final: 0.0509 (mmt180) REVERT: C 96 ARG cc_start: 0.8136 (ptt180) cc_final: 0.7715 (ptm160) REVERT: C 147 LEU cc_start: 0.6903 (tp) cc_final: 0.6665 (tp) REVERT: D 144 PHE cc_start: 0.7019 (p90) cc_final: 0.6382 (p90) REVERT: D 164 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7527 (tp40) outliers start: 42 outliers final: 25 residues processed: 121 average time/residue: 0.1827 time to fit residues: 29.3642 Evaluate side-chains 114 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 381 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 462 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 352 THR 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 42 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 100 TRP 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 141 VAL Chi-restraints excluded: chain D residue 164 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5037 moved from start: 0.3882 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= 0.197 Angle : 0.650 11.090 8933 Z= 0.321 Chirality : 0.045 0.230 1037 Planarity : 0.005 0.061 1133 Dihedral : 6.306 56.924 961 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 6.07 % Allowed : 22.60 % Favored : 71.33 % 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: -0.21 (0.30), residues: 793 helix: 1.18 (0.35), residues: 198 sheet: -0.56 (0.33), residues: 259 loop : -0.45 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 100 HIS 0.010 0.001 HIS D 49 PHE 0.017 0.002 PHE B 460 TYR 0.021 0.001 TYR B 254 ARG 0.003 0.000 ARG A 346 *********************** 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 133 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 90 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3094 (t-100) cc_final: 0.1956 (t60) REVERT: B 351 VAL cc_start: 0.7460 (t) cc_final: 0.7123 (m) REVERT: B 364 SER cc_start: 0.6407 (OUTLIER) cc_final: 0.6144 (t) REVERT: B 381 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7689 (m) REVERT: B 450 TRP cc_start: 0.7086 (t60) cc_final: 0.6720 (t60) REVERT: B 462 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6181 (tp) REVERT: A 240 LYS cc_start: 0.6117 (tmtt) cc_final: 0.5753 (tmtt) REVERT: A 356 LYS cc_start: 0.7861 (tttt) cc_final: 0.7596 (tmtt) REVERT: A 456 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6774 (t80) REVERT: C 55 ARG cc_start: 0.1122 (mtt180) cc_final: 0.0208 (mmt180) REVERT: C 128 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4462 (pt) REVERT: D 118 TYR cc_start: 0.7277 (m-80) cc_final: 0.6761 (m-10) REVERT: D 144 PHE cc_start: 0.7153 (p90) cc_final: 0.6519 (p90) REVERT: D 148 ASP cc_start: 0.7482 (t0) cc_final: 0.7237 (t0) REVERT: D 177 PHE cc_start: 0.3835 (m-10) cc_final: 0.3310 (t80) outliers start: 43 outliers final: 27 residues processed: 118 average time/residue: 0.1871 time to fit residues: 29.0316 Evaluate side-chains 116 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 381 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 462 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 352 THR 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 42 LEU Chi-restraints excluded: chain C residue 60 THR 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 D residue 49 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 141 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 0.0770 overall best weight: 1.3544 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5125 moved from start: 0.4391 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= 0.250 Angle : 0.716 12.927 8933 Z= 0.353 Chirality : 0.047 0.268 1037 Planarity : 0.005 0.064 1133 Dihedral : 6.262 56.285 958 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.78 % Allowed : 23.31 % Favored : 69.92 % 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: -0.45 (0.30), residues: 793 helix: 0.81 (0.36), residues: 199 sheet: -0.67 (0.33), residues: 262 loop : -0.51 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 100 HIS 0.012 0.002 HIS D 49 PHE 0.018 0.002 PHE A 456 TYR 0.019 0.002 TYR B 254 ARG 0.006 0.001 ARG C 55 *********************** 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 142 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 94 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3135 (t-100) cc_final: 0.2895 (t-100) REVERT: B 351 VAL cc_start: 0.7470 (t) cc_final: 0.7113 (m) REVERT: B 364 SER cc_start: 0.6580 (OUTLIER) cc_final: 0.6346 (t) REVERT: B 381 THR cc_start: 0.7946 (OUTLIER) cc_final: 0.7691 (m) REVERT: B 450 TRP cc_start: 0.7207 (t60) cc_final: 0.6776 (t60) REVERT: A 240 LYS cc_start: 0.5898 (tmtt) cc_final: 0.5686 (tmtt) REVERT: A 276 MET cc_start: 0.4651 (mmp) cc_final: 0.4322 (mmp) REVERT: A 356 LYS cc_start: 0.7881 (tttt) cc_final: 0.7623 (tmtt) REVERT: A 456 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6872 (t80) REVERT: A 476 LYS cc_start: 0.4014 (tptp) cc_final: 0.2162 (ptmm) REVERT: C 55 ARG cc_start: 0.1294 (mtt180) cc_final: 0.0385 (mmt-90) REVERT: C 100 TRP cc_start: 0.6957 (OUTLIER) cc_final: 0.6513 (p-90) REVERT: C 128 LEU cc_start: 0.4891 (OUTLIER) cc_final: 0.4471 (pt) REVERT: C 138 ILE cc_start: 0.7558 (tt) cc_final: 0.7267 (tp) REVERT: D 138 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6859 (tm-30) REVERT: D 144 PHE cc_start: 0.7039 (p90) cc_final: 0.6426 (p90) REVERT: D 148 ASP cc_start: 0.7511 (t0) cc_final: 0.7290 (t0) REVERT: D 177 PHE cc_start: 0.3342 (m-10) cc_final: 0.3093 (t80) outliers start: 48 outliers final: 34 residues processed: 123 average time/residue: 0.2046 time to fit residues: 