Starting phenix.real_space_refine on Tue Jul 29 07:09:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z85_39838/07_2025/8z85_39838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z85_39838/07_2025/8z85_39838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z85_39838/07_2025/8z85_39838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z85_39838/07_2025/8z85_39838.map" model { file = "/net/cci-nas-00/data/ceres_data/8z85_39838/07_2025/8z85_39838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z85_39838/07_2025/8z85_39838.cif" } resolution = 2.3 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= 0.006 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 1075 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: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 63 5.16 5 C 6585 2.51 5 N 1804 2.21 5 O 1998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10467 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4771 Classifications: {'peptide': 591} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 561} Chain breaks: 2 Chain: "B" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4702 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 31, 'TRANS': 558} Chain breaks: 2 Chain: "C" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 608 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain breaks: 1 Chain: "D" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 283 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "E" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Time building chain proxies: 6.80, per 1000 atoms: 0.65 Number of scatterers: 10467 At special positions: 0 Unit cell: (92.402, 100.708, 126.663, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 17 15.00 O 1998 8.00 N 1804 7.00 C 6585 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: 2.86 Conformation dependent library (CDL) restraints added in 2.3 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 49.6% alpha, 11.6% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.752A pdb=" N LEU A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 155 removed outlier: 4.745A pdb=" N GLY A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N CYS A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.965A pdb=" N GLN A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.526A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.999A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.433A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.710A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 517 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.810A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 4.014A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 13 through 20 removed outlier: 4.244A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 47 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 95 through 108 removed outlier: 3.622A pdb=" N LYS B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.713A pdb=" N LYS B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.652A pdb=" N GLU B 117 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.543A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.127A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.728A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 Proline residue: B 338 - end of helix removed outlier: 3.557A pdb=" N SER B 344 " --> pdb=" O MET B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 removed outlier: 4.429A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 3.618A pdb=" N SER B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 449 removed outlier: 3.552A pdb=" N LYS B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 459 removed outlier: 3.774A pdb=" N CYS B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.674A pdb=" N TYR B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.594A pdb=" N MET B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'C' and resid 52 through 55 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.921A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.688A pdb=" N LYS C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.782A pdb=" N LEU A 117 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 removed outlier: 4.503A pdb=" N ASN B 453 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 238 removed outlier: 4.253A pdb=" N ILE A 450 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 423 through 431 current: chain 'A' and resid 463 through 469 removed outlier: 6.757A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.141A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 442 through 451 current: chain 'A' and resid 290 through 291 Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245 removed outlier: 4.587A pdb=" N THR B 228 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 469 Processing sheet with id=AB3, first strand: chain 'B' and resid 633 through 634 removed outlier: 4.697A pdb=" N THR B 633 " --> pdb=" O SER C 68 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2846 1.33 - 1.45: 1854 1.45 - 1.57: 5896 