Starting phenix.real_space_refine on Sat Mar 16 17:10:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/03_2024/8omr_16976_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/03_2024/8omr_16976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/03_2024/8omr_16976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/03_2024/8omr_16976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/03_2024/8omr_16976_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/03_2024/8omr_16976_updated.pdb" } resolution = 3.3 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= -0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7626 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 75 5.49 5 S 48 5.16 5 C 4520 2.51 5 N 1341 2.21 5 O 1640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 376": "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: 7626 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 390, 3000 Classifications: {'peptide': 390} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 368} Conformer: "B" Number of residues, atoms: 390, 3000 Classifications: {'peptide': 390} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 368} bond proxies already assigned to first conformer: 3053 Chain: "B" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3014 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 365} Chain breaks: 1 Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1589 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 63} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' ZN': 1, '9DG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2336 SG CYS A 317 50.960 46.783 79.155 1.00 71.53 S ATOM 2349 SG CYS A 319 48.135 45.426 76.966 1.00 57.96 S ATOM 2369 SG CYS A 322 51.015 47.274 75.471 1.00 66.05 S ATOM 5496 SG CYS B 351 26.013 26.939 71.448 1.00 61.72 S ATOM 5508 SG CYS B 353 27.602 29.987 72.683 1.00 70.08 S ATOM 5532 SG CYS B 356 24.182 29.011 73.915 1.00 67.56 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 335 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 335 " occ=0.50 Time building chain proxies: 6.44, per 1000 atoms: 0.84 Number of scatterers: 7626 At special positions: 0 Unit cell: (72.54, 99.06, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 48 16.00 P 75 15.00 O 1640 8.00 N 1341 7.00 C 4520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 348 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 319 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 322 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 317 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 382 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 351 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 356 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 353 " Number of angles added : 6 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 11 sheets defined 40.3% alpha, 10.9% beta 23 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.913A pdb=" N SER A 113 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 170 through 188 Processing helix chain 'A' and resid 207 through 217 Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.649A pdb=" N ARG A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.855A pdb=" N GLN A 323 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 324 " --> pdb=" O THR A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 324' Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.785A pdb=" N AHIS A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 365 removed outlier: 3.905A pdb=" N HIS A 344 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU A 345 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR A 346 " --> pdb=" O HIS A 343 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 357 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.555A pdb=" N VAL A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 removed outlier: 3.639A pdb=" N ASP A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 394 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.781A pdb=" N ASN B 52 " --> pdb=" O HIS B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 157 through 180 Processing helix chain 'B' and resid 183 through 186 removed outlier: 3.718A pdb=" N LYS B 186 " --> pdb=" O VAL B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'B' and resid 199 through 209 removed outlier: 4.159A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 257 through 266 removed outlier: 3.987A pdb=" N LEU B 261 " --> pdb=" O PRO B 257 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 361 through 369 Processing