Starting phenix.real_space_refine on Thu Sep 26 21:03:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/09_2024/8omr_16976.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/09_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_16976/09_2024/8omr_16976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/09_2024/8omr_16976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/09_2024/8omr_16976.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omr_16976/09_2024/8omr_16976.cif" } 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. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 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: 6.78, per 1000 atoms: 0.89 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 35 helices and 10 sheets defined 47.9% alpha, 11.8% beta 23 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.581A pdb=" N GLY A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.571A pdb=" N ILE A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 169 through 189 Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 235 through 250 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 263 through 274 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.554A pdb=" N ARG A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.911A pdb=" N PHE A 306 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 removed outlier: 4.065A pdb=" N LYS A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 325' Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.625A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N AHIS A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 341 through 366 removed outlier: 4.244A pdb=" N LEU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 347 " --> pdb=" O HIS A 343 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 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 383 through 387 removed outlier: 4.216A pdb=" N CYS A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 399 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 46 through 51 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.521A pdb=" N PHE B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.071A pdb=" N SER B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS B 151 " --> pdb=" O GLU B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 156 through 181 removed outlier: 3.820A pdb=" N VAL B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.718A pdb=" N LYS B 186 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 4.159A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.830A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 264 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) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 373 through 401 removed outlier: 3.844A pdb=" N VAL B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) 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 402 through 412 removed outlier: 3.874A pdb=" N LEU B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 6.732A pdb=" N MET A 17 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TRP A 34 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A 19 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU A 32 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing sheet with id=AA2, 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=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 72 removed outlier: 3.562A pdb=" N ILE A 154 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET A 156 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 224 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 199 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 9 removed outlier: 5.665A pdb=" N LEU B 5 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS B 16 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 7 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 9 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 15 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.825A pdb=" N GLY B 32 " --> pdb=" O PHE B 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.917A pdb=" N LEU B 35 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR B 63 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 93 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS B 94 " --> pdb=" O TRP B 140 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 142 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE B 141 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N VAL B 192 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 113 through 117 Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 286 244 hydrogen bonds defined for protein. 699 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: 2.17 Time building geometry restraints manager: 2.09 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: 0.00 - 2.42: 10715 2.42 - 4.83: 345 4.83 - 7.25: 41 7.25 - 9.66: 4 9.66 - 12.08: 1 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: 2730 2.87 - 3.54: 10057 3.54 - 4.22: 17336 4.22 - 4.90: 28650 Nonbonded interactions: 58774 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 3.120 nonbonded pdb=" O MET A 175 " pdb=" OG SER A 178 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN B 110 " pdb=" NE ARG B 166 " model vdw 2.232 3.120 ... (remaining 58769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.040 Find NCS groups from input model: 0.090 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- 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= 0.617 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 : 0.742 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: 0.2146 time to fit residues: 25.7113 Evaluate side-chains 79 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 40 