Starting phenix.real_space_refine on Wed Aug 5 18:16:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z85_39838/08_2026/8z85_39838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z85_39838/08_2026/8z85_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_39838/08_2026/8z85_39838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z85_39838/08_2026/8z85_39838.map" model { file = "/net/cci-nas-00/data/ceres_data/8z85_39838/08_2026/8z85_39838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z85_39838/08_2026/8z85_39838.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 2.63, per 1000 atoms: 0.25 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: 0.76 Conformation dependent library (CDL) restraints added in 374.7 milliseconds 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: 1.15 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: 1.57 Time building geometry restraints manager: 1.08 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: 14260 1.38 - 2.76: 287 2.76 - 4.14: 60 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=" O5' A D 7 " pdb=" C5' A D 7 " pdb=" C4' A D 7 " ideal model delta sigma weight residual 109.40 112.48 -3.08 8.00e-01 1.56e+00 1.48e+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=" O5' G E 15 " pdb=" C5' G E 15 " pdb=" C4' G E 15 " ideal model delta sigma weight residual 109.40 111.93 -2.53 8.00e-01 1.56e+00 1.00e+01 angle pdb=" O5' C E 16 " pdb=" C5' C E 16 " pdb=" C4' C E 16 " ideal model delta sigma weight residual 109.40 111.77 -2.37 8.00e-01 1.56e+00 8.78e+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 - 0.028: 1015 0.028 - 0.055: 391 0.055 - 0.083: 128 0.083 - 0.111: 77 0.111 - 0.138: 34 Chirality restraints: 1645 Sorted by residual: chirality pdb=" C2' G D 2 " pdb=" C3' G D 2 " pdb=" O2' G D 2 " pdb=" C1' G D 2 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" C2' G D 13 " pdb=" C3' G D 13 " pdb=" O2' G D 13 " pdb=" C1' G D 13 " both_signs ideal model delta sigma weight residual False -2.62 -2.75 0.14 2.00e-01 2.50e+01 4.65e-01 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 ... (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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.270 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 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= 0.099 Angle : 0.501 6.893 14623 Z= 0.273 Chirality : 0.040 0.138 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.000 ARG B 131 TYR 0.015 0.001 TYR B 22 PHE 0.017 0.001 PHE A 483 TRP 0.008 0.001 TRP C 65 HIS 0.006 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (10734) covalent geometry : angle 0.50119 / 0.27 (14623) hydrogen bonds : bond 0.24420 / 16.50 ( 455) hydrogen bonds : angle 7.23443 / 5.04 ( 1288) *********************** 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 : 0.404 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: 0.6564 time to fit residues: 111.6330 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 : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN A 311 GLN A 516 ASN 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 = 0.3631 r_free = 0.3631 target = 0.123269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.084306 restraints weight = 14003.165| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.09 r_work: 0.2902 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10734 Z= 0.141 Angle : 0.577 7.490 14623 Z= 0.299 Chirality : 0.042 0.184 1645 Planarity : 0.005 0.062 1804 Dihedral : 10.200 73.004 1629 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.69 % Allowed : 6.87 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.24), residues: 1240 helix: 1.23 (0.22), residues: 557 sheet: 0.26 (0.46), residues: 124 loop : -0.42 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 536 TYR 0.017 0.002 TYR A 489 PHE 0.017 0.001 PHE A 483 TRP 0.010 0.001 TRP B 330 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (10734) covalent geometry : angle 0.57691 / 0.30 (14623) hydrogen bonds : bond 0.05578 / 3.77 ( 455) hydrogen bonds : angle 5.01424 / 3.49 ( 1288) *********************** 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 147 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.8789 (m110) cc_final: 0.8303 (m110) REVERT: B 93 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7908 (mpp80) REVERT: B 332 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.7782 (mmm) REVERT: B 422 ASP cc_start: 0.8132 (p0) cc_final: 0.7642 (p0) REVERT: C 68 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8468 (p) REVERT: C 116 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8497 (tm) outliers start: 19 outliers final: 4 residues processed: 133 average time/residue: 0.6816 time to fit residues: 96.4427 Evaluate side-chains 132 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 625 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 26 optimal weight: 0.0980 chunk 124 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN A 311 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.079722 restraints weight = 14092.678| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.09 r_work: 0.2813 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10734 Z= 0.183 Angle : 0.574 8.411 14623 Z= 0.297 Chirality : 0.044 0.201 1645 Planarity : 0.005 0.040 1804 Dihedral : 10.292 73.026 1629 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.05 % Allowed : 8.65 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.23), residues: 1240 helix: 1.44 (0.22), residues: 556 sheet: -0.28 (0.43), residues: 130 loop : -0.43 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 151 TYR 0.016 0.002 TYR B 22 PHE 0.019 0.002 PHE A 483 TRP 0.011 0.001 TRP A 426 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (10734) covalent geometry : angle 0.57360 / 0.30 (14623) hydrogen bonds : bond 0.05094 / 3.47 ( 455) hydrogen bonds : angle 4.64932 / 3.23 ( 1288) *********************** 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 153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: B 17 GLU cc_start: 0.8588 (pt0) cc_final: 0.8283 (pt0) REVERT: B 213 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8520 (ttmm) REVERT: B 332 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.7888 (mmm) REVERT: B 383 ASN cc_start: 0.8731 (t0) cc_final: 0.8236 (t0) REVERT: B 422 ASP cc_start: 0.8530 (p0) cc_final: 0.8096 (p0) REVERT: C 68 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8623 (p) outliers start: 23 outliers final: 10 residues processed: 138 average time/residue: 0.6438 time to fit residues: 94.3560 Evaluate side-chains 141 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 213 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 67 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN A 516 ASN B 148 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.082149 restraints weight = 14067.411| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.10 r_work: 0.2857 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10734 Z= 0.107 Angle : 0.507 6.890 14623 Z= 0.262 Chirality : 0.040 0.160 1645 Planarity : 0.004 0.039 1804 Dihedral : 10.181 73.122 1629 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.14 % Allowed : 9.55 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1240 helix: 1.61 (0.22), residues: 558 sheet: -0.40 (0.43), residues: 130 loop : -0.39 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 151 TYR 0.020 0.001 TYR A 489 PHE 0.012 0.001 PHE A 483 TRP 0.011 0.001 TRP B 330 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10734) covalent geometry : angle 0.50689 / 0.26 (14623) hydrogen bonds : bond 0.03893 / 2.62 ( 455) hydrogen bonds : angle 4.42440 / 3.07 ( 1288) *********************** 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 155 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8463 (mmmm) REVERT: B 17 GLU cc_start: 0.8591 (pt0) cc_final: 0.8265 (pt0) REVERT: B 93 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8082 (mtp-110) REVERT: B 131 ARG cc_start: 0.8559 (ptt90) cc_final: 0.8276 (ptt90) REVERT: B 151 ARG cc_start: 0.8602 (mmt90) cc_final: 0.8374 (mmm160) REVERT: B 383 ASN cc_start: 0.8797 (t0) cc_final: 0.8234 (t0) REVERT: C 116 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8510 (tt) REVERT: C 127 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8045 (t70) outliers start: 24 outliers final: 9 residues processed: 141 average time/residue: 0.6431 time to fit residues: 96.1395 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 : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 327 GLN 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 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3603 r_free = 0.3603 target = 0.121157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081774 restraints weight = 13957.376| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.08 r_work: 0.2854 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10734 Z= 0.119 Angle : 0.514 6.833 14623 Z= 0.264 Chirality : 0.040 0.168 1645 Planarity : 0.004 0.047 1804 Dihedral : 10.155 73.146 1629 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.41 % Allowed : 9.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1240 helix: 1.69 (0.22), residues: 559 sheet: -0.54 (0.43), residues: 130 loop : -0.37 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 536 TYR 0.016 0.001 TYR B 533 PHE 0.011 0.001 PHE A 483 TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10734) covalent geometry : angle 0.51373 / 0.26 (14623) hydrogen bonds : bond 0.03851 / 2.60 ( 455) hydrogen bonds : angle 4.32325 / 3.00 ( 1288) *********************** 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 155 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8436 (mmmm) REVERT: B 17 GLU cc_start: 0.8590 (pt0) cc_final: 0.8266 (pt0) REVERT: B 131 ARG cc_start: 0.8531 (ptt90) cc_final: 0.8259 (ptt90) REVERT: B 148 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: B 332 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8327 (mtm) REVERT: B 369 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8687 (mmm) REVERT: B 383 ASN cc_start: 0.8803 (t0) cc_final: 0.8230 (t0) REVERT: C 116 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8514 (tt) outliers start: 27 outliers final: 11 residues processed: 138 average time/residue: 0.7058 time to fit residues: 103.4803 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 : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 327 GLN 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 148 GLN 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 369 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 102 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 116 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 