Starting phenix.real_space_refine on Mon Mar 11 00:45:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/03_2024/8e4c_27888.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/03_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_27888/03_2024/8e4c_27888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/03_2024/8e4c_27888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/03_2024/8e4c_27888.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4c_27888/03_2024/8e4c_27888.pdb" } 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 Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.94, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 2.18 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.68 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: 1.76 Time building geometry restraints manager: 2.41 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: 100.40 - 107.17: 278 107.17 - 113.93: 3726 113.93 - 120.70: 2569 120.70 - 127.47: 2275 127.47 - 134.23: 85 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 2.440 nonbonded pdb=" OG1 THR A 414 " pdb=" O ARG A 429 " model vdw 2.258 2.440 nonbonded pdb=" O SER A 382 " pdb=" OG1 THR A 396 " model vdw 2.294 2.440 nonbonded pdb=" O VAL C 152 " pdb=" OG1 THR C 155 " model vdw 2.353 2.440 nonbonded pdb=" O CYS D 43 " pdb=" OG1 THR D 132 " model vdw 2.357 2.440 ... (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 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: 1.970 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: 7.560 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.200 Find NCS groups from input model: 0.250 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- 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 : 0.709 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: 0.2269 time to fit residues: 46.4042 Evaluate side-chains 95 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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: 5.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN B 279 HIS A 372 GLN C 52 ASN C 95 HIS C 165 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5092 moved from start: 0.2728 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= 0.273 Angle : 0.756 12.055 8933 Z= 0.372 Chirality : 0.050 0.297 1037 Planarity : 0.006 0.076 1133 Dihedral : 6.745 60.225 962 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.79 % Allowed : 22.32 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.30), residues: 793 helix: 1.06 (0.36), residues: 198 sheet: -0.72 (0.34), residues: 244 loop : -0.71 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 100 HIS 0.014 0.002 HIS D 49 PHE 0.022 0.002 PHE B 303 TYR 0.018 0.002 TYR B 254 ARG 0.005 0.001 ARG C 55 *********************** 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 148 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 107 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3246 (t-100) cc_final: 0.2157 (t60) REVERT: B 351 VAL cc_start: 0.7306 (t) cc_final: 0.6966 (m) REVERT: B 381 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7689 (m) REVERT: B 450 TRP cc_start: 0.6994 (t60) cc_final: 0.6681 (t60) REVERT: A 399 ILE cc_start: 0.8955 (mt) cc_final: 0.8685 (mm) REVERT: C 55 ARG cc_start: 0.1342 (mtt180) cc_final: 0.0775 (mmt180) REVERT: C 111 ARG cc_start: 0.6080 (ttt-90) cc_final: 0.5606 (mpt180) REVERT: C 147 LEU cc_start: 0.7087 (tp) cc_final: 0.6725 (tp) REVERT: C 162 ARG cc_start: 0.1914 (ttp-110) cc_final: 0.0815 (mmt180) REVERT: D 103 TYR cc_start: 0.5602 (m-80) cc_final: 0.4895 (m-80) REVERT: D 138 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6726 (tm-30) REVERT: D 144 PHE cc_start: 0.6874 (p90) cc_final: 0.6347 (p90) REVERT: D 164 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7294 (tm-30) outliers start: 41 outliers final: 19 residues processed: 133 average time/residue: 0.2462 time to fit residues: 41.8586 Evaluate side-chains 111 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 448 ASN 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 A residue 415 CYS Chi-restraints excluded: chain C residue 42 LEU 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 69 HIS 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: 1.