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1347 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= 0.206 Angle : 0.596 7.031 11106 Z= 0.308 Chirality : 0.040 0.208 1313 Planarity : 0.004 0.038 1148 Dihedral : 19.085 132.675 2095 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.76 % Allowed : 10.83 % Favored : 85.41 % 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: -0.85 (0.30), residues: 769 helix: 0.62 (0.30), residues: 325 sheet: -0.81 (0.54), residues: 100 loop : -1.66 (0.31), residues: 344 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 0.014 0.001 PHE A 127 TYR 0.012 0.001 TYR B 354 ARG 0.010 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 73 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 48 time to evaluate : 0.775 Fit side-chains REVERT: A 135 GLU cc_start: 0.8109 (tt0) cc_final: 0.7777 (pm20) REVERT: A 368 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6883 (ptm160) REVERT: B 1 MET cc_start: 0.4159 (mtm) cc_final: 0.3456 (mtp) REVERT: B 97 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7342 (p90) REVERT: B 123 GLU cc_start: 0.8315 (pm20) cc_final: 0.8037 (pt0) REVERT: B 230 GLU cc_start: 0.8753 (tp30) cc_final: 0.8540 (mm-30) REVERT: B 249 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7528 (mmt-90) REVERT: B 393 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7128 (t80) outliers start: 25 outliers final: 16 residues processed: 70 average time/residue: 0.1905 time to fit residues: 18.4086 Evaluate side-chains 60 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 40 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 182 LEU 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 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 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: 6.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 0.0270 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1770 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= 0.170 Angle : 0.538 6.398 11106 Z= 0.274 Chirality : 0.037 0.201 1313 Planarity : 0.004 0.034 1148 Dihedral : 18.946 105.695 2067 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.01 % Allowed : 12.93 % Favored : 84.06 % 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: -0.60 (0.31), residues: 769 helix: 0.74 (0.30), residues: 341 sheet: -0.73 (0.51), residues: 110 loop : -1.51 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 240 HIS 0.003 0.001 HIS B 365 PHE 0.012 0.001 PHE A 127 TYR 0.010 0.001 TYR B 354 ARG 0.005 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 67 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 0.738 Fit side-chains REVERT: A 135 GLU cc_start: 0.8197 (tt0) cc_final: 0.7819 (pm20) REVERT: A 197 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8591 (tt) REVERT: B 1 MET cc_start: 0.4196 (mtm) cc_final: 0.3533 (mtp) REVERT: B 97 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7351 (p90) REVERT: B 123 GLU cc_start: 0.8274 (pm20) cc_final: 0.7970 (pt0) REVERT: B 249 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.5534 (mmt-90) REVERT: B 393 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7101 (t80) outliers start: 20 outliers final: 13 residues processed: 65 average time/residue: 0.1957 time to fit residues: 17.7190 Evaluate side-chains 60 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 197 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 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: 10.0000 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 8 optimal weight: 0.0970 chunk 36 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7938 Z= 0.338 Angle : 0.620 6.564 11106 Z= 0.320 Chirality : 0.041 0.211 1313 Planarity : 0.004 0.035 1148 Dihedral : 18.998 89.506 2056 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.91 % Allowed : 13.23 % Favored : 82.86 % 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: -0.87 (0.30), residues: 769 helix: 0.58 (0.30), residues: 341 sheet: -0.83 (0.58), residues: 86 loop : -1.70 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 240 HIS 0.005 0.001 HIS B 366 PHE 0.017 0.002 PHE B 331 TYR 0.013 0.002 TYR B 354 ARG 0.005 0.000 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 70 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 44 time to evaluate : 0.739 Fit side-chains REVERT: A 135 GLU cc_start: 0.8182 (tt0) cc_final: 0.7830 (pm20) REVERT: B 1 MET cc_start: 0.4159 (mtm) cc_final: 0.3523 (mtp) REVERT: B 97 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7433 (p90) REVERT: B 123 GLU cc_start: 0.8363 (pm20) cc_final: 0.7958 (pt0) REVERT: B 230 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8468 (mm-30) REVERT: B 249 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7579 (mmt-90) REVERT: B 264 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7468 (mt) REVERT: B 393 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7124 (t80) outliers start: 26 outliers final: 19 residues processed: 65 average time/residue: 0.1977 time to fit residues: 17.5672 Evaluate side-chains 64 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 41 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain A residue 112 VAL 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 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 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: 6.