helix chain 'B' and resid 374 through 400 removed outlier: 3.713A pdb=" N HIS B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 385 " --> pdb=" O MET B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 Processing sheet with id= A, first strand: chain 'A' and resid 39 through 42 removed outlier: 6.500A pdb=" N GLU A 32 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A 19 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TRP A 34 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET A 17 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.546A pdb=" N PHE A 278 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 46 " --> pdb=" O PHE A 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.674A pdb=" N ASN A 101 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY A 72 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 103 " --> pdb=" O GLY A 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 118 through 121 Processing sheet with id= E, first strand: chain 'A' and resid 154 through 156 removed outlier: 5.455A pdb=" N ASN A 196 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY A 224 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE A 201 " --> pdb=" O GLY A 224 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 226 " --> pdb=" O ILE A 201 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 292 through 294 Processing sheet with id= G, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.619A pdb=" N GLY B 15 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 9 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 7 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS B 16 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU B 5 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 113 through 117 Processing sheet with id= I, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.877A pdb=" N VAL B 188 " --> pdb=" O PHE B 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 191 through 193 removed outlier: 7.976A pdb=" N LEU B 219 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 250 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 284 through 286 193 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 3.70 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: 1581 1.33 - 1.45: 2123 1.45 - 1.57: 4014 1.57 - 1.69: 149 1.69 - 1.81: 71 Bond restraints: 7938 Sorted by residual: bond pdb=" CG ASP A 279 " pdb=" OD2 ASP A 279 " ideal model delta sigma weight residual 1.249 1.359 -0.110 1.90e-02 2.77e+03 3.34e+01 bond pdb=" O5' C C 48 " pdb=" C5' C C 48 " ideal model delta sigma weight residual 1.420 1.454 -0.034 1.50e-02 4.44e+03 5.29e+00 bond pdb=" O5' A C 1 " pdb=" C5' A C 1 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.83e+00 bond pdb=" O5' U C 58 " pdb=" C5' U C 58 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.68e+00 bond pdb=" O5' G C 15 " pdb=" C5' G C 15 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.63e+00 ... (remaining 7933 not shown) Histogram of bond angle deviations from ideal: 95.43 - 103.17: 282 103.17 - 110.91: 3333 110.91 - 118.65: 3232 118.65 - 126.40: 3978 126.40 - 134.14: 281 Bond angle restraints: 11106 Sorted by residual: angle pdb=" O3' A C 57 " pdb=" P U C 58 " pdb=" O5' U C 58 " ideal model delta sigma weight residual 104.00 95.43 8.57 1.50e+00 4.44e-01 3.26e+01 angle pdb=" O3' U C 58 " pdb=" P U C 59 " pdb=" O5' U C 59 " ideal model delta sigma weight residual 104.00 96.91 7.09 1.50e+00 4.44e-01 2.23e+01 angle pdb=" C4' G C 56 " pdb=" C3' G C 56 " pdb=" O3' G C 56 " ideal model delta sigma weight residual 113.00 106.87 6.13 1.50e+00 4.44e-01 1.67e+01 angle pdb=" O3' A C 57 " pdb=" P U C 58 " pdb=" OP1 U C 58 " ideal model delta sigma weight residual 108.00 120.08 -12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C2' A C 12 " pdb=" C1' A C 12 " pdb=" N9 A C 12 " ideal model delta sigma weight residual 112.00 117.40 -5.40 1.50e+00 4.44e-01 1.30e+01 ... (remaining 11101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 4618 29.64 - 59.28: 208 59.28 - 88.93: 81 88.93 - 118.57: 0 118.57 - 148.21: 1 Dihedral angle restraints: 4908 sinusoidal: 2691 harmonic: 2217 Sorted by residual: dihedral pdb=" C4' G C 34 " pdb=" C3' G C 34 " pdb=" C2' G C 34 " pdb=" C1' G C 34 " ideal model delta sinusoidal sigma weight residual 36.00 -21.05 57.05 1 8.00e+00 1.56e-02 6.84e+01 dihedral pdb=" O4' G C 34 " pdb=" C2' G C 34 " pdb=" C1' G C 34 " pdb=" C3' G C 34 " ideal model delta sinusoidal sigma weight residual 25.00 -30.91 55.91 1 8.00e+00 1.56e-02 6.59e+01 dihedral pdb=" C5' G C 34 " pdb=" C4' G C 34 " pdb=" C3' G C 34 " pdb=" O3' G C 34 " ideal model delta sinusoidal sigma weight residual 82.00 123.89 -41.89 1 8.00e+00 1.56e-02 3.83e+01 ... (remaining 4905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1215 0.114 - 0.227: 85 0.227 - 0.341: 4 0.341 - 0.454: 3 0.454 - 0.568: 6 Chirality restraints: 1313 Sorted by residual: chirality pdb=" P A C 1 " pdb=" OP1 A C 1 " pdb=" OP2 A C 1 " pdb=" O5' A C 1 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" P C C 47 " pdb=" OP1 C C 47 " pdb=" OP2 C C 47 " pdb=" O5' C C 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" P U C 16 " pdb=" OP1 U C 16 " pdb=" OP2 U C 16 " pdb=" O5' U C 16 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.64e+00 ... (remaining 1310 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 21 " -0.037 2.00e-02 2.50e+03 2.20e-02 1.33e+01 pdb=" N9 A C 21 " 0.061 2.00e-02 2.50e+03 pdb=" C8 A C 21 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A C 21 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A C 21 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A C 21 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A C 21 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A C 21 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A C 21 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A C 21 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A C 21 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 12 " 0.037 2.00e-02 2.50e+03 1.98e-02 1.07e+01 pdb=" N9 A C 12 " -0.052 2.00e-02 2.50e+03 pdb=" C8 A C 12 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A C 12 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A C 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A C 12 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A C 12 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A C 12 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A C 12 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A C 12 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A C 12 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 42 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C THR A 42 " -0.053 2.00e-02 2.50e+03 pdb=" O THR A 42 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO A 43 " 0.018 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 1 2.19 - 2.87: 2735 2.87 - 3.54: 10110 3.54 - 4.22: 17424 4.22 - 4.90: 28708 Nonbonded interactions: 58978 Sorted by model distance: nonbonded pdb=" OD2 ASP A 279 " pdb=" C1' G C 34 " model vdw 1.512 3.470 nonbonded pdb=" OD2 ASP A 279 " pdb=" O4' G C 34 " model vdw 2.196 3.040 nonbonded pdb=" OG SER B 181 " pdb=" N GLU B 182 " model vdw 2.199 2.520 nonbonded pdb=" O MET A 175 " pdb=" OG SER A 178 " model vdw 2.218 2.440 nonbonded pdb=" OD1 ASN B 110 " pdb=" NE ARG B 166 " model vdw 2.232 2.520 ... (remaining 58973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.180 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.160 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.010 0.110 7938 Z= 0.623 Angle : 1.004 12.077 11106 Z= 0.569 Chirality : 0.073 0.568 1313 Planarity : 0.008 0.075 1148 Dihedral : 17.486 148.211 3480 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 6.62 % Allowed : 7.67 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.83 (0.28), residues: 769 helix: -0.33 (0.28), residues: 325 sheet: -1.15 (0.61), residues: 70 loop : -2.04 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 240 HIS 0.008 0.002 HIS B 359 PHE 0.028 0.003 PHE B 331 TYR 0.018 0.004 TYR B 354 ARG 0.018 0.003 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 51 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 71 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6854 (mp) REVERT: A 197 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8583 (tt) REVERT: A 368 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7145 (ptm160) REVERT: B 1 MET cc_start: 0.4226 (mtm) cc_final: 0.3501 (mtp) REVERT: B 97 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7507 (p90) REVERT: B 123 GLU cc_start: 0.8388 (pm20) cc_final: 0.7945 (pt0) REVERT: B 228 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7371 (p) REVERT: B 249 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.6373 (mtt-85) REVERT: B 393 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7009 (t80) REVERT: B 405 GLN cc_start: 0.7883 (tp40) cc_final: 0.7663 (tm-30) outliers start: 44 outliers final: 32 residues processed: 90 average time/residue: 0.2319 time to fit residues: 27.7460 Evaluate side-chains 79 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 40 