19 optimal weight: 0.2980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3600 r_free = 0.3600 target = 0.120873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.081531 restraints weight = 14063.515| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.09 r_work: 0.2818 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1982 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= 0.124 Angle : 0.516 7.383 14623 Z= 0.265 Chirality : 0.040 0.176 1645 Planarity : 0.004 0.049 1804 Dihedral : 10.148 73.138 1629 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.78 % Allowed : 10.70 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1240 helix: 1.71 (0.22), residues: 561 sheet: -0.55 (0.43), residues: 130 loop : -0.36 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 536 TYR 0.019 0.001 TYR A 489 PHE 0.011 0.001 PHE B 145 TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (10734) covalent geometry : angle 0.51564 / 0.27 (14623) hydrogen bonds : bond 0.03795 / 2.56 ( 455) hydrogen bonds : angle 4.27552 / 2.97 ( 1288) *********************** 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 147 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8418 (mmmm) REVERT: B 17 GLU cc_start: 0.8608 (pt0) cc_final: 0.8276 (pt0) REVERT: B 93 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7997 (mtp-110) REVERT: B 131 ARG cc_start: 0.8520 (ptt90) cc_final: 0.8251 (ptt90) REVERT: B 369 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8696 (mmm) REVERT: B 383 ASN cc_start: 0.8786 (t0) cc_final: 0.8221 (t0) REVERT: C 116 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8552 (tt) outliers start: 20 outliers final: 11 residues processed: 136 average time/residue: 0.6718 time to fit residues: 97.2259 Evaluate side-chains 140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 327 GLN 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 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 393 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 102 VAL Chi-restraints excluded: chain C residue 116 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 120 optimal weight: 0.0070 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3587 r_free = 0.3587 target = 0.119908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.080468 restraints weight = 13893.340| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.08 r_work: 0.2800 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2047 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= 0.139 Angle : 0.530 7.549 14623 Z= 0.273 Chirality : 0.041 0.190 1645 Planarity : 0.004 0.052 1804 Dihedral : 10.179 73.159 1629 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1240 helix: 1.70 (0.22), residues: 561 sheet: -0.55 (0.43), residues: 130 loop : -0.39 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 536 TYR 0.016 0.001 TYR B 533 PHE 0.011 0.001 PHE B 145 TRP 0.011 0.001 TRP A 336 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (10734) covalent geometry : angle 0.53023 / 0.27 (14623) hydrogen bonds : bond 0.03925 / 2.67 ( 455) hydrogen bonds : angle 4.25299 / 2.96 ( 1288) *********************** 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 153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8418 (mmmm) REVERT: A 515 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: B 17 GLU cc_start: 0.8616 (pt0) cc_final: 0.8278 (pt0) REVERT: B 93 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8059 (mtp85) REVERT: B 383 ASN cc_start: 0.8877 (t0) cc_final: 0.8355 (t0) REVERT: B 436 MET cc_start: 0.9061 (ttp) cc_final: 0.8843 (ttp) outliers start: 23 outliers final: 11 residues processed: 140 average time/residue: 0.7411 time to fit residues: 110.4330 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 327 GLN 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 93 ARG 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 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 8 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 74 optimal weight: 0.3980 chunk 110 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 13 optimal weight: 0.0170 chunk 70 optimal weight: 0.1980 chunk 87 optimal weight: 0.0470 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.084377 restraints weight = 13809.870| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.07 r_work: 0.2902 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10734 Z= 0.095 Angle : 0.498 7.244 14623 Z= 0.257 Chirality : 0.039 0.160 1645 Planarity : 0.004 0.048 1804 Dihedral : 10.062 73.277 1629 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.25 % Allowed : 11.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.24), residues: 1240 helix: 1.85 (0.22), residues: 554 sheet: -0.58 (0.43), residues: 130 loop : -0.36 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 536 TYR 0.017 0.001 TYR A 489 PHE 0.010 0.001 PHE B 214 TRP 0.014 0.001 TRP B 330 HIS 0.004 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (10734) covalent geometry : angle 0.49812 / 0.26 (14623) hydrogen bonds : bond 0.03257 / 2.17 ( 455) hydrogen bonds : angle 4.16830 / 2.91 ( 1288) *********************** 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 146 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8438 (mmmm) REVERT: A 516 ASN cc_start: 0.8714 (m-40) cc_final: 0.7958 (m110) REVERT: B 17 GLU cc_start: 0.8583 (pt0) cc_final: 0.8239 (pt0) REVERT: B 148 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: B 383 ASN cc_start: 0.8772 (t0) cc_final: 0.8152 (t0) outliers start: 14 outliers final: 6 residues processed: 139 average time/residue: 0.7322 time to fit residues: 108.2071 Evaluate side-chains 135 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 148 GLN 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 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 0.0060 chunk 21 optimal weight: 0.0570 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 79 optimal weight: 0.0020 chunk 15 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 116 optimal weight: 0.0370 overall best weight: 0.