Starting phenix.real_space_refine on Fri Jul 3 00:25:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z85_39838/07_2026/8z85_39838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z85_39838/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z85_39838/07_2026/8z85_39838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z85_39838/07_2026/8z85_39838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z85_39838/07_2026/8z85_39838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z85_39838/07_2026/8z85_39838.map" } 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-dev-6108/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: 2.35, per 1000 atoms: 0.22 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: 0.81 Conformation dependent library (CDL) restraints added in 366.6 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: 1.23 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: 1.78 Time building geometry restraints manager: 1.12 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.670 Find NCS groups from input model: 0.050 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- 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= 0.097 Angle : 0.484 6.893 14623 Z= 0.252 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 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 0.00209 / 0.10 (10734) covalent geometry : angle 0.48408 / 0.25 (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 : 0.315 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: 0.6721 time to fit residues: 114.1857 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 : 0.333 ------------------------------------------------------------------------------- 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 A 542 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.084291 restraints weight = 14065.370| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.10 r_work: 0.2868 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1211 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= 0.142 Angle : 0.574 7.263 14623 Z= 0.298 Chirality : 0.042 0.184 1645 Planarity : 0.005 0.058 1804 Dihedral : 10.223 73.056 1629 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.69 % Allowed : 7.05 % Favored : 91.26 % 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: 0.54 (0.24), residues: 1240 helix: 1.21 (0.22), residues: 557 sheet: 0.25 (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 0.00305 / 0.14 (10734) covalent geometry : angle 0.57450 / 0.30 (14623) hydrogen bonds : bond 0.05731 / 3.88 ( 455) hydrogen bonds : angle 5.02565 / 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 : 0.391 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.8766 (m110) cc_final: 0.8276 (m110) REVERT: B 93 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7896 (mpp80) REVERT: B 332 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.7760 (mmm) REVERT: B 422 ASP cc_start: 0.8120 (p0) cc_final: 0.7624 (p0) REVERT: B 588 GLU cc_start: 0.7603 (tp30) cc_final: 0.7391 (tp30) REVERT: C 68 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8439 (p) REVERT: C 116 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8544 (tm) outliers start: 19 outliers final: 4 residues processed: 133 average time/residue: 0.6334 time to fit residues: 89.7949 Evaluate side-chains 133 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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: 9.9990 chunk 91 optimal weight: 10.0000 chunk 2 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 GLN A 311 GLN A 516 ASN A 577 HIS B 148 GLN B 476 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.077157 restraints weight = 14092.326| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.10 r_work: 0.2766 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10734 Z= 0.265 Angle : 0.646 10.123 14623 Z= 0.336 Chirality : 0.047 0.219 1645 Planarity : 0.005 0.043 1804 Dihedral : 10.429 73.051 1629 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.32 % Allowed : 8.74 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.31 (0.23), residues: 1240 helix: 1.16 (0.22), residues: 565 sheet: -0.30 (0.43), residues: 130 loop : -0.62 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 151 TYR 0.020 0.002 TYR B 22 PHE 0.020 0.002 PHE A 483 TRP 0.015 0.002 TRP A 426 HIS 0.009 0.002 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.26 (10734) covalent geometry : angle 0.64626 / 0.34 (14623) hydrogen bonds : bond 0.05612 / 3.85 ( 455) hydrogen bonds : angle 4.72101 / 3.28 ( 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 157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.8731 (m110) cc_final: 0.8498 (m110) REVERT: B 213 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8563 (ttmm) REVERT: B 332 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8027 (mmm) REVERT: B 383 ASN cc_start: 0.8894 (t0) cc_final: 0.8694 (t0) REVERT: B 422 ASP cc_start: 0.8727 (p0) cc_final: 0.8286 (p0) REVERT: C 68 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8728 (p) outliers start: 26 outliers final: 11 residues processed: 140 average time/residue: 0.6765 time to fit residues: 100.5754 Evaluate side-chains 141 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 327 GLN Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 22 TYR 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 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: 0.8980 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN A 516 ASN B 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.080240 restraints weight = 14040.869| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.08 r_work: 0.2822 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10734 Z= 0.120 Angle : 0.524 6.976 14623 