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.5132 moved from start: 0.3499 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= 0.252 Angle : 0.726 12.423 8933 Z= 0.359 Chirality : 0.047 0.285 1037 Planarity : 0.006 0.065 1133 Dihedral : 7.091 59.287 961 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.05 % Favored : 93.82 % Rotamer: Outliers : 7.63 % Allowed : 21.05 % 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: -0.60 (0.30), residues: 793 helix: 0.94 (0.36), residues: 199 sheet: -0.79 (0.32), residues: 255 loop : -0.76 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 100 HIS 0.010 0.002 HIS D 49 PHE 0.027 0.002 PHE A 456 TYR 0.011 0.001 TYR A 466 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 155 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 101 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 ILE cc_start: -0.0746 (OUTLIER) cc_final: -0.0983 (pt) REVERT: B 297 TRP cc_start: 0.3275 (t-100) cc_final: 0.2123 (t60) REVERT: B 351 VAL cc_start: 0.7223 (t) cc_final: 0.6931 (m) REVERT: B 381 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7743 (m) REVERT: B 450 TRP cc_start: 0.7013 (t60) cc_final: 0.6583 (t60) REVERT: A 399 ILE cc_start: 0.8892 (mt) cc_final: 0.8641 (mm) REVERT: A 476 LYS cc_start: 0.3837 (tptp) cc_final: 0.2236 (ptmm) REVERT: C 55 ARG cc_start: 0.1352 (mtt180) cc_final: 0.0269 (mmt-90) REVERT: C 111 ARG cc_start: 0.6159 (ttt-90) cc_final: 0.5885 (mpt180) REVERT: C 147 LEU cc_start: 0.7125 (tp) cc_final: 0.6906 (tp) REVERT: D 103 TYR cc_start: 0.5673 (m-80) cc_final: 0.5043 (m-80) REVERT: D 138 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6748 (tm-30) REVERT: D 144 PHE cc_start: 0.7280 (p90) cc_final: 0.6464 (p90) REVERT: D 164 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: D 168 ILE cc_start: 0.5907 (OUTLIER) cc_final: 0.5655 (pt) outliers start: 54 outliers final: 31 residues processed: 136 average time/residue: 0.2007 time to fit residues: 35.5691 Evaluate side-chains 129 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 448 ASN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 463 SER 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 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 C residue 37 SER Chi-restraints excluded: chain C residue 39 THR 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 D residue 69 HIS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 174 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5088 moved from start: 0.3875 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= 0.187 Angle : 0.649 10.245 8933 Z= 0.320 Chirality : 0.045 0.253 1037 Planarity : 0.005 0.062 1133 Dihedral : 6.425 50.392 961 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 5.37 % Allowed : 22.74 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.30), residues: 793 helix: 1.18 (0.36), residues: 199 sheet: -0.72 (0.33), residues: 255 loop : -0.65 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 367 HIS 0.006 0.001 HIS D 49 PHE 0.027 0.002 PHE B 460 TYR 0.016 0.001 TYR D 66 ARG 0.003 0.000 ARG C 111 *********************** 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 134 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3293 (t-100) cc_final: 0.2077 (t60) REVERT: B 351 VAL cc_start: 0.7291 (t) cc_final: 0.6977 (m) REVERT: B 443 GLU cc_start: 0.6597 (pp20) cc_final: 0.6224 (pp20) REVERT: B 450 TRP cc_start: 0.7007 (t60) cc_final: 0.6610 (t60) REVERT: A 356 LYS cc_start: 0.7933 (tttt) cc_final: 0.7535 (tmtt) REVERT: A 456 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6841 (t80) REVERT: C 55 ARG cc_start: 0.1430 (mtt180) cc_final: 0.0455 (mmt180) REVERT: C 147 LEU cc_start: 0.6944 (tp) cc_final: 0.6704 (tp) REVERT: D 103 TYR cc_start: 0.5582 (m-80) cc_final: 0.5284 (m-80) REVERT: D 138 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6856 (tm-30) REVERT: D 144 PHE cc_start: 0.7411 (p90) cc_final: 0.6694 (p90) REVERT: D 177 PHE cc_start: 0.3789 (m-10) cc_final: 0.3378 (t80) outliers start: 38 outliers final: 26 residues processed: 119 average time/residue: 0.2023 time to fit residues: 31.8153 Evaluate side-chains 115 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET 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 