Starting phenix.real_space_refine on Thu Nov 14 17:18:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orj_17127/11_2024/8orj_17127_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orj_17127/11_2024/8orj_17127.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/8orj_17127/11_2024/8orj_17127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orj_17127/11_2024/8orj_17127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orj_17127/11_2024/8orj_17127_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orj_17127/11_2024/8orj_17127_trim.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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 50 5.16 5 C 4372 2.51 5 N 1188 2.21 5 O 1314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6930 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3521 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 441} Chain breaks: 1 Chain: "B" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3310 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FDA': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 904 SG CYS A 122 38.366 31.493 70.225 1.00 51.16 S ATOM 904 SG CYS A 122 38.366 31.493 70.225 1.00 51.16 S Time building chain proxies: 5.01, per 1000 atoms: 0.72 Number of scatterers: 6930 At special positions: 0 Unit cell: (75.4, 77.35, 111.15, 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) S 50 16.00 P 4 15.00 Mg 2 11.99 O 1314 8.00 N 1188 7.00 C 4372 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: 1.90 Conformation dependent library (CDL) restraints added in 1.0 seconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1594 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 36.2% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.793A pdb=" N GLN A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 56 removed outlier: 3.736A pdb=" N LYS A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 50 " --> pdb=" O MET A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 164 through 175 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.758A pdb=" N SER A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 208 through 219 Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 264 through 284 removed outlier: 3.859A pdb=" N LYS A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 336 Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'B' and resid 19 through 33 Processing helix chain 'B' and resid 133 through 145 Processing helix chain 'B' and resid 156 through 166 removed outlier: 4.129A pdb=" N TYR B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 198 removed outlier: 3.572A pdb=" N LYS B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 323 through 328 removed outlier: 3.957A pdb=" N HIS B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 396 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 467 through 478 Processing helix chain 'B' and resid 481 through 490 removed outlier: 6.322A pdb=" N GLU B 486 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 488 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 489 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.646A pdb=" N CYS A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 13.429A pdb=" N ILE A 83 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 12.018A pdb=" N PHE A 102 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N LEU A 85 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 11.450A pdb=" N ALA A 100 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N ASP A 87 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN A 98 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 98 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 375 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 374 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.694A pdb=" N VAL A 347 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG A 128 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 349 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG A 125 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N SER A 260 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LEU A 127 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE A 258 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR A 129 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL A 256 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU A 131 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLN A 