1.57 - 1.69: 33 1.69 - 1.81: 105 Bond restraints: 10734 Sorted by residual: bond pdb=" CA LYS A 170 " pdb=" CB LYS A 170 " ideal model delta sigma weight residual 1.518 1.541 -0.023 2.08e-02 2.31e+03 1.27e+00 bond pdb=" C ALA A 169 " pdb=" N LYS A 170 " ideal model delta sigma weight residual 1.325 1.338 -0.013 1.14e-02 7.69e+03 1.25e+00 bond pdb=" CA VAL B 491 " pdb=" CB VAL B 491 " ideal model delta sigma weight residual 1.546 1.538 0.009 8.80e-03 1.29e+04 9.61e-01 bond pdb=" CA ILE A 414 " pdb=" CB ILE A 414 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 8.37e-01 bond pdb=" CB MET B 526 " pdb=" CG MET B 526 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.58e-01 ... (remaining 10729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 14303 1.38 - 2.76: 245 2.76 - 4.14: 59 4.14 - 5.51: 13 5.51 - 6.89: 3 Bond angle restraints: 14623 Sorted by residual: angle pdb=" N GLY B 352 " pdb=" CA GLY B 352 " pdb=" C GLY B 352 " ideal model delta sigma weight residual 112.04 116.98 -4.94 1.02e+00 9.61e-01 2.35e+01 angle pdb=" C LYS A 170 " pdb=" CA LYS A 170 " pdb=" CB LYS A 170 " ideal model delta sigma weight residual 115.79 111.83 3.96 1.19e+00 7.06e-01 1.11e+01 angle pdb=" C SER B 8 " pdb=" N GLU B 9 " pdb=" CA GLU B 9 " ideal model delta sigma weight residual 121.54 126.53 -4.99 1.91e+00 2.74e-01 6.82e+00 angle pdb=" C TYR B 210 " pdb=" N THR B 211 " pdb=" CA THR B 211 " ideal model delta sigma weight residual 121.54 126.05 -4.51 1.91e+00 2.74e-01 5.58e+00 angle pdb=" CB MET A 546 " pdb=" CG MET A 546 " pdb=" SD MET A 546 " ideal model delta sigma weight residual 112.70 105.81 6.89 3.00e+00 1.11e-01 5.28e+00 ... (remaining 14618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5978 17.19 - 34.38: 428 34.38 - 51.58: 80 51.58 - 68.77: 29 68.77 - 85.96: 15 Dihedral angle restraints: 6530 sinusoidal: 2854 harmonic: 3676 Sorted by residual: dihedral pdb=" CA MET A 546 " pdb=" C MET A 546 " pdb=" N ILE A 547 " pdb=" CA ILE A 547 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ILE B 212 " pdb=" C ILE B 212 " pdb=" N LYS B 213 " pdb=" CA LYS B 213 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CG ARG A 570 " pdb=" CD ARG A 570 " pdb=" NE ARG A 570 " pdb=" CZ ARG A 570 " ideal model delta sinusoidal sigma weight residual 180.00 135.09 44.91 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 6527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1025 0.027 - 0.055: 390 0.055 - 0.082: 132 0.082 - 0.109: 73 0.109 - 0.136: 25 Chirality restraints: 1645 Sorted by residual: chirality pdb=" CA ILE B 460 " pdb=" N ILE B 460 " pdb=" C ILE B 460 " pdb=" CB ILE B 460 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE A 480 " pdb=" N ILE A 480 " pdb=" C ILE A 480 " pdb=" CB ILE A 480 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1642 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 555 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO B 556 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 556 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 556 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 418 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 419 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 108 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO A 109 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.023 5.00e-02 4.00e+02 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1798 2.77 - 3.30: 10157 3.30 - 3.83: 18189 3.83 - 4.37: 22434 4.37 - 4.90: 36834 Nonbonded interactions: 89412 Sorted by model distance: nonbonded pdb=" O SER A 482 " pdb=" O2' A D 3 " model vdw 2.234 3.040 nonbonded pdb=" OE2 GLU A 122 " pdb=" NZ LYS B 109 " model vdw 2.263 3.120 nonbonded pdb=" NH2 ARG A 264 " pdb=" O TYR A 459 " model vdw 2.292 3.120 nonbonded pdb=" OD2 ASP B 362 " pdb=" NZ LYS B 364 " model vdw 2.296 3.120 nonbonded pdb=" OD1 ASN B 11 " pdb=" OG1 THR B 14 " model vdw 2.298 3.040 ... (remaining 89407 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.350 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 : 0.002 0.029 10734 Z= 0.095 Angle : 0.484 6.893 14623 Z= 0.249 Chirality : 0.038 0.136 1645 Planarity : 0.004 0.044 1804 Dihedral : 13.262 85.961 4144 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.02 (0.23), residues: 1240 helix: 0.58 (0.22), residues: 543 sheet: 0.43 (0.46), residues: 123 loop : -0.55 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.006 0.001 HIS B 476 PHE 0.017 0.001 PHE A 483 TYR 0.015 0.001 TYR B 22 ARG 0.008 0.000 ARG B 131 Details of bonding type rmsd hydrogen bonds : bond 0.24420 ( 455) hydrogen bonds : angle 7.23443 ( 1288) covalent geometry : bond 0.00209 (10734) covalent geometry : angle 0.48408 (14623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.7519 (m110) cc_final: 0.7080 (m110) REVERT: B 422 ASP cc_start: 0.7675 (p0) cc_final: 0.7249 (p0) REVERT: B 575 ASP cc_start: 0.8128 (t70) cc_final: 0.7884 (t70) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 1.5428 time to fit residues: 262.2927 Evaluate side-chains 130 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 