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1828 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= 0.207 Angle : 0.538 6.350 11106 Z= 0.277 Chirality : 0.038 0.217 1313 Planarity : 0.004 0.034 1148 Dihedral : 18.987 74.060 2056 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.16 % Allowed : 13.83 % Favored : 83.01 % 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: -0.67 (0.31), residues: 769 helix: 0.73 (0.30), residues: 341 sheet: -0.70 (0.51), residues: 107 loop : -1.62 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 240 HIS 0.003 0.001 HIS A 344 PHE 0.013 0.001 PHE A 127 TYR 0.010 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 67 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 46 time to evaluate : 0.731 Fit side-chains REVERT: A 135 GLU cc_start: 0.8183 (tt0) cc_final: 0.7817 (pm20) REVERT: B 1 MET cc_start: 0.4135 (mtm) cc_final: 0.3499 (mtp) REVERT: B 97 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7363 (p90) REVERT: B 123 GLU cc_start: 0.8299 (pm20) cc_final: 0.7936 (pt0) REVERT: B 230 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8487 (mm-30) REVERT: B 249 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.6015 (mmt-90) REVERT: B 393 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.7049 (t80) outliers start: 21 outliers final: 18 residues processed: 64 average time/residue: 0.2077 time to fit residues: 18.2013 Evaluate side-chains 64 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain A residue 112 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 0.0070 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2292 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= 0.129 Angle : 0.474 6.145 11106 Z= 0.242 Chirality : 0.036 0.221 1313 Planarity : 0.004 0.034 1148 Dihedral : 18.900 73.933 2056 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.01 % Allowed : 13.83 % 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: -0.35 (0.31), residues: 769 helix: 1.04 (0.31), residues: 339 sheet: -0.78 (0.48), residues: 119 loop : -1.40 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 240 HIS 0.002 0.000 HIS B 359 PHE 0.011 0.001 PHE A 127 TYR 0.008 0.001 TYR B 354 ARG 0.008 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 67 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 0.738 Fit side-chains REVERT: A 135 GLU cc_start: 0.8228 (tt0) cc_final: 0.7779 (pm20) REVERT: A 197 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8603 (tt) REVERT: B 1 MET cc_start: 0.4190 (mtm) cc_final: 0.3560 (mtp) REVERT: B 123 GLU cc_start: 0.8250 (pm20) cc_final: 0.7961 (pt0) REVERT: B 230 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8530 (mm-30) REVERT: B 249 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6207 (mmt-90) REVERT: B 393 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7076 (t80) outliers start: 20 outliers final: 14 residues processed: 65 average time/residue: 0.1853 time to fit residues: 16.8817 Evaluate side-chains 60 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain A residue 197 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 37 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7938 Z= 0.281 Angle : 0.557 6.470 11106 Z= 0.288 Chirality : 0.039 0.222 1313 Planarity : 0.004 0.045 1148 Dihedral : 18.969 74.065 2053 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.76 % Allowed : 13.68 % Favored : 82.56 % 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: -0.60 (0.31), residues: 769 helix: 0.82 (0.30), residues: 341 sheet: -0.77 (0.50), residues: 107 loop : -1.59 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 240 HIS 0.004 0.001 HIS A 344 PHE 0.014 0.002 PHE A 127 TYR 0.012 0.001 TYR B 354 ARG 0.005 0.000 ARG A 18 *********************** 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 67 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 42 time to evaluate : 0.725 Fit side-chains REVERT: A 135 GLU cc_start: 0.8178 (tt0) cc_final: 0.7801 (pm20) REVERT: A 197 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8586 (tt) REVERT: B 1 MET cc_start: 0.4180 (mtm) cc_final: 0.3543 (mtp) REVERT: B 97 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7390 (p90) REVERT: B 123 GLU cc_start: 0.8273 (pm20) cc_final: 0.7881 (pt0) REVERT: B 230 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8516 (mm-30) REVERT: B 249 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.5976 (mmt-90) REVERT: B 393 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7048 (t80) outliers start: 25 outliers final: 21 residues processed: 63 average time/residue: 0.1977 time to fit residues: 17.3668 Evaluate side-chains 66 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 41 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 LEU 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 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 97 HIS Chi-restraints excluded: chain B residue 155 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 369 VAL 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: 0.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 0.0170 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7938 Z= 0.176 Angle : 0.508 6.264 11106 Z= 0.261 Chirality : 0.037 0.233 1313 Planarity : 0.004 0.033 1148 Dihedral : 18.931 74.035 2053 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.91 % Allowed : 13.53 % Favored : 82.56 % 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: -0.44 (0.31), residues: 769 helix: 0.93 (0.31), residues: 341 sheet: -0.70 (0.50), residues: 112 loop : -1.49 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 240 HIS 0.003 0.001 HIS B 359 PHE 0.011 0.001 PHE A 127 TYR 0.009 0.001 TYR B 354 ARG 0.006 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 70 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 44 time to evaluate : 0.726 Fit side-chains REVERT: A 135 GLU cc_start: 0.8184 (tt0) cc_final: 0.7804 (pm20) REVERT: A 197 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8574 (tt) REVERT: B 1 MET cc_start: 0.4143 (mtm) cc_final: 0.3514 (mtp) REVERT: B 97 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7365 (p90) REVERT: B 123 GLU cc_start: 0.8224 (pm20) cc_final: 