32.5375 Evaluate side-chains 124 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 381 THR 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 472 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 352 THR 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 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 100 TRP 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 128 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 141 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 440 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5145 moved from start: 0.4851 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= 0.241 Angle : 0.703 12.952 8933 Z= 0.345 Chirality : 0.047 0.274 1037 Planarity : 0.005 0.067 1133 Dihedral : 6.344 54.509 958 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 6.21 % Allowed : 24.15 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.30), residues: 793 helix: 0.66 (0.36), residues: 198 sheet: -0.82 (0.32), residues: 262 loop : -0.59 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 61 HIS 0.013 0.002 HIS D 49 PHE 0.017 0.002 PHE A 456 TYR 0.018 0.002 TYR B 254 ARG 0.006 0.001 ARG C 55 *********************** 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 131 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 87 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3323 (t-100) cc_final: 0.3015 (t-100) REVERT: B 351 VAL cc_start: 0.7490 (t) cc_final: 0.7104 (m) REVERT: B 450 TRP cc_start: 0.7145 (t60) cc_final: 0.6727 (t60) REVERT: B 462 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6606 (tp) REVERT: A 356 LYS cc_start: 0.7849 (tttt) cc_final: 0.7607 (tmtt) REVERT: A 456 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6992 (t80) REVERT: C 55 ARG cc_start: 0.0998 (mtt180) cc_final: 0.0442 (mmt180) REVERT: C 100 TRP cc_start: 0.6944 (OUTLIER) cc_final: 0.6678 (p-90) REVERT: C 128 LEU cc_start: 0.4838 (OUTLIER) cc_final: 0.4573 (pt) REVERT: C 138 ILE cc_start: 0.7576 (tt) cc_final: 0.7333 (tp) REVERT: D 138 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6955 (tm-30) REVERT: D 144 PHE cc_start: 0.7207 (p90) cc_final: 0.6513 (p90) REVERT: D 177 PHE cc_start: 0.3331 (m-10) cc_final: 0.3010 (t80) outliers start: 44 outliers final: 30 residues processed: 114 average time/residue: 0.2074 time to fit residues: 30.4652 Evaluate side-chains 112 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 78 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 462 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 352 THR 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 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 100 TRP 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 128 LEU Chi-restraints excluded: chain C residue 152 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 440 ASN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5103 moved from start: 0.5064 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= 0.193 Angle : 0.674 12.758 8933 Z= 0.330 Chirality : 0.045 0.278 1037 Planarity : 0.005 0.071 1133 Dihedral : 6.076 54.848 958 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.65 % Allowed : 24.86 % 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: -0.46 (0.30), residues: 793 helix: 0.96 (0.36), residues: 197 sheet: -0.75 (0.33), residues: 262 loop : -0.54 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 261 HIS 0.012 0.001 HIS D 49 PHE 0.020 0.001 PHE B 303 TYR 0.018 0.001 TYR B 254 ARG 0.014 0.001 ARG A 346 *********************** 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 126 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 86 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3228 (t-100) cc_final: 0.1903 (t60) REVERT: B 351 VAL cc_start: 0.7473 (t) cc_final: 0.7132 (m) REVERT: B 450 TRP cc_start: 0.7175 (t60) cc_final: 0.6778 (t60) REVERT: B 462 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6527 (tp) REVERT: A 456 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6904 (t80) REVERT: C 55 ARG cc_start: 0.1161 (mtt180) cc_final: 0.0343 (mmt180) REVERT: C 128 LEU cc_start: 0.4845 (OUTLIER) cc_final: 0.4430 (pt) REVERT: C 138 ILE cc_start: 0.7569 (tt) cc_final: 0.7348 (tp) REVERT: D 118 TYR cc_start: 0.7118 (m-80) cc_final: 0.6835 (m-10) REVERT: D 138 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6973 (tm-30) REVERT: D 144 PHE cc_start: 0.6976 (p90) cc_final: 0.6245 (p90) REVERT: D 164 GLN cc_start: 0.6827 (tm-30) cc_final: 0.6602 (tm-30) REVERT: D 177 PHE cc_start: 0.3530 (m-10) cc_final: 0.3003 (t80) outliers start: 40 outliers final: 31 residues processed: 112 average time/residue: 0.2140 time to fit residues: 30.8543 Evaluate side-chains 115 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 81 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 278 SER 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 444 GLU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 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 350 THR Chi-restraints excluded: chain A residue 352 THR 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 456 PHE 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 69 HIS Chi-restraints excluded: chain D residue 79 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5147 moved from start: 0.5286 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= 0.224 Angle : 0.709 13.442 8933 Z= 0.346 Chirality : 0.047 0.277 1037 Planarity : 0.005 0.071 1133 Dihedral : 6.209 56.074 958 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.79 % Allowed : 