311 GLN A 516 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 132 ASN B 148 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082925 restraints weight = 13926.169| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.09 r_work: 0.2843 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10734 Z= 0.153 Angle : 0.581 7.407 14623 Z= 0.299 Chirality : 0.043 0.182 1645 Planarity : 0.005 0.049 1804 Dihedral : 10.234 73.017 1629 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.61 % Allowed : 7.23 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1240 helix: 1.21 (0.22), residues: 559 sheet: -0.02 (0.45), residues: 128 loop : -0.40 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.005 0.001 HIS A 577 PHE 0.018 0.002 PHE A 483 TYR 0.018 0.002 TYR A 489 ARG 0.013 0.001 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 455) hydrogen bonds : angle 4.84865 ( 1288) covalent geometry : bond 0.00349 (10734) covalent geometry : angle 0.58114 (14623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.8740 (m110) cc_final: 0.8523 (m110) REVERT: B 93 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7888 (mpp80) REVERT: B 332 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8003 (mmm) REVERT: C 68 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8489 (p) outliers start: 18 outliers final: 5 residues processed: 138 average time/residue: 1.7371 time to fit residues: 254.5321 Evaluate side-chains 138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 25 optimal weight: 8.9990 chunk 59 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 311 GLN A 358 ASN A 516 ASN B 148 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.119607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.080562 restraints weight = 14179.999| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.10 r_work: 0.2826 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10734 Z= 0.150 Angle : 0.541 7.865 14623 Z= 0.279 Chirality : 0.042 0.177 1645 Planarity : 0.004 0.038 1804 Dihedral : 10.251 73.107 1629 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.32 % Allowed : 8.74 % Favored : 88.94 % 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: 0.66 (0.24), residues: 1240 helix: 1.47 (0.22), residues: 559 sheet: -0.27 (0.43), residues: 130 loop : -0.41 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS B 476 PHE 0.016 0.001 PHE A 483 TYR 0.015 0.001 TYR B 533 ARG 0.007 0.000 ARG B 151 Details of bonding type rmsd hydrogen bonds : bond 0.04572 ( 455) hydrogen bonds : angle 4.51082 ( 1288) covalent geometry : bond 0.00344 (10734) covalent geometry : angle 0.54094 (14623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8438 (mmmm) REVERT: B 17 GLU cc_start: 0.8595 (pt0) cc_final: 0.8286 (pt0) REVERT: B 131 ARG cc_start: 0.8571 (ptt90) cc_final: 0.8311 (ptt90) REVERT: B 332 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7729 (mmm) REVERT: B 383 ASN cc_start: 0.8797 (t0) cc_final: 0.8343 (t0) REVERT: B 588 GLU cc_start: 0.7889 (tp30) cc_final: 0.7615 (tp30) outliers start: 26 outliers final: 12 residues processed: 147 average time/residue: 1.5942 time to fit residues: 248.9322 Evaluate side-chains 140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 516 ASN A 577 HIS B 148 GLN B 476 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.077428 restraints weight = 13900.319| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.07 r_work: 0.2772 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10734 Z= 0.228 Angle : 0.589 7.232 14623 Z= 0.306 Chirality : 0.045 0.177 1645 Planarity : 0.005 0.046 1804 Dihedral : 10.374 72.931 1629 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.59 % Allowed : 9.37 % Favored : 88.05 % 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: 0.50 (0.23), residues: 1240 helix: 1.38 (0.22), residues: 559 sheet: -0.45 (0.43), residues: 130 loop : -0.51 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 426 HIS 0.005 0.001 HIS A 577 PHE 0.015 0.002 PHE B 48 TYR 0.026 0.002 TYR A 489 ARG 0.010 0.001 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 455) hydrogen bonds : angle 4.50443 ( 1288) covalent geometry : bond 0.00536 (10734) covalent geometry : angle 0.58949 (14623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8420 (mmmm) REVERT: B 17 GLU cc_start: 0.8671 (pt0) cc_final: 0.8336 (pt0) REVERT: B 151 ARG cc_start: 0.8588 (mmt90) cc_final: 0.8374 (mmm160) REVERT: B 332 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.7914 (mmm) REVERT: B 436 MET cc_start: 0.9129 (ttp) cc_final: 0.8896 (ttp) outliers start: 29 outliers final: 12 residues processed: 142 average time/residue: 1.6714 time to fit residues: 251.5829 Evaluate side-chains 141 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 7 optimal weight: 40.0000 chunk 105 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.081076 restraints weight = 13846.946| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.06 r_work: 0.2847 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10734 Z= 0.107 Angle : 0.496 5.195 14623 Z= 0.256 Chirality : 0.040 0.160 1645 Planarity : 