0.7848 (pt0) REVERT: B 230 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8516 (mm-30) REVERT: B 249 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6315 (mmt-90) REVERT: B 393 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.7073 (t80) outliers start: 26 outliers final: 22 residues processed: 67 average time/residue: 0.1800 time to fit residues: 17.1432 Evaluate side-chains 70 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 44 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 LEU 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 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 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 91 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 155 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 369 VAL 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: 7.9990 chunk 77 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2226 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= 0.172 Angle : 0.502 6.279 11106 Z= 0.257 Chirality : 0.037 0.237 1313 Planarity : 0.004 0.033 1148 Dihedral : 18.869 73.989 2053 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.06 % Allowed : 13.23 % Favored : 82.71 % 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: -0.36 (0.31), residues: 769 helix: 0.98 (0.31), residues: 341 sheet: -0.68 (0.49), residues: 112 loop : -1.40 (0.32), residues: 316 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 0.012 0.001 PHE A 127 TYR 0.009 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 71 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 44 time to evaluate : 0.735 Fit side-chains REVERT: A 135 GLU cc_start: 0.8200 (tt0) cc_final: 0.7808 (pm20) REVERT: A 197 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8564 (tt) REVERT: B 1 MET cc_start: 0.4127 (mtm) cc_final: 0.3503 (mtp) REVERT: B 97 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7338 (p90) REVERT: B 123 GLU cc_start: 0.8212 (pm20) cc_final: 0.7838 (pt0) REVERT: B 230 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8532 (mm-30) REVERT: B 249 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6389 (mmt-90) REVERT: B 393 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7083 (t80) outliers start: 27 outliers final: 23 residues processed: 68 average time/residue: 0.1809 time to fit residues: 17.5735 Evaluate side-chains 69 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 42 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 LEU 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 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 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 91 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 155 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 369 VAL 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: 0.7980 chunk 55 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2097 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= 0.235 Angle : 0.539 6.351 11106 Z= 0.278 Chirality : 0.038 0.233 1313 Planarity : 0.004 0.033 1148 Dihedral : 18.902 74.045 2053 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.21 % Allowed : 13.68 % Favored : 82.11 % 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: -0.55 (0.31), residues: 769 helix: 0.85 (0.30), residues: 341 sheet: -0.86 (0.51), residues: 102 loop : -1.51 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 240 HIS 0.004 0.001 HIS A 344 PHE 0.012 0.002 PHE A 127 TYR 0.010 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 70 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 42 time to evaluate : 0.663 Fit side-chains REVERT: A 135 GLU cc_start: 0.8222 (tt0) cc_final: 0.7834 (pm20) REVERT: A 197 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8576 (tt) REVERT: B 1 MET cc_start: 0.4168 (mtm) cc_final: 0.3552 (mtp) REVERT: B 97 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7362 (p90) REVERT: B 123 GLU cc_start: 0.8230 (pm20) cc_final: 0.7833 (pt0) REVERT: B 230 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8531 (mm-30) REVERT: B 249 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6125 (mmt-90) REVERT: B 393 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7065 (t80) outliers start: 28 outliers final: 23 residues processed: 66 average time/residue: 0.1819 time to fit residues: 16.9351 Evaluate side-chains 68 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 41 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 LEU 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 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 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 91 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 155 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 369 VAL 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: 5.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.113315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.084430 restraints weight = 28705.049| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.23 r_work: 0.3070 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7938 Z= 0.146 Angle : 0.484 6.223 11106 Z= 0.248 Chirality : 0.036 0.235 1313 Planarity : 0.004 0.033 1148 Dihedral : 18.867 74.016 2053 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.46 % Allowed : 14.44 % Favored : 82.11 % 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: -0.27 (0.31), residues: 769 helix: 1.04 (0.31), residues: 342 sheet: -0.74 (0.51), residues: 107 loop : -1.28 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 240 HIS 0.003 0.001 HIS B 359 PHE 0.011 0.001 PHE A 127 TYR 0.008 0.001 TYR B 354 ARG 0.005 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1610.39 seconds wall clock time: 29 minutes 29.24 seconds (1769.24 seconds total)