24.44 % Favored : 69.77 % 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: -0.51 (0.30), residues: 793 helix: 0.96 (0.36), residues: 197 sheet: -0.78 (0.32), residues: 263 loop : -0.61 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 100 HIS 0.013 0.002 HIS D 49 PHE 0.017 0.002 PHE A 456 TYR 0.017 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 127 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 86 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3223 (t-100) cc_final: 0.2858 (t-100) REVERT: B 351 VAL cc_start: 0.7503 (t) cc_final: 0.7136 (m) REVERT: B 450 TRP cc_start: 0.7157 (t60) cc_final: 0.6739 (t60) REVERT: B 462 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6556 (tp) REVERT: A 456 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6909 (t80) REVERT: C 55 ARG cc_start: 0.1169 (mtt180) cc_final: 0.0497 (mmt180) REVERT: C 128 LEU cc_start: 0.4731 (OUTLIER) cc_final: 0.4456 (pt) REVERT: C 138 ILE cc_start: 0.7624 (tt) cc_final: 0.7387 (tp) REVERT: D 118 TYR cc_start: 0.7246 (m-80) cc_final: 0.6874 (m-10) REVERT: D 138 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6961 (tm-30) REVERT: D 144 PHE cc_start: 0.7199 (p90) cc_final: 0.6457 (p90) REVERT: D 164 GLN cc_start: 0.6813 (tm-30) cc_final: 0.6597 (tm-30) REVERT: D 177 PHE cc_start: 0.3493 (m-10) cc_final: 0.2996 (t80) outliers start: 41 outliers final: 33 residues processed: 114 average time/residue: 0.1883 time to fit residues: 28.0783 Evaluate side-chains 122 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 278 SER 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 416 VAL Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 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 350 THR Chi-restraints excluded: chain A residue 352 THR 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 456 PHE 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 128 LEU Chi-restraints excluded: chain C residue 152 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 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5125 moved from start: 0.5388 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= 0.200 Angle : 0.701 13.636 8933 Z= 0.341 Chirality : 0.046 0.275 1037 Planarity : 0.006 0.071 1133 Dihedral : 6.086 56.252 958 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.65 % Allowed : 25.00 % 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: -0.40 (0.30), residues: 793 helix: 1.08 (0.36), residues: 197 sheet: -0.70 (0.33), residues: 263 loop : -0.57 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 100 HIS 0.012 0.002 HIS D 49 PHE 0.015 0.001 PHE A 456 TYR 0.017 0.001 TYR B 254 ARG 0.009 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 123 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 83 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3214 (t-100) cc_final: 0.2848 (t-100) REVERT: B 351 VAL cc_start: 0.7519 (t) cc_final: 0.7174 (m) REVERT: B 450 TRP cc_start: 0.7143 (t60) cc_final: 0.6692 (t60) REVERT: B 462 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6476 (tp) REVERT: A 456 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6933 (t80) REVERT: C 55 ARG cc_start: 0.1087 (mtt180) cc_final: 0.0369 (mmt180) REVERT: C 105 GLU cc_start: 0.4286 (tp30) cc_final: 0.2497 (tt0) REVERT: C 128 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4512 (pt) REVERT: C 138 ILE cc_start: 0.7622 (tt) cc_final: 0.7379 (tp) REVERT: D 118 TYR cc_start: 0.7207 (m-80) cc_final: 0.6829 (m-10) REVERT: D 138 GLU cc_start: 0.7279 (tm-30) cc_final: 0.7002 (tm-30) REVERT: D 144 PHE cc_start: 0.7155 (p90) cc_final: 0.6428 (p90) outliers start: 40 outliers final: 32 residues processed: 109 average time/residue: 0.1949 time to fit residues: 27.8171 Evaluate side-chains 110 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 75 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 444 GLU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 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 350 THR Chi-restraints excluded: chain A residue 352 THR 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 456 PHE 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 128 LEU Chi-restraints excluded: chain C residue 152 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 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 64 optimal weight: 0.0980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4555 r_free = 0.4555 target = 0.186641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.179614 restraints weight = 18564.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.177003 restraints weight = 27778.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 118)---------------| | r_work = 0.4431 r_free = 0.4431 target = 0.176704 restraints weight = 29938.213| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4831 moved from start: 0.5680 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= 0.250 Angle : 0.750 15.307 8933 Z= 0.367 Chirality : 0.047 0.293 1037 Planarity : 0.006 0.072 1133 Dihedral : 6.430 58.592 958 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 6.21 % Allowed : 24.72 % Favored : 69.07 % 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: 0.86 (0.36), residues: 197 sheet: -0.72 (0.33), residues: 258 loop : -0.63 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 100 HIS 0.014 0.002 HIS D 49 PHE 0.018 0.002 PHE A 456 TYR 0.017 0.001 TYR B 254 ARG 0.007 0.001 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.59 seconds wall clock time: 30 minutes 51.69 seconds (1851.69 seconds total)