Starting phenix.real_space_refine on Fri Jan 17 17:53:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z85_39838/01_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_39838/01_2025/8z85_39838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.map" model { file = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_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-5571/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: 6.52, per 1000 atoms: 0.62 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: 2.58 Conformation dependent library (CDL) restraints added in 1.3 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: 3.52 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: 3.34 Time building geometry restraints manager: 2.97 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.380 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.290 ------------------------------------------------------------------------------- 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= 0.136 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 *********************** 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 : 1.333 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: 1.6655 time to fit residues: 282.9072 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 : 1.231 ------------------------------------------------------------------------------- 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 = 0.122058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082927 restraints weight = 13926.512| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.09 r_work: 0.2844 rms_B_bonded: 2.54 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= 0.230 Angle : 0.581 7.408 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 *********************** 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 : 1.260 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.8737 (m110) cc_final: 0.8520 (m110) REVERT: B 93 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7887 (mpp80) REVERT: B 332 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8002 (mmm) REVERT: C 68 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8490 (p) outliers start: 18 outliers final: 5 residues processed: 138 average time/residue: 1.6615 time to fit residues: 243.6433 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 : 1.180 ------------------------------------------------------------------------------- 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: 0.0470 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 40.0000 chunk 34 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 overall best weight: 1.2684 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.120505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.081664 restraints weight = 14128.615| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.09 r_work: 0.2847 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1721 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= 0.193 Angle : 0.525 7.808 14623 Z= 0.270 Chirality : 0.041 0.164 1645 Planarity : 0.004 0.038 1804 Dihedral : 10.214 73.146 1629 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.05 % Allowed : 8.74 % Favored : 89.21 % 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: 0.71 (0.24), residues: 1240 helix: 1.51 (0.22), residues: 560 sheet: -0.24 (0.43), residues: 130 loop : -0.38 (0.26), residues: 550 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 0.015 0.001 PHE A 483 TYR 0.014 0.001 TYR B 533 ARG 0.006 0.000 ARG B 151 *********************** 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 156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8439 (mmmm) REVERT: A 489 TYR cc_start: 0.9034 (t80) cc_final: 0.8833 (t80) REVERT: A 546 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8634 (ptm) REVERT: B 17 GLU cc_start: 0.8549 (pt0) cc_final: 0.8207 (pt0) REVERT: B 131 ARG cc_start: 0.8555 (ptt90) cc_final: 0.8298 (ptt90) REVERT: B 383 ASN cc_start: 0.8736 (t0) cc_final: 0.8302 (t0) REVERT: B 436 MET cc_start: 0.9156 (ttp) cc_final: 0.8870 (ttp) REVERT: B 588 GLU cc_start: 0.7772 (tp30) cc_final: 0.7490 (tp30) outliers start: 23 outliers final: 11 residues processed: 143 average time/residue: 1.5983 time to fit residues: 242.7567 Evaluate side-chains 140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 515 GLU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS 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: 0.6980 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.080015 restraints weight = 13908.035| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.07 r_work: 0.2817 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10734 Z= 0.220 Angle : 0.530 7.773 14623 Z= 0.273 Chirality : 0.042 0.176 1645 Planarity : 0.004 0.038 1804 Dihedral : 10.240 73.101 1629 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.68 % Allowed : 8.92 % Favored : 88.40 % 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: 0.71 (0.24), residues: 1240 helix: 1.57 (0.22), residues: 560 sheet: -0.39 (0.43), residues: 130 loop : -0.41 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 426 HIS 0.004 0.001 HIS B 476 PHE 0.013 0.001 PHE A 483 TYR 0.016 0.001 TYR B 533 ARG 0.008 0.000 ARG A 536 *********************** 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 162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8438 (mmmm) REVERT: A 516 ASN cc_start: 0.8780 (m-40) cc_final: 0.8210 (m110) REVERT: A 546 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8672 (ptm) REVERT: B 17 GLU cc_start: 0.8612 (pt0) cc_final: 0.8292 (pt0) REVERT: B 131 ARG cc_start: 0.8510 (ptt90) cc_final: 0.8248 (ptt90) REVERT: B 383 ASN cc_start: 0.8855 (t0) cc_final: 0.8386 (t0) outliers start: 30 outliers final: 12 residues processed: 145 average time/residue: 1.6053 time to fit residues: 247.6644 Evaluate side-chains 142 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 