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 99 PRO Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7938 Z= 0.220 Angle : 0.578 7.102 11106 Z= 0.297 Chirality : 0.040 0.206 1313 Planarity : 0.004 0.038 1148 Dihedral : 19.076 133.376 2095 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.66 % Allowed : 11.43 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.09 (0.30), residues: 769 helix: 0.26 (0.30), residues: 316 sheet: -0.99 (0.59), residues: 90 loop : -1.52 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 240 HIS 0.004 0.001 HIS B 359 PHE 0.016 0.002 PHE A 127 TYR 0.013 0.001 TYR B 354 ARG 0.007 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 46 time to evaluate : 0.742 Fit side-chains REVERT: A 135 GLU cc_start: 0.8086 (tt0) cc_final: 0.7749 (pm20) REVERT: A 197 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8454 (tt) REVERT: A 368 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7093 (ptm160) REVERT: B 1 MET cc_start: 0.4131 (mtm) cc_final: 0.3416 (mtp) REVERT: B 97 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7308 (p90) REVERT: B 123 GLU cc_start: 0.8294 (pm20) cc_final: 0.8024 (pt0) REVERT: B 230 GLU cc_start: 0.8781 (tp30) cc_final: 0.8568 (mm-30) REVERT: B 249 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6387 (mmt-90) REVERT: B 393 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7049 (t80) outliers start: 31 outliers final: 19 residues processed: 73 average time/residue: 0.1923 time to fit residues: 19.5019 Evaluate side-chains 66 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 42 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 61 optimal weight: 0.0050 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7938 Z= 0.251 Angle : 0.568 6.621 11106 Z= 0.290 Chirality : 0.039 0.202 1313 Planarity : 0.004 0.032 1148 Dihedral : 18.989 107.631 2075 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.06 % Allowed : 12.78 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.02 (0.31), residues: 769 helix: 0.27 (0.31), residues: 315 sheet: -0.89 (0.53), residues: 101 loop : -1.45 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.003 0.001 HIS B 359 PHE 0.015 0.002 PHE A 127 TYR 0.014 0.001 TYR B 354 ARG 0.004 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 45 time to evaluate : 0.755 Fit side-chains REVERT: A 135 GLU cc_start: 0.8117 (tt0) cc_final: 0.7770 (pm20) REVERT: A 197 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8484 (tt) REVERT: A 368 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6993 (ptm160) REVERT: B 1 MET cc_start: 0.4169 (mtm) cc_final: 0.3512 (mtp) REVERT: B 97 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.7309 (p90) REVERT: B 123 GLU cc_start: 0.8317 (pm20) cc_final: 0.7983 (pt0) REVERT: B 230 GLU cc_start: 0.8784 (tp30) cc_final: 0.8580 (mm-30) REVERT: B 249 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.6306 (mmt-90) REVERT: B 393 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7008 (t80) REVERT: B 405 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7346 (tm-30) outliers start: 27 outliers final: 20 residues processed: 68 average time/residue: 0.2011 time to fit residues: 18.9566 Evaluate side-chains 68 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 43 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 7938 Z= 0.476 Angle : 0.682 6.698 11106 Z= 0.351 Chirality : 0.044 0.208 1313 Planarity : 0.005 0.037 1148 Dihedral : 19.143 92.722 2072 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.81 % Allowed : 14.14 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -1.45 (0.30), residues: 769 helix: -0.06 (0.30), residues: 316 sheet: -0.84 (0.58), residues: 86 loop : -1.80 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 240 HIS 0.005 0.001 HIS B 359 PHE 0.021 0.003 PHE B 331 TYR 0.017 0.002 TYR B 354 ARG 0.006 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 43 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8085 (tt0) cc_final: 0.7739 (pm20) REVERT: A 197 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8553 (tt) REVERT: A 368 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7232 (ptm160) REVERT: B 1 MET cc_start: 0.4066 (mtm) cc_final: 0.3450 (mtp) REVERT: B 97 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7493 (p90) REVERT: B 123 GLU cc_start: 0.8338 (pm20) cc_final: 0.7848 (pt0) REVERT: B 249 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7462 (mmt-90) REVERT: B 264 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7440 (mt) REVERT: B 393 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.6970 (t80) REVERT: B 405 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7093 (tm-30) outliers start: 32 outliers final: 26 residues processed: 69 average time/residue: 0.2063 time to fit residues: 19.4405 Evaluate side-chains 74 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 42 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7938 Z= 0.170 Angle : 0.507 6.254 11106 Z= 0.259 Chirality : 0.037 0.194 1313 Planarity : 0.004 0.038 1148 Dihedral : 18.996 73.964 2072 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.21 % Allowed : 14.74 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 (0.31), residues: 769 helix: 0.36 (0.31), residues: 313 sheet: -0.80 (0.52), residues: 102 loop : -1.45 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 240 HIS 0.004 0.001 HIS B 365 PHE 0.013 0.001 PHE A 127 TYR 0.011 0.001 TYR B 354 ARG 0.004 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 47 time to evaluate : 0.823 Fit side-chains REVERT: A 135 GLU cc_start: 0.8073 (tt0) cc_final: 0.7751 (pm20) REVERT: A 197 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8434 (tt) REVERT: B 1 MET cc_start: 0.4026 (mtm) cc_final: 0.3406 (mtp) REVERT: B 97 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7296 (p90) REVERT: B 123 GLU cc_start: 0.8219 (pm20) cc_final: 0.7832 (pt0) REVERT: B 230 GLU cc_start: 0.8839 (tp30) cc_final: 0.8607 (mm-30) REVERT: B 393 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.7026 (t80) outliers start: 28 outliers final: 22 residues processed: 72 average time/residue: 0.1904 time to fit residues: 19.3440 Evaluate side-chains 67 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 42 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7938 Z= 0.134 Angle : 0.464 6.343 11106 Z= 0.235 Chirality : 0.035 0.214 1313 Planarity : 0.004 0.036 1148 Dihedral : 18.851 73.911 2063 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.46 % Allowed : 15.64 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.31), residues: 769 helix: 0.55 (0.31), residues: 316 sheet: -0.64 (0.53), residues: 102 loop : -1.18 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 240 HIS 0.004 0.001 HIS B 365 PHE 0.012 0.001 PHE A 127 TYR 0.011 0.001 TYR B 354 ARG 0.007 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 47 time to evaluate : 0.769 Fit side-chains REVERT: A 135 GLU cc_start: 0.8172 (tt0) cc_final: 0.7864 (pm20) REVERT: B 1 MET cc_start: 0.4073 (mtm) cc_final: 0.3477 (mtp) REVERT: B 97 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7237 (p90) REVERT: B 123 GLU cc_start: 0.8111 (pm20) cc_final: 0.7730 (pt0) REVERT: B 249 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.5961 (mmt-90) REVERT: B 393 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7005 (t80) outliers start: 23 outliers final: 16 residues processed: 68 average time/residue: 0.2050 time to fit residues: 18.9929 Evaluate side-chains 63 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 44 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 46 optimal weight: 0.0170 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 68 optimal weight: 0.0050 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 0.0370 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.2510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 GLN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7938 Z= 0.104 Angle : 0.449 6.688 11106 Z= 0.223 Chirality : 0.034 0.229 1313 Planarity : 0.004 0.035 1148 Dihedral : 18.769 73.844 2052 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.65 % Allowed : 17.14 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.35 (0.32), residues: 769 helix: 0.70 (0.31), residues: 324 sheet: -0.40 (0.51), residues: 107 loop : -1.03 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 240 HIS 0.004 0.000 HIS B 365 PHE 0.010 0.001 PHE A 127 TYR 0.009 0.001 TYR B 354 ARG 0.004 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.852 Fit side-chains REVERT: A 135 GLU cc_start: 0.8168 (tt0) cc_final: 0.7677 (pm20) REVERT: B 1 MET cc_start: 0.4131 (mtm) cc_final: 0.3518 (mtp) REVERT: B 123 GLU cc_start: 0.8025 (pm20) cc_final: 0.7785 (pt0) REVERT: B 249 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.5805 (mmt-90) REVERT: B 393 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.6906 (t80) outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.1877 time to fit residues: 16.0159 Evaluate side-chains 59 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.0050 chunk 51 optimal weight: 0.0470 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 0.8894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7938 