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN B 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.084802 restraints weight = 13837.118| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.06 r_work: 0.2881 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2211 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= 0.092 Angle : 0.497 7.489 14623 Z= 0.255 Chirality : 0.039 0.163 1645 Planarity : 0.004 0.053 1804 Dihedral : 10.036 73.280 1629 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.34 % Allowed : 12.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.24), residues: 1240 helix: 1.90 (0.22), residues: 553 sheet: -0.60 (0.43), residues: 130 loop : -0.32 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 536 TYR 0.016 0.001 TYR B 533 PHE 0.010 0.001 PHE B 214 TRP 0.011 0.001 TRP B 330 HIS 0.003 0.000 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (10734) covalent geometry : angle 0.49668 / 0.26 (14623) hydrogen bonds : bond 0.03191 / 2.13 ( 455) hydrogen bonds : angle 4.12687 / 2.89 ( 1288) *********************** 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 147 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8428 (mmmm) REVERT: B 17 GLU cc_start: 0.8617 (pt0) cc_final: 0.8281 (pt0) REVERT: B 383 ASN cc_start: 0.8769 (t0) cc_final: 0.8168 (t0) outliers start: 15 outliers final: 8 residues processed: 141 average time/residue: 0.7328 time to fit residues: 110.1865 Evaluate side-chains 137 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 393 MET Chi-restraints excluded: chain B residue 475 HIS 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 41 optimal weight: 7.9990 chunk 116 optimal weight: 0.0370 chunk 31 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 117 optimal weight: 0.0770 overall best weight: 2.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3588 r_free = 0.3588 target = 0.119897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.080569 restraints weight = 13775.533| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.05 r_work: 0.2837 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10734 Z= 0.178 Angle : 0.557 7.969 14623 Z= 0.285 Chirality : 0.042 0.198 1645 Planarity : 0.005 0.059 1804 Dihedral : 10.132 73.195 1629 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.34 % Allowed : 12.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1240 helix: 1.81 (0.22), residues: 556 sheet: -0.56 (0.43), residues: 130 loop : -0.38 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 536 TYR 0.018 0.002 TYR A 489 PHE 0.015 0.002 PHE B 569 TRP 0.013 0.001 TRP A 426 HIS 0.026 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (10734) covalent geometry : angle 0.55669 / 0.29 (14623) hydrogen bonds : bond 0.03973 / 2.70 ( 455) hydrogen bonds : angle 4.21714 / 2.94 ( 1288) ********************** 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 143 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8415 (mmmm) REVERT: B 17 GLU cc_start: 0.8629 (pt0) cc_final: 0.8303 (pt0) REVERT: B 383 ASN cc_start: 0.8928 (t0) cc_final: 0.8407 (t0) REVERT: B 572 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8063 (mmt) REVERT: C 131 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7974 (mp10) outliers start: 15 outliers final: 8 residues processed: 136 average time/residue: 0.7287 time to fit residues: 105.6618 Evaluate side-chains 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 393 MET Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 625 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 80 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3609 r_free = 0.3609 target = 0.121509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.082331 restraints weight = 13985.897| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.06 r_work: 0.2869 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10734 Z= 0.106 Angle : 0.517 8.185 14623 Z= 0.265 Chirality : 0.040 0.179 1645 Planarity : 0.004 0.056 1804 Dihedral : 10.102 73.218 1629 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.16 % Allowed : 12.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1240 helix: 1.90 (0.22), residues: 552 sheet: -0.62 (0.43), residues: 130 loop : -0.35 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 536 TYR 0.016 0.001 TYR A 489 PHE 0.012 0.001 PHE B 569 TRP 0.009 0.001 TRP B 330 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10734) covalent geometry : angle 0.51688 / 0.27 (14623) hydrogen bonds : bond 0.03509 / 2.35 ( 455) hydrogen bonds : angle 4.19613 / 2.93 ( 1288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4686.35 seconds wall clock time: 80 minutes 18.05 seconds (4818.05 seconds total)