546 MET 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 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: 6.9990 chunk 108 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 40.0000 chunk 105 optimal weight: 0.8980 chunk 117 optimal weight: 0.0970 chunk 25 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.120840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.081588 restraints weight = 13891.959| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.07 r_work: 0.2852 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10734 Z= 0.166 Angle : 0.505 7.025 14623 Z= 0.259 Chirality : 0.040 0.166 1645 Planarity : 0.004 0.042 1804 Dihedral : 10.181 73.190 1629 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.32 % Allowed : 9.81 % Favored : 87.87 % 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: 0.80 (0.24), residues: 1240 helix: 1.70 (0.22), residues: 561 sheet: -0.44 (0.43), residues: 130 loop : -0.39 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS B 476 PHE 0.012 0.001 PHE B 214 TYR 0.019 0.001 TYR A 489 ARG 0.010 0.000 ARG A 536 *********************** 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 158 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8447 (mmmm) REVERT: A 489 TYR cc_start: 0.9063 (t80) cc_final: 0.8851 (t80) REVERT: A 546 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8604 (ptm) REVERT: B 17 GLU cc_start: 0.8573 (pt0) cc_final: 0.8279 (pt0) REVERT: B 131 ARG cc_start: 0.8449 (ptt90) cc_final: 0.8217 (ptt90) REVERT: B 383 ASN cc_start: 0.8914 (t0) cc_final: 0.8430 (t0) REVERT: B 588 GLU cc_start: 0.7640 (tp30) cc_final: 0.7315 (tp30) outliers start: 26 outliers final: 9 residues processed: 144 average time/residue: 1.6435 time to fit residues: 251.3408 Evaluate side-chains 140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 546 MET 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 74 GLU 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: 1.9990 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3595 r_free = 0.3595 target = 0.120484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.081147 restraints weight = 13866.556| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.06 r_work: 0.2814 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10734 Z= 0.177 Angle : 0.505 7.215 14623 Z= 0.258 Chirality : 0.040 0.167 1645 Planarity : 0.004 0.042 1804 Dihedral : 10.166 73.184 1629 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.96 % Allowed : 10.79 % 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: 0.84 (0.24), residues: 1240 helix: 1.75 (0.22), residues: 561 sheet: -0.48 (0.43), residues: 130 loop : -0.39 (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 B 476 PHE 0.011 0.001 PHE B 214 TYR 0.017 0.001 TYR A 489 ARG 0.012 0.000 ARG A 536 *********************** 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 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8414 (mmmm) REVERT: A 546 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8631 (ptm) REVERT: B 17 GLU cc_start: 0.8588 (pt0) cc_final: 0.8276 (pt0) REVERT: B 131 ARG cc_start: 0.8427 (ptt90) cc_final: 0.8122 (ptt90) REVERT: B 151 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7580 (mmm160) REVERT: B 332 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8281 (mtm) REVERT: B 383 ASN cc_start: 0.8917 (t0) cc_final: 0.8377 (t0) REVERT: B 588 GLU cc_start: 0.7770 (tp30) cc_final: 0.7471 (tp30) outliers start: 22 outliers final: 12 residues processed: 138 average time/residue: 1.7107 time to fit residues: 250.9011 Evaluate side-chains 138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 546 MET 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 67 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 74 GLU 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: 8.9990 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN B 475 HIS C 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.081455 restraints weight = 13974.845| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.06 r_work: 0.2853 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10734 Z= 0.164 Angle : 0.499 6.993 14623 Z= 0.255 Chirality : 0.040 0.164 1645 Planarity : 0.004 0.051 1804 Dihedral : 10.139 73.200 1629 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.05 % Allowed : 10.70 % 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: 0.89 (0.24), residues: 1240 helix: 1.86 (0.22), residues: 553 sheet: -0.50 (0.43), residues: 130 loop : -0.39 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS B 476 PHE 0.011 0.001 PHE B 214 TYR 0.016 0.001 TYR B 533 ARG 0.014 0.000 ARG A 536 *********************** 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 149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8448 (mmmm) REVERT: A 546 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8617 (ptm) REVERT: B 17 GLU cc_start: 0.8598 (pt0) cc_final: 0.8295 (pt0) REVERT: B 131 ARG cc_start: 0.8441 (ptt90) cc_final: 0.8158 (ptt90) REVERT: B 151 ARG cc_start: 0.7836 (mmm160) cc_final: 0.7615 (mmm160) REVERT: B 383 ASN cc_start: 0.8885 (t0) cc_final: 0.8342 (t0) REVERT: B 588 GLU cc_start: 0.7810 (tp30) cc_final: 0.7447 (tp30) REVERT: C 72 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8741 (p) outliers start: 23 outliers final: 9 residues processed: 138 average time/residue: 1.6277 time to fit residues: 238.7613 Evaluate side-chains 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 546 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 30 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A 577 HIS B 148 GLN B 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.078110 restraints weight = 13780.826| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.05 r_work: 0.2757 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10734 Z= 0.298 Angle : 0.571 8.370 14623 Z= 0.293 Chirality : 0.043 0.190 1645 Planarity : 0.005 0.055 1804 Dihedral : 10.283 