0.004 0.037 1804 Dihedral : 10.195 73.281 1629 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.87 % Allowed : 10.17 % Favored : 87.96 % 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: 0.74 (0.24), residues: 1240 helix: 1.65 (0.22), residues: 560 sheet: -0.50 (0.43), residues: 130 loop : -0.43 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 330 HIS 0.003 0.001 HIS A 577 PHE 0.012 0.001 PHE B 214 TYR 0.016 0.001 TYR B 533 ARG 0.009 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 455) hydrogen bonds : angle 4.27127 ( 1288) covalent geometry : bond 0.00237 (10734) covalent geometry : angle 0.49643 (14623) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8461 (mmmm) REVERT: A 489 TYR cc_start: 0.9130 (t80) cc_final: 0.8922 (t80) REVERT: B 17 GLU cc_start: 0.8575 (pt0) cc_final: 0.8273 (pt0) REVERT: B 93 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7969 (mtm-85) REVERT: B 131 ARG cc_start: 0.8454 (ptt90) cc_final: 0.8204 (ptt90) outliers start: 21 outliers final: 9 residues processed: 139 average time/residue: 1.8283 time to fit residues: 269.4034 Evaluate side-chains 138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.120066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.080736 restraints weight = 13847.013| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.06 r_work: 0.2836 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10734 Z= 0.118 Angle : 0.501 5.157 14623 Z= 0.257 Chirality : 0.040 0.155 1645 Planarity : 0.004 0.050 1804 Dihedral : 10.176 73.180 1629 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.23 % Allowed : 10.53 % Favored : 87.24 % 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: 0.78 (0.24), residues: 1240 helix: 1.71 (0.22), residues: 561 sheet: -0.50 (0.43), residues: 130 loop : -0.42 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS A 577 PHE 0.011 0.001 PHE B 214 TYR 0.016 0.001 TYR A 489 ARG 0.012 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 455) hydrogen bonds : angle 4.21154 ( 1288) covalent geometry : bond 0.00269 (10734) covalent geometry : angle 0.50057 (14623) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8433 (mmmm) REVERT: B 17 GLU cc_start: 0.8581 (pt0) cc_final: 0.8274 (pt0) REVERT: B 131 ARG cc_start: 0.8409 (ptt90) cc_final: 0.8116 (ptt90) REVERT: B 332 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8296 (mtm) REVERT: C 56 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7800 (ttp-110) outliers start: 25 outliers final: 10 residues processed: 143 average time/residue: 1.5219 time to fit residues: 231.3568 Evaluate side-chains 138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 516 ASN B 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.079742 restraints weight = 13951.203| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.06 r_work: 0.2788 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10734 Z= 0.138 Angle : 0.521 6.166 14623 Z= 0.267 Chirality : 0.041 0.158 1645 Planarity : 0.004 0.051 1804 Dihedral : 10.196 73.157 1629 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.05 % Allowed : 11.33 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1240 helix: 1.69 (0.22), residues: 562 sheet: -0.56 (0.43), residues: 130 loop : -0.42 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.006 0.001 HIS B 475 PHE 0.011 0.001 PHE B 214 TYR 0.016 0.001 TYR B 533 ARG 0.012 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 455) hydrogen bonds : angle 4.21233 ( 1288) covalent geometry : bond 0.00320 (10734) covalent geometry : angle 0.52092 (14623) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8409 (mmmm) REVERT: B 17 GLU cc_start: 0.8589 (pt0) cc_final: 0.8282 (pt0) REVERT: B 131 ARG cc_start: 0.8394 (ptt90) cc_final: 0.8186 (ptt90) REVERT: C 56 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7840 (ttp-110) REVERT: C 131 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7987 (mp10) outliers start: 23 outliers final: 11 residues processed: 140 average time/residue: 1.5001 time to fit residues: 223.2423 Evaluate side-chains 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 131 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 32 optimal weight: 0.0270 chunk 70 optimal weight: 5.9990 chunk 66 optimal weight: 0.0060 overall best weight: 0.7056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN B 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081974 restraints weight = 13819.740| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.06 r_work: 0.2859 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10734 Z= 0.101 Angle : 0.498 6.854 14623 Z= 0.254 Chirality : 0.039 0.149 1645 Planarity : 0.004 0.051 1804 Dihedral : 10.112 73.267 1629 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.78 % Allowed : 11.60 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1240 helix: 1.86 (0.22), residues: 554 sheet: -0.55 (0.43), residues: 130 loop : -0.40 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.005 0.001 HIS B 475 PHE 0.010 0.001 PHE B 214 TYR 0.016 0.001 TYR B 533 ARG 0.013 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 