448 ASN Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain A residue 276 MET 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 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 139 ILE Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 0.0370 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5092 moved from start: 0.4137 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= 0.192 Angle : 0.642 10.915 8933 Z= 0.315 Chirality : 0.045 0.254 1037 Planarity : 0.005 0.062 1133 Dihedral : 6.164 59.991 958 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 6.21 % Allowed : 23.16 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.30), residues: 793 helix: 1.19 (0.37), residues: 199 sheet: -0.69 (0.33), residues: 256 loop : -0.56 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 100 HIS 0.005 0.001 HIS D 49 PHE 0.021 0.002 PHE B 460 TYR 0.012 0.001 TYR D 66 ARG 0.003 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 94 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: -0.0617 (OUTLIER) cc_final: -0.0878 (pt) REVERT: B 297 TRP cc_start: 0.3183 (t-100) cc_final: 0.1970 (t60) REVERT: B 351 VAL cc_start: 0.7357 (t) cc_final: 0.7048 (m) REVERT: B 381 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7703 (m) REVERT: B 450 TRP cc_start: 0.7041 (t60) cc_final: 0.6627 (t60) REVERT: A 240 LYS cc_start: 0.6282 (tmtt) cc_final: 0.5993 (tmtt) REVERT: A 356 LYS cc_start: 0.7898 (tttt) cc_final: 0.7442 (tmtt) REVERT: A 440 ASN cc_start: 0.6788 (t0) cc_final: 0.6466 (t0) REVERT: A 456 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6832 (t80) REVERT: A 476 LYS cc_start: 0.3951 (tptp) cc_final: 0.2094 (ptmm) REVERT: C 55 ARG cc_start: 0.1361 (mtt180) cc_final: 0.0358 (mmt180) REVERT: C 100 TRP cc_start: 0.6803 (OUTLIER) cc_final: 0.6577 (p-90) REVERT: C 138 ILE cc_start: 0.7505 (tt) cc_final: 0.7209 (tp) REVERT: D 103 TYR cc_start: 0.5519 (m-80) cc_final: 0.5230 (m-80) REVERT: D 144 PHE cc_start: 0.7368 (p90) cc_final: 0.6625 (p90) REVERT: D 148 ASP cc_start: 0.7550 (t0) cc_final: 0.7293 (t0) REVERT: D 177 PHE cc_start: 0.3737 (m-10) cc_final: 0.3314 (t80) outliers start: 44 outliers final: 33 residues processed: 125 average time/residue: 0.2081 time to fit residues: 34.0961 Evaluate side-chains 126 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 89 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 377 GLU 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 448 ASN Chi-restraints excluded: chain B residue 462 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 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 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 91 VAL Chi-restraints excluded: chain C residue 100 TRP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 69 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.0000 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.5095 moved from start: 0.4444 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= 0.195 Angle : 0.646 11.658 8933 Z= 0.313 Chirality : 0.045 0.278 1037 Planarity : 0.005 0.064 1133 Dihedral : 5.984 54.435 958 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.50 % Allowed : 24.01 % 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: -0.31 (0.31), residues: 793 helix: 1.19 (0.36), residues: 199 sheet: -0.64 (0.33), residues: 260 loop : -0.55 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 367 HIS 0.006 0.001 HIS D 49 PHE 0.019 0.001 PHE B 460 TYR 0.013 0.001 TYR D 66 ARG 0.006 0.000 ARG D 51 *********************** 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 139 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 93 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: B 273 ILE cc_start: -0.0626 (OUTLIER) cc_final: -0.0909 (pt) REVERT: B 297 TRP cc_start: 0.3232 (t-100) cc_final: 0.1967 (t60) REVERT: B 351 VAL cc_start: 0.7418 (t) cc_final: 0.7092 (m) REVERT: B 450 TRP cc_start: 0.7017 (t60) cc_final: 0.6611 (t60) REVERT: A 356 LYS cc_start: 0.7872 (tttt) cc_final: 0.7421 (tmtt) REVERT: A 456 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6794 (t80) REVERT: A 476 LYS cc_start: 0.4148 (tptp) cc_final: 0.2153 (ptmm) REVERT: C 55 ARG cc_start: 0.1306 (mtt180) cc_final: 