253 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 233 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASP A 235 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A 497 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 379 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 91 removed outlier: 3.768A pdb=" N GLN B 89 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 129 removed outlier: 5.907A pdb=" N LEU B 129 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET B 151 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 171 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLU B 258 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP B 173 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.847A pdb=" N LYS B 265 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 298 " --> pdb=" O CYS B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 340 through 342 removed outlier: 6.030A pdb=" N LEU B 340 " --> pdb=" O THR B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 409 through 414 removed outlier: 4.249A pdb=" N LYS B 418 " --> pdb=" O GLY B 463 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1389 1.33 - 1.45: 1641 1.45 - 1.57: 3954 1.57 - 1.70: 8 1.70 - 1.82: 80 Bond restraints: 7072 Sorted by residual: bond pdb=" N ILE B 255 " pdb=" CA ILE B 255 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.14e-02 7.69e+03 1.48e+01 bond pdb=" N ILE A 500 " pdb=" CA ILE A 500 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.06e-02 8.90e+03 1.37e+01 bond pdb=" N GLU B 468 " pdb=" CA GLU B 468 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.14e+01 bond pdb=" CZ ARG A 263 " pdb=" NH2 ARG A 263 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" N THR A 129 " pdb=" CA THR A 129 " ideal model delta sigma weight residual 1.455 1.496 -0.040 1.21e-02 6.83e+03 1.11e+01 ... (remaining 7067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6483 1.64 - 3.28: 2483 3.28 - 4.91: 506 4.91 - 6.55: 78 6.55 - 8.19: 14 Bond angle restraints: 9564 Sorted by residual: angle pdb=" CA LYS A 496 " pdb=" C LYS A 496 " pdb=" O LYS A 496 " ideal model delta sigma weight residual 121.11 113.88 7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" CB HIS A 150 " pdb=" CG HIS A 150 " pdb=" CD2 HIS A 150 " ideal model delta sigma weight residual 131.20 124.03 7.17 1.30e+00 5.92e-01 3.04e+01 angle pdb=" CB HIS B 32 " pdb=" CG HIS B 32 " pdb=" CD2 HIS B 32 " ideal model delta sigma weight residual 131.20 124.28 6.92 1.30e+00 5.92e-01 2.83e+01 angle pdb=" CA GLY A 123 " pdb=" C GLY A 123 " pdb=" O GLY A 123 " ideal model delta sigma weight residual 121.38 116.40 4.98 9.40e-01 1.13e+00 2.81e+01 angle pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " pdb=" CG ASP A 189 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.00e+00 1.00e+00 2.71e+01 ... (remaining 9559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3794 17.80 - 35.60: 327 35.60 - 53.39: 96 53.39 - 71.19: 36 71.19 - 88.99: 10 Dihedral angle restraints: 4263 sinusoidal: 1767 harmonic: 2496 Sorted by residual: dihedral pdb=" CA PHE A 118 " pdb=" C PHE A 118 " pdb=" N ASP A 119 " pdb=" CA ASP A 119 " ideal model delta harmonic sigma weight residual 180.00 156.96 23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLN B 89 " pdb=" C GLN B 89 " pdb=" N LEU B 90 " pdb=" CA LEU B 90 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" C LEU A 42 " pdb=" N LEU A 42 " pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " ideal model delta harmonic sigma weight residual -122.60 -133.96 11.36 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 4260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 554 0.070 - 0.140: 332 0.140 - 0.210: 128 0.210 - 0.280: 25 0.280 - 0.350: 7 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA LEU A 42 " pdb=" N LEU A 42 " pdb=" C LEU A 42 " pdb=" CB LEU A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA MET B 346 " pdb=" N MET B 346 " pdb=" C MET B 346 " pdb=" CB MET B 346 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA THR A 484 " pdb=" N THR A 484 " pdb=" C THR A 484 " pdb=" CB THR A 484 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1043 not shown) Planarity restraints: 1227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FDA B 602 " 0.405 2.00e-02 2.50e+03 1.74e-01 1.44e+03 pdb=" C10 FDA B 602 " 0.060 2.00e-02 2.50e+03 pdb=" C2 FDA B 602 " -0.182 2.00e-02 2.50e+03 pdb=" C4 FDA B 602 " 0.019 