455) hydrogen bonds : angle 4.10195 ( 1288) covalent geometry : bond 0.00226 (10734) covalent geometry : angle 0.49788 (14623) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8430 (mmmm) REVERT: B 17 GLU cc_start: 0.8597 (pt0) cc_final: 0.8290 (pt0) REVERT: B 131 ARG cc_start: 0.8372 (ptt90) cc_final: 0.8109 (ptt90) REVERT: C 72 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8786 (p) REVERT: C 131 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7989 (mp10) outliers start: 20 outliers final: 9 residues processed: 134 average time/residue: 1.6058 time to fit residues: 228.8521 Evaluate side-chains 135 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 131 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 114 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.082709 restraints weight = 14008.249| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.07 r_work: 0.2877 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10734 Z= 0.097 Angle : 0.499 7.514 14623 Z= 0.254 Chirality : 0.039 0.141 1645 Planarity : 0.004 0.058 1804 Dihedral : 10.069 73.268 1629 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.43 % Allowed : 12.13 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1240 helix: 1.95 (0.23), residues: 553 sheet: -0.54 (0.43), residues: 133 loop : -0.34 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 330 HIS 0.005 0.001 HIS B 475 PHE 0.010 0.001 PHE B 214 TYR 0.016 0.001 TYR B 533 ARG 0.013 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 455) hydrogen bonds : angle 4.07487 ( 1288) covalent geometry : bond 0.00214 (10734) covalent geometry : angle 0.49899 (14623) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.8643 (pt0) cc_final: 0.8283 (pt0) REVERT: B 131 ARG cc_start: 0.8417 (ptt90) cc_final: 0.8157 (ptt90) REVERT: C 72 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8822 (p) REVERT: C 98 ARG cc_start: 0.8441 (ptm-80) cc_final: 0.8086 (mtm-85) REVERT: C 131 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8023 (mp10) outliers start: 16 outliers final: 8 residues processed: 133 average time/residue: 2.2088 time to fit residues: 312.2673 Evaluate side-chains 133 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 131 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 120 optimal weight: 0.0060 chunk 66 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.083211 restraints weight = 13914.257| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.06 r_work: 0.2853 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10734 Z= 0.097 Angle : 0.498 7.287 14623 Z= 0.253 Chirality : 0.039 0.143 1645 Planarity : 0.004 0.058 1804 Dihedral : 10.040 73.277 1629 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.16 % Allowed : 12.58 % Favored : 86.26 % 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: 1.02 (0.24), residues: 1240 helix: 1.99 (0.23), residues: 553 sheet: -0.55 (0.43), residues: 133 loop : -0.31 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 330 HIS 0.005 0.001 HIS B 475 PHE 0.010 0.001 PHE B 214 TYR 0.016 0.001 TYR B 533 ARG 0.015 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 455) hydrogen bonds : angle 4.05756 ( 1288) covalent geometry : bond 0.00217 (10734) covalent geometry : angle 0.49835 (14623) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8411 (mmmm) REVERT: B 17 GLU cc_start: 0.8635 (pt0) cc_final: 0.8303 (pt0) REVERT: B 131 ARG cc_start: 0.8390 (ptt90) cc_final: 0.8136 (ptt90) REVERT: B 148 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: C 68 SER cc_start: 0.8901 (p) cc_final: 0.8557 (p) REVERT: C 72 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8815 (p) REVERT: C 98 ARG cc_start: 0.8419 (ptm-80) cc_final: 0.8068 (mtm-85) REVERT: C 131 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8041 (mp10) outliers start: 13 outliers final: 5 residues processed: 131 average time/residue: 1.9263 time to fit residues: 268.0470 Evaluate side-chains 130 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 131 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.079908 restraints weight = 13685.542| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.04 r_work: 0.2826 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10734 Z= 0.161 Angle : 0.545 6.603 14623 Z= 0.278 Chirality : 0.042 0.150 1645 Planarity : 0.005 0.064 1804 Dihedral : 10.154 73.171 1629 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.34 % Allowed : 12.58 % Favored : 86.08 % 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: 0.82 (0.24), residues: 1240 helix: 1.78 (0.22), residues: 559 sheet: -0.59 (0.43), residues: 135 loop : -0.42 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 426 HIS 0.006 0.001 HIS B 475 PHE 0.013 0.001 PHE B 48 TYR 0.015 0.002 TYR B 533 ARG 0.014 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 455) hydrogen bonds : angle 4.15412 ( 1288) covalent geometry : bond 0.00378 (10734) covalent geometry : angle 0.54460 (14623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11891.72 seconds wall clock time: 210 minutes 39.08 seconds (12639.08 seconds total)