Z= 0.131 Angle : 0.450 6.244 11106 Z= 0.225 Chirality : 0.035 0.229 1313 Planarity : 0.004 0.033 1148 Dihedral : 18.739 73.886 2045 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.41 % Allowed : 16.39 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.32), residues: 769 helix: 0.74 (0.31), residues: 325 sheet: -0.33 (0.50), residues: 107 loop : -0.99 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 240 HIS 0.003 0.001 HIS B 365 PHE 0.011 0.001 PHE A 127 TYR 0.010 0.001 TYR B 354 ARG 0.005 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.820 Fit side-chains REVERT: A 135 GLU cc_start: 0.8235 (tt0) cc_final: 0.7701 (pm20) REVERT: B 1 MET cc_start: 0.4151 (mtm) cc_final: 0.3550 (mtp) REVERT: B 123 GLU cc_start: 0.8046 (pm20) cc_final: 0.7816 (pt0) REVERT: B 249 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.5791 (mmt-90) REVERT: B 393 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.6887 (t80) outliers start: 16 outliers final: 14 residues processed: 60 average time/residue: 0.1823 time to fit residues: 15.2357 Evaluate side-chains 62 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 71 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7938 Z= 0.175 Angle : 0.487 6.301 11106 Z= 0.246 Chirality : 0.036 0.224 1313 Planarity : 0.004 0.032 1148 Dihedral : 18.753 73.992 2045 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.71 % Allowed : 16.24 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.38 (0.32), residues: 769 helix: 0.63 (0.31), residues: 326 sheet: -0.31 (0.51), residues: 107 loop : -1.06 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.004 0.001 HIS B 70 PHE 0.011 0.001 PHE A 127 TYR 0.011 0.001 TYR B 354 ARG 0.005 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 0.800 Fit side-chains REVERT: A 135 GLU cc_start: 0.8182 (tt0) cc_final: 0.7771 (pm20) REVERT: B 1 MET cc_start: 0.4156 (mtm) cc_final: 0.3557 (mtp) REVERT: B 123 GLU cc_start: 0.8114 (pm20) cc_final: 0.7890 (pt0) REVERT: B 249 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.6385 (mmt-90) REVERT: B 393 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6847 (t80) outliers start: 18 outliers final: 16 residues processed: 60 average time/residue: 0.1985 time to fit residues: 16.7505 Evaluate side-chains 63 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.0270 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 0.0870 chunk 20 optimal weight: 0.1980 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7938 Z= 0.127 Angle : 0.451 6.246 11106 Z= 0.226 Chirality : 0.035 0.231 1313 Planarity : 0.004 0.032 1148 Dihedral : 18.734 73.920 2044 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.26 % Allowed : 17.14 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 (0.32), residues: 769 helix: 0.70 (0.31), residues: 328 sheet: -0.32 (0.51), residues: 107 loop : -1.08 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 240 HIS 0.003 0.000 HIS B 365 PHE 0.010 0.001 PHE A 127 TYR 0.009 0.001 TYR B 354 ARG 0.005 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.793 Fit side-chains REVERT: A 18 ARG cc_start: 0.8202 (tmm160) cc_final: 0.7746 (ppt170) REVERT: A 135 GLU cc_start: 0.8201 (tt0) cc_final: 0.7704 (pm20) REVERT: B 1 MET cc_start: 0.4146 (mtm) cc_final: 0.3550 (mtp) REVERT: B 249 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.5917 (mmt-90) REVERT: B 341 GLN cc_start: 0.7882 (pt0) cc_final: 0.7624 (tt0) REVERT: B 393 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.6871 (t80) outliers start: 15 outliers final: 13 residues processed: 58 average time/residue: 0.2123 time to fit residues: 17.1697 Evaluate side-chains 59 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.112943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083757 restraints weight = 29281.918| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.27 r_work: 0.3053 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7938 Z= 0.167 Angle : 0.469 6.285 11106 Z= 0.236 Chirality : 0.036 0.226 1313 Planarity : 0.004 0.031 1148 Dihedral : 18.735 73.966 2044 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.86 % Allowed : 16.54 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.38 (0.31), residues: 769 helix: 0.68 (0.31), residues: 329 sheet: -0.38 (0.50), residues: 107 loop : -1.10 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.002 0.001 HIS B 359 PHE 0.011 0.001 PHE A 127 TYR 0.011 0.001 TYR B 354 ARG 0.006 0.000 ARG A 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.35 seconds wall clock time: 30 minutes 33.98 seconds (1833.98 seconds total)