2.00e-02 2.50e+03 pdb=" C4X FDA B 602 " 0.111 2.00e-02 2.50e+03 pdb=" C5X FDA B 602 " 0.134 2.00e-02 2.50e+03 pdb=" C6 FDA B 602 " 0.065 2.00e-02 2.50e+03 pdb=" C7 FDA B 602 " -0.067 2.00e-02 2.50e+03 pdb=" C7M FDA B 602 " -0.150 2.00e-02 2.50e+03 pdb=" C8 FDA B 602 " -0.122 2.00e-02 2.50e+03 pdb=" C8M FDA B 602 " -0.261 2.00e-02 2.50e+03 pdb=" C9 FDA B 602 " -0.048 2.00e-02 2.50e+03 pdb=" C9A FDA B 602 " 0.082 2.00e-02 2.50e+03 pdb=" N1 FDA B 602 " -0.084 2.00e-02 2.50e+03 pdb=" N10 FDA B 602 " 0.171 2.00e-02 2.50e+03 pdb=" N3 FDA B 602 " -0.122 2.00e-02 2.50e+03 pdb=" N5 FDA B 602 " 0.263 2.00e-02 2.50e+03 pdb=" O2 FDA B 602 " -0.315 2.00e-02 2.50e+03 pdb=" O4 FDA B 602 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 601 " 0.174 2.00e-02 2.50e+03 1.26e-01 3.18e+02 pdb=" C2N NAD B 601 " -0.268 2.00e-02 2.50e+03 pdb=" C3N NAD B 601 " -0.037 2.00e-02 2.50e+03 pdb=" C4N NAD B 601 " 0.051 2.00e-02 2.50e+03 pdb=" C5N NAD B 601 " 0.017 2.00e-02 2.50e+03 pdb=" C6N NAD B 601 " -0.017 2.00e-02 2.50e+03 pdb=" C7N NAD B 601 " 0.133 2.00e-02 2.50e+03 pdb=" N1N NAD B 601 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 239 " 0.104 2.00e-02 2.50e+03 5.01e-02 6.26e+01 pdb=" CG TRP B 239 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 239 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 239 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP B 239 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP B 239 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 239 " -0.063 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 239 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 239 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 239 " 0.046 2.00e-02 2.50e+03 ... (remaining 1224 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 12 2.51 - 3.11: 4725 3.11 - 3.71: 10441 3.71 - 4.30: 15330 4.30 - 4.90: 25231 Nonbonded interactions: 55739 Sorted by model distance: nonbonded pdb=" OD2 ASP A 119 " pdb="MG MG A 602 " model vdw 1.914 2.170 nonbonded pdb=" OD2 ASP B 500 " pdb="MG MG A 602 " model vdw 1.993 2.170 nonbonded pdb=" NE2 HIS A 353 " pdb="MG MG A 601 " model vdw 2.023 2.250 nonbonded pdb=" NE2 HIS A 259 " pdb="MG MG A 601 " model vdw 2.054 2.250 nonbonded pdb=" SG CYS A 122 " pdb="MG MG A 601 " model vdw 2.064 2.530 ... (remaining 55734 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=1.00 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.890 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.012 0.060 7072 Z= 0.778 Angle : 1.751 8.188 9564 Z= 1.208 Chirality : 0.098 0.350 1046 Planarity : 0.012 0.174 1227 Dihedral : 16.332 88.988 2669 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.16 % Allowed : 9.63 % Favored : 87.21 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.27), residues: 870 helix: -0.12 (0.28), residues: 281 sheet: -0.91 (0.38), residues: 172 loop : -0.34 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.018 TRP B 239 HIS 0.015 0.004 HIS A 373 PHE 0.076 0.012 PHE B 332 TYR 0.088 0.013 TYR B 484 ARG 0.005 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 286 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7562 (mtm-85) REVERT: A 363 VAL cc_start: 0.8715 (t) cc_final: 0.8482 (t) REVERT: A 371 LEU cc_start: 0.8285 (tp) cc_final: 0.7960 (tp) REVERT: B 165 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8393 (mm-30) REVERT: B 240 HIS cc_start: 0.7058 (p-80) cc_final: 0.6126 (p-80) REVERT: B 384 TRP cc_start: 0.7699 (t60) cc_final: 0.6964 (t60) outliers start: 23 outliers final: 8 residues processed: 304 average time/residue: 0.2393 time to fit residues: 91.6084 Evaluate side-chains 160 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 29 ASN A 232 GLN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 269 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7072 Z= 0.237 Angle : 0.712 9.064 9564 Z= 0.371 Chirality : 0.048 0.210 1046 Planarity : 0.004 0.042 1227 Dihedral : 9.802 105.140 1061 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.71 % Allowed : 20.22 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 870 helix: 1.58 (0.30), residues: 282 sheet: -0.83 (0.42), residues: 152 loop : -0.43 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 364 HIS 0.008 0.001 HIS B 240 PHE 0.019 0.002 PHE B 312 TYR 0.013 0.001 TYR A 392 ARG 0.010 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8921 (mt) cc_final: 0.8692 (mt) REVERT: B 149 ARG cc_start: 0.8763 (tpp80) cc_final: 0.8429 (tpp-160) REVERT: B 170 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6873 (tp30) outliers start: 27 outliers final: 13 residues processed: 172 average time/residue: 0.2322 time to fit residues: 51.6563 Evaluate side-chains 136 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 0.0050 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7072 Z= 0.194 Angle : 0.624 7.167 9564 Z= 0.325 Chirality : 0.046 0.161 1046 Planarity : 0.003 0.031 1227 Dihedral : 8.593 109.130 1049 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.89 % Allowed : 22.28 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.28), residues: 870 helix: 1.70 (0.31), residues: 282 sheet: -0.62 (0.42), residues: 155 loop : -0.55 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 364 HIS 0.007 0.001 HIS B 32 PHE 0.025 0.002 PHE B 185 TYR 0.011 0.001 TYR A 392 ARG 0.006 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8906 (mt) cc_final: 0.8686 (mt) REVERT: A 163 MET cc_start: 0.8137 (mmp) cc_final: 0.7716 (mpp) REVERT: B 170 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: B 421 LEU cc_start: 0.8533 (mt) cc_final: 0.8240 (mt) outliers start: 21 outliers final: 12 residues processed: 141 average time/residue: 0.2129 time to fit residues: 38.7195 Evaluate side-chains 130 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 470 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 371 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7072 Z= 0.297 Angle : 0.646 10.549 9564 Z= 0.334 Chirality : 0.046 0.163 1046 Planarity : 0.004 0.042 1227 Dihedral : 8.496 116.876 1049 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.95 % Allowed : 22.70 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 870 helix: 1.53 (0.31), residues: 282 sheet: -0.48 (0.41), residues: 167 loop : -0.54 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 364 HIS 0.005 0.001 HIS B 240 PHE 0.023 0.002 PHE B 185 TYR 0.013 0.001 TYR A 392 ARG 0.005 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7534 (t0) REVERT: A 163 MET cc_start: 0.8188 (mmp) cc_final: 0.7814 (mpp) REVERT: B 170 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6861 (tp30) outliers start: 36 outliers final: 23 residues processed: 139 average time/residue: 0.2336 time to fit residues: 42.6199 Evaluate side-chains 136 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 470 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7072 Z= 0.250 Angle : 0.618 10.487 9564 Z= 0.318 Chirality : 0.045 0.137 1046 Planarity : 0.003 0.028 1227 Dihedral : 8.129 119.398 1047 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.58 % Allowed : 23.11 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.28), residues: 870 helix: 1.64 (0.31), residues: 282 sheet: -0.22 (0.45), residues: 144 loop : -0.51 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 384 HIS 0.003 0.001 HIS A 267 PHE 0.022 0.002 PHE B 185 TYR 0.011 0.001 TYR A 392 ARG 0.005 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.8698 (tpp) cc_final: 0.8438 (mmt) REVERT: B 494 ASP cc_start: 0.7439 (t0) cc_final: 0.6988 (t0) outliers start: 26 outliers final: 19 residues processed: 131 average time/residue: 0.2214 time to fit residues: 37.7130 Evaluate side-chains 127 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7072 Z= 0.274 Angle : 0.617 9.981 9564 Z= 0.319 Chirality : 0.045 0.136 1046 Planarity : 0.003 0.026 1227 Dihedral : 8.005 121.848 1047 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.85 % Allowed : 22.97 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 870 helix: 1.59 (0.31), residues: 281 sheet: -0.22 (0.45), residues: 144 loop : -0.56 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 384 HIS 0.005 0.001 HIS A 267 PHE 0.023 0.002 PHE B 185 TYR 0.012 0.001 TYR A 392 ARG 0.008 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.803 Fit side-chains REVERT: A 12 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 121 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7593 (t0) REVERT: B 494 ASP cc_start: 0.7428 (t0) cc_final: 0.7187 (t70) outliers start: 28 outliers final: 24 residues processed: 127 average time/residue: 0.2249 time to fit residues: 36.9807 Evaluate side-chains 126 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7072 Z= 0.288 Angle : 0.637 9.841 9564 Z= 0.328 Chirality : 0.045 0.137 1046 Planarity : 0.003 0.032 1227 Dihedral : 7.954 122.616 1047 