0.0322 (mmt180) REVERT: C 100 TRP cc_start: 0.6777 (OUTLIER) cc_final: 0.6440 (p-90) REVERT: C 128 LEU cc_start: 0.4939 (OUTLIER) cc_final: 0.4357 (pt) REVERT: C 138 ILE cc_start: 0.7498 (tt) cc_final: 0.7292 (tp) REVERT: D 103 TYR cc_start: 0.5614 (m-80) cc_final: 0.5296 (m-80) REVERT: D 144 PHE cc_start: 0.7346 (p90) cc_final: 0.6589 (p90) REVERT: D 148 ASP cc_start: 0.7451 (t0) cc_final: 0.7208 (t0) REVERT: D 168 ILE cc_start: 0.5928 (OUTLIER) cc_final: 0.5484 (pt) REVERT: D 177 PHE cc_start: 0.3594 (m-10) cc_final: 0.3232 (t80) outliers start: 46 outliers final: 34 residues processed: 124 average time/residue: 0.2612 time to fit residues: 41.7782 Evaluate side-chains 121 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 82 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 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 427 THR Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 462 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 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 91 VAL Chi-restraints excluded: chain C residue 100 TRP 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 139 ILE 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 113 GLU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 168 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5221 moved from start: 0.5075 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= 0.270 Angle : 0.740 15.500 8933 Z= 0.364 Chirality : 0.048 0.295 1037 Planarity : 0.006 0.066 1133 Dihedral : 6.562 54.100 958 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 6.92 % Allowed : 23.59 % 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: -0.73 (0.30), residues: 793 helix: 0.74 (0.36), residues: 199 sheet: -0.99 (0.32), residues: 266 loop : -0.63 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 261 HIS 0.009 0.002 HIS D 129 PHE 0.020 0.002 PHE A 456 TYR 0.015 0.002 TYR A 466 ARG 0.009 0.001 ARG A 346 *********************** 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 141 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 92 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3284 (t-100) cc_final: 0.1844 (t60) REVERT: B 351 VAL cc_start: 0.7318 (t) cc_final: 0.7037 (m) REVERT: B 450 TRP cc_start: 0.7138 (t60) cc_final: 0.6647 (t60) REVERT: A 356 LYS cc_start: 0.7943 (tttt) cc_final: 0.7661 (tmtt) REVERT: A 456 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6974 (t80) REVERT: C 55 ARG cc_start: 0.1264 (OUTLIER) cc_final: 0.0437 (mmt180) REVERT: C 100 TRP cc_start: 0.7077 (OUTLIER) cc_final: 0.6777 (p-90) REVERT: C 128 LEU cc_start: 0.4811 (OUTLIER) cc_final: 0.4540 (pt) REVERT: C 137 ARG cc_start: 0.6759 (tpp-160) cc_final: 0.6194 (ttp-170) REVERT: C 138 ILE cc_start: 0.7665 (tt) cc_final: 0.7374 (tp) REVERT: D 103 TYR cc_start: 0.5767 (m-80) cc_final: 0.5181 (m-80) REVERT: D 138 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6865 (tm-30) REVERT: D 144 PHE cc_start: 0.7404 (p90) cc_final: 0.6889 (p90) REVERT: D 148 ASP cc_start: 0.7550 (t0) cc_final: 0.7335 (t0) REVERT: D 168 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5537 (pt) REVERT: D 177 PHE cc_start: 0.3338 (m-10) cc_final: 0.3036 (t80) outliers start: 49 outliers final: 35 residues processed: 124 average time/residue: 0.2347 time to fit residues: 37.0699 Evaluate side-chains 125 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 85 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 462 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 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 456 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 55 ARG 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 102 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 168 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN ** B 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5166 moved from start: 0.5269 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= 0.201 Angle : 0.685 12.815 8933 Z= 0.338 Chirality : 0.046 0.290 1037 Planarity : 0.005 0.067 1133 Dihedral : 5.858 56.001 956 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.78 % Allowed : 24.29 % 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: -0.61 (0.30), residues: 793 helix: 