73.015 1629 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.23 % Allowed : 10.70 % Favored : 87.07 % 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: 0.60 (0.23), residues: 1240 helix: 1.54 (0.22), residues: 567 sheet: -0.54 (0.43), residues: 130 loop : -0.55 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 426 HIS 0.004 0.001 HIS B 531 PHE 0.013 0.002 PHE B 48 TYR 0.018 0.002 TYR A 489 ARG 0.013 0.001 ARG A 536 *********************** 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 148 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8402 (mmmm) REVERT: A 472 LYS cc_start: 0.8512 (mtmp) cc_final: 0.8128 (mtpp) REVERT: B 17 GLU cc_start: 0.8607 (pt0) cc_final: 0.8307 (pt0) REVERT: B 93 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8042 (mtp85) REVERT: B 131 ARG cc_start: 0.8417 (ptt90) cc_final: 0.8167 (ptt90) REVERT: B 151 ARG cc_start: 0.7852 (mmm160) cc_final: 0.7585 (mmm160) REVERT: B 383 ASN cc_start: 0.9019 (t0) cc_final: 0.8734 (t0) REVERT: C 98 ARG cc_start: 0.8483 (ptm-80) cc_final: 0.8038 (mtm-85) outliers start: 25 outliers final: 11 residues processed: 139 average time/residue: 1.6352 time to fit residues: 241.3184 Evaluate side-chains 134 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 VAL 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 93 ARG Chi-restraints excluded: chain B residue 211 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.080900 restraints weight = 14004.622| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.08 r_work: 0.2843 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2376 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= 0.161 Angle : 0.510 5.604 14623 Z= 0.261 Chirality : 0.040 0.158 1645 Planarity : 0.004 0.056 1804 Dihedral : 10.152 73.265 1629 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.52 % Allowed : 11.69 % Favored : 86.80 % 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: 0.85 (0.24), residues: 1240 helix: 1.83 (0.22), residues: 553 sheet: -0.55 (0.43), residues: 130 loop : -0.40 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 330 HIS 0.003 0.001 HIS A 577 PHE 0.011 0.001 PHE B 214 TYR 0.017 0.001 TYR B 533 ARG 0.014 0.000 ARG A 536 *********************** 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 141 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8470 (mmmm) REVERT: B 17 GLU cc_start: 0.8598 (pt0) cc_final: 0.8299 (pt0) REVERT: B 131 ARG cc_start: 0.8407 (ptt90) cc_final: 0.8203 (ptt90) REVERT: B 151 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7593 (mmm160) REVERT: B 383 ASN cc_start: 0.8934 (t0) cc_final: 0.8631 (t0) REVERT: B 588 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7178 (tp30) REVERT: C 72 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8758 (p) REVERT: C 98 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8115 (mtm-85) outliers start: 17 outliers final: 8 residues processed: 134 average time/residue: 1.6576 time to fit residues: 236.4499 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 : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 591 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 chunk 78 optimal weight: 0.0270 chunk 110 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 overall best weight: 1.0042 ------------------------------------------------------------------------------- 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 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.080920 restraints weight = 13917.194| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.06 r_work: 0.2844 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10734 Z= 0.170 Angle : 0.511 6.304 14623 Z= 0.260 Chirality : 0.040 0.152 1645 Planarity : 0.004 0.060 1804 Dihedral : 10.122 73.178 1629 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.16 % Allowed : 11.95 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1240 helix: 1.86 (0.22), residues: 553 sheet: -0.54 (0.43), residues: 130 loop : -0.36 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS B 476 PHE 0.011 0.001 PHE B 214 TYR 0.016 0.001 TYR B 533 ARG 0.015 0.000 ARG A 536 ********************** 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 133 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8468 (mmmm) REVERT: B 17 GLU cc_start: 0.8579 (pt0) cc_final: 0.8274 (pt0) REVERT: B 93 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7942 (mtp85) REVERT: B 131 ARG cc_start: 0.8413 (ptt90) cc_final: 0.8140 (ptt90) REVERT: B 151 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7583 (mmm160) REVERT: B 383 ASN cc_start: 0.8953 (t0) cc_final: 0.8656 (t0) REVERT: C 72 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8810 (p) REVERT: C 98 ARG cc_start: 0.8469 (ptm-80) cc_final: 0.8099 (mtm-85) outliers start: 13 outliers final: 6 residues processed: 129 average time/residue: 1.6633 time to fit residues: 228.0369 Evaluate side-chains 129 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 93 ARG Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 591 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.078110 restraints weight = 13726.960| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.04 r_work: 0.2759 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10734 Z= 0.306 Angle : 0.571 7.236 14623 Z= 0.293 Chirality : 0.043 0.169 1645 Planarity : 0.005 0.064 1804 Dihedral : 10.246 73.050 1629 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.52 % Allowed : 11.69 % Favored : 86.80 % 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: 0.61 (0.24), residues: 1240 helix: 1.56 (0.22), residues: 567 sheet: -0.58 (0.44), residues: 133 loop : -0.52 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 426 HIS 0.006 0.001 HIS A 577 PHE 0.013 0.002 PHE B 48 TYR 0.018 0.002 TYR A 489 ARG 0.015 0.000 ARG A 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10247.22 seconds wall clock time: 183 minutes 27.47 seconds (11007.47 seconds total)