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.13 % Allowed : 23.11 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 870 helix: 1.60 (0.31), residues: 281 sheet: -0.36 (0.45), residues: 146 loop : -0.59 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 384 HIS 0.005 0.001 HIS A 267 PHE 0.024 0.002 PHE B 185 TYR 0.011 0.001 TYR A 392 ARG 0.009 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.941 Fit side-chains REVERT: A 12 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8613 (mp) REVERT: A 99 MET cc_start: 0.8707 (ppp) cc_final: 0.8476 (ppp) REVERT: B 421 LEU cc_start: 0.8556 (mt) cc_final: 0.8118 (mt) outliers start: 30 outliers final: 24 residues processed: 124 average time/residue: 0.2204 time to fit residues: 36.1796 Evaluate side-chains 124 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7072 Z= 0.192 Angle : 0.637 10.245 9564 Z= 0.321 Chirality : 0.045 0.156 1046 Planarity : 0.003 0.028 1227 Dihedral : 7.640 118.537 1047 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.03 % Allowed : 24.48 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 870 helix: 1.65 (0.31), residues: 281 sheet: -0.22 (0.46), residues: 143 loop : -0.65 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 384 HIS 0.006 0.001 HIS A 267 PHE 0.027 0.001 PHE B 185 TYR 0.012 0.001 TYR B 425 ARG 0.017 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.810 Fit side-chains REVERT: A 12 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8406 (mp) REVERT: A 66 MET cc_start: 0.8034 (mtt) cc_final: 0.7793 (mtt) REVERT: A 99 MET cc_start: 0.8735 (ppp) cc_final: 0.8532 (ppp) REVERT: B 172 ILE cc_start: 0.8643 (pt) cc_final: 0.8284 (pt) outliers start: 22 outliers final: 18 residues processed: 137 average time/residue: 0.2110 time to fit residues: 37.8539 Evaluate side-chains 124 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7072 Z= 0.271 Angle : 0.694 9.810 9564 Z= 0.354 Chirality : 0.046 0.185 1046 Planarity : 0.003 0.031 1227 Dihedral : 7.715 119.728 1047 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.71 % Allowed : 24.48 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 870 helix: 1.50 (0.31), residues: 282 sheet: -0.23 (0.45), residues: 143 loop : -0.63 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 384 HIS 0.005 0.001 HIS A 267 PHE 0.024 0.002 PHE B 185 TYR 0.011 0.001 TYR B 425 ARG 0.013 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.826 Fit side-chains REVERT: A 12 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 66 MET cc_start: 0.8064 (mtt) cc_final: 0.7818 (mtt) outliers start: 27 outliers final: 21 residues processed: 131 average time/residue: 0.2077 time to fit residues: 36.1323 Evaluate side-chains 130 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 495 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7072 Z= 0.218 Angle : 0.680 10.185 9564 Z= 0.346 Chirality : 0.046 0.185 1046 Planarity : 0.003 0.032 1227 Dihedral : 7.698 121.103 1047 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.03 % Allowed : 24.90 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.28), residues: 870 helix: 1.40 (0.31), residues: 282 sheet: -0.30 (0.45), residues: 141 loop : -0.58 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 384 HIS 0.006 0.001 HIS A 267 PHE 0.025 0.001 PHE B 185 TYR 0.013 0.001 TYR B 425 ARG 0.014 0.001 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.830 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 125 average time/residue: 0.2079 time to fit residues: 34.4394 Evaluate side-chains 126 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.0370 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.062365 restraints weight = 20653.533| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.84 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7072 Z= 0.192 Angle : 0.678 10.280 9564 Z= 0.346 Chirality : 0.046 0.177 1046 Planarity : 0.003 0.031 1227 Dihedral : 7.554 119.104 1047 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.48 % Allowed : 25.58 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.28), residues: 870 helix: 1.38 (0.30), residues: 287 sheet: -0.25 (0.45), residues: 143 loop : -0.56 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 384 HIS 0.005 0.001 HIS A 267 PHE 0.024 0.001 PHE B 185 TYR 0.020 0.001 TYR A 241 ARG 0.013 0.001 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1749.08 seconds wall clock time: 39 minutes 46.83 seconds (2386.83 seconds total)