0.96 (0.36), residues: 199 sheet: -0.69 (0.32), residues: 268 loop : -0.87 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 261 HIS 0.006 0.001 HIS D 49 PHE 0.017 0.002 PHE A 456 TYR 0.013 0.001 TYR D 66 ARG 0.009 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 134 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 86 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.1573 (mt) cc_final: 0.1182 (tp) REVERT: B 297 TRP cc_start: 0.3206 (t-100) cc_final: 0.1889 (t60) REVERT: B 351 VAL cc_start: 0.7444 (t) cc_final: 0.7163 (m) REVERT: B 450 TRP cc_start: 0.7068 (t60) cc_final: 0.6605 (t60) REVERT: A 456 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6911 (t80) REVERT: C 55 ARG cc_start: 0.1393 (OUTLIER) cc_final: 0.0606 (mmt180) REVERT: C 100 TRP cc_start: 0.7151 (OUTLIER) cc_final: 0.6843 (p-90) REVERT: C 128 LEU cc_start: 0.4802 (OUTLIER) cc_final: 0.4505 (pt) REVERT: C 137 ARG cc_start: 0.6736 (tpp-160) cc_final: 0.6153 (ttp-170) REVERT: C 162 ARG cc_start: 0.1930 (ttp-110) cc_final: 0.0459 (mmt180) REVERT: D 69 HIS cc_start: 0.1880 (OUTLIER) cc_final: 0.0246 (t70) REVERT: D 103 TYR cc_start: 0.5664 (m-80) cc_final: 0.5184 (m-80) REVERT: D 138 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6875 (tm-30) REVERT: D 144 PHE cc_start: 0.7309 (p90) cc_final: 0.6416 (p90) REVERT: D 168 ILE cc_start: 0.6040 (OUTLIER) cc_final: 0.5600 (pt) REVERT: D 177 PHE cc_start: 0.3316 (m-10) cc_final: 0.2964 (t80) outliers start: 48 outliers final: 35 residues processed: 119 average time/residue: 0.2225 time to fit residues: 33.6946 Evaluate side-chains 123 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 82 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 320 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 462 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 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 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 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 55 ARG Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 100 TRP 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 D residue 49 HIS Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 168 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.0050 chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.7800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5254 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 6557 Z= 0.298 Angle : 0.788 16.719 8933 Z= 0.387 Chirality : 0.050 0.312 1037 Planarity : 0.006 0.067 1133 Dihedral : 6.467 59.359 956 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.78 % Allowed : 23.87 % 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: -0.95 (0.30), residues: 793 helix: 0.66 (0.35), residues: 198 sheet: -0.86 (0.31), residues: 270 loop : -1.10 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 261 HIS 0.009 0.002 HIS A 397 PHE 0.021 0.002 PHE A 456 TYR 0.015 0.002 TYR D 66 ARG 0.007 0.001 ARG C 55 *********************** 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 137 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 89 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3157 (t-100) cc_final: 0.1728 (t60) REVERT: B 351 VAL cc_start: 0.7471 (t) cc_final: 0.7137 (m) REVERT: B 450 TRP cc_start: 0.7148 (t60) cc_final: 0.6689 (t60) REVERT: A 456 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6992 (t80) REVERT: C 55 ARG cc_start: 0.1288 (OUTLIER) cc_final: 0.0295 (mmt-90) REVERT: C 100 TRP cc_start: 0.7269 (OUTLIER) cc_final: 0.7019 (p-90) REVERT: C 128 LEU cc_start: 0.4827 (OUTLIER) cc_final: 0.4560 (pt) REVERT: C 137 ARG cc_start: 0.6864 (tpp-160) cc_final: 0.6223 (ttp-170) REVERT: C 162 ARG cc_start: 0.1812 (ttp-110) cc_final: 0.0502 (mmt180) REVERT: D 69 HIS cc_start: 0.1946 (OUTLIER) cc_final: 0.0361 (t70) REVERT: D 103 TYR cc_start: 0.5779 (m-80) cc_final: 0.5063 (m-80) REVERT: D 138 GLU cc_start: 0.7563 (tm-30) cc_final: 0.6858 (tm-30) REVERT: D 144 PHE cc_start: 0.7389 (p90) cc_final: 0.6733 (p90) REVERT: D 168 ILE cc_start: 0.6144 (OUTLIER) cc_final: 0.5648 (pt) REVERT: D 177 PHE cc_start: 0.3263 (m-10) cc_final: 0.3011 (t80) outliers start: 48 outliers final: 38 residues processed: 122 average time/residue: 0.2127 time to fit residues: 33.1837 Evaluate side-chains 129 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 85 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 355 VAL 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 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 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 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 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 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 55 ARG 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 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 102 VAL Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 overall best weight: 0.5016 ------------------------------------------------------------------------------- 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 136 ASN D 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5150 moved from start: 0.5691 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= 0.189 Angle : 0.686 13.303 8933 Z= 0.337 Chirality : 0.047 0.299 1037 Planarity : 0.005 0.068 1133 Dihedral : 5.891 59.930 956 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.08 % Allowed : 26.13 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.30), residues: 793 helix: 1.10 (0.36), residues: 198 sheet: -0.68 (0.32), residues: 270 loop : -0.90 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 297 HIS 0.006 0.001 HIS D 49 PHE 0.015 0.001 PHE A 456 TYR 0.013 0.001 TYR D 66 ARG 0.005 0.000 ARG D 51 ********************** 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 127 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 91 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 TRP cc_start: 0.3132 (t-100) cc_final: 0.1774 (t60) REVERT: B 351 VAL cc_start: 0.7506 (t) cc_final: 0.7176 (m) REVERT: B 450 TRP cc_start: 0.7000 (t60) cc_final: 0.6596 (t60) REVERT: A 456 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.7005 (t80) REVERT: C 55 ARG cc_start: 0.1399 (mtt180) cc_final: 0.0376 (mmt180) REVERT: C 105 GLU cc_start: 0.4127 (tp30) cc_final: 0.2435 (tt0) REVERT: C 128 LEU cc_start: 0.4732 (OUTLIER) cc_final: 0.4447 (pt) REVERT: C 137 ARG cc_start: 0.6846 (tpp-160) cc_final: 0.6167 (ttp-170) REVERT: C 162 ARG cc_start: 0.1706 (ttp-110) cc_final: 0.0301 (mmt180) REVERT: D 103 TYR cc_start: 0.5616 (m-80) cc_final: 0.5153 (m-80) REVERT: D 138 GLU cc_start: 0.7514 (tm-30) cc_final: 0.6950 (tm-30) REVERT: D 144 PHE cc_start: 0.7297 (p90) cc_final: 0.6342 (p90) REVERT: D 168 ILE cc_start: 0.6122 (OUTLIER) cc_final: 0.5668 (pt) outliers start: 36 outliers final: 28 residues processed: 117 average time/residue: 0.2501 time to fit residues: 37.4136 Evaluate side-chains 119 residues out of total 721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 355 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 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 373 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 60 THR 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 D residue 49 HIS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.186559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.177790 restraints weight = 18979.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.177068 restraints weight = 29003.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.177277 restraints weight = 25936.527| |-----------------------------------------------------------------------------| r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4859 moved from start: 0.5964 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= 0.239 Angle : 0.739 15.034 8933 Z= 0.361 Chirality : 0.049 0.323 1037 Planarity : 0.006 0.067 1133 Dihedral : 6.164 58.737 956 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.65 % Allowed : 25.71 % 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: -0.70 (0.30), residues: 793 helix: 0.94 (0.35), residues: 198 sheet: -0.75 (0.32), residues: 270 loop : -0.96 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 100 HIS 0.006 0.002 HIS D 49 PHE 0.019 0.002 PHE A 456 TYR 0.013 0.001 TYR D 66 ARG 0.008 0.001 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1756.70 seconds wall clock time: 32 minutes 53.42 seconds (1973.42 seconds total)