Z= 0.272 Chirality : 0.041 0.168 1645 Planarity : 0.004 0.038 1804 Dihedral : 10.313 73.087 1629 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.23 % Allowed : 9.19 % Favored : 88.58 % 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: 1.51 (0.22), residues: 558 sheet: -0.46 (0.43), residues: 130 loop : -0.47 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 151 TYR 0.015 0.001 TYR B 533 PHE 0.012 0.001 PHE A 483 TRP 0.012 0.001 TRP B 330 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10734) covalent geometry : angle 0.52433 / 0.27 (14623) hydrogen bonds : bond 0.04138 / 2.79 ( 455) hydrogen bonds : angle 4.47791 / 3.11 ( 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 153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASN cc_start: 0.8664 (m110) cc_final: 0.8403 (m110) REVERT: A 468 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8435 (mmmm) REVERT: B 17 GLU cc_start: 0.8608 (pt0) cc_final: 0.8295 (pt0) REVERT: B 93 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8062 (mtm-85) REVERT: B 151 ARG cc_start: 0.8619 (mmt90) cc_final: 0.8383 (mmm160) REVERT: B 383 ASN cc_start: 0.8916 (t0) cc_final: 0.8494 (t0) REVERT: B 588 GLU cc_start: 0.7724 (tp30) cc_final: 0.7450 (tp30) REVERT: C 127 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7936 (t70) outliers start: 25 outliers final: 12 residues processed: 140 average time/residue: 0.7359 time to fit residues: 108.9919 Evaluate side-chains 137 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain 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 127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 5.9990 chunk 88 optimal weight: 0.0030 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN A 516 ASN B 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.080720 restraints weight = 13889.702| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.06 r_work: 0.2804 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10734 Z= 0.121 Angle : 0.515 6.880 14623 Z= 0.266 Chirality : 0.041 0.171 1645 Planarity : 0.004 0.047 1804 Dihedral : 10.253 73.180 1629 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.23 % Allowed : 10.26 % 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: 0.73 (0.24), residues: 1240 helix: 1.64 (0.22), residues: 557 sheet: -0.52 (0.43), residues: 130 loop : -0.41 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 536 TYR 0.022 0.001 TYR A 489 PHE 0.011 0.001 PHE B 214 TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10734) covalent geometry : angle 0.51542 / 0.27 (14623) hydrogen bonds : bond 0.03907 / 2.65 ( 455) hydrogen bonds : angle 4.34972 / 3.02 ( 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 152 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8412 (mmmm) REVERT: B 17 GLU cc_start: 0.8642 (pt0) cc_final: 0.8324 (pt0) REVERT: B 148 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: B 151 ARG cc_start: 0.8605 (mmt90) cc_final: 0.8356 (mmm160) REVERT: B 332 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8333 (mtm) REVERT: B 369 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8707 (mmm) REVERT: B 383 ASN cc_start: 0.8908 (t0) cc_final: 0.8435 (t0) outliers start: 25 outliers final: 10 residues processed: 137 average time/residue: 0.6687 time to fit residues: 97.4016 Evaluate side-chains 141 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 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 68 SER Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.120639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.081242 restraints weight = 14054.861| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.09 r_work: 0.2814 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10734 Z= 0.109 Angle : 0.509 6.954 14623 Z= 0.262 Chirality : 0.040 0.169 1645 Planarity : 0.004 0.049 1804 Dihedral : 10.216 73.149 1629 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.87 % Allowed : 10.97 % Favored : 87.15 % 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: 0.77 (0.24), residues: 1240 helix: 1.65 (0.22), residues: 562 sheet: -0.52 (0.43), residues: 130 loop : -0.37 (0.26), residues: 548 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 0.012 0.001 PHE B 214 TRP 0.010 0.001 TRP B 330 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10734) covalent geometry : angle 0.50860 / 0.26 (14623) hydrogen bonds : bond 0.03704 / 2.50 ( 455) hydrogen bonds : angle 4.27299 / 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 153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8413 (mmmm) REVERT: B 17 GLU cc_start: 0.8645 (pt0) cc_final: 0.8298 (pt0) REVERT: B 93 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8000 (mtp-110) REVERT: B 148 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: B 151 ARG cc_start: 0.8530 (mmt90) cc_final: 0.8319 (mmm160) REVERT: B 332 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8285 (mtm) REVERT: B 383 ASN cc_start: 0.8885 (t0) cc_final: 0.8408 (t0) REVERT: C 131 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8018 (mp10) outliers start: 21 outliers final: 10 residues processed: 142 average time/residue: 0.6612 time to fit residues: 99.9143 Evaluate side-chains 144 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 93 ARG 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 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 131 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 121 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN A 516 ASN ** B 148 GLN ** 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 = 0.3569 r_free = 0.3569 target = 0.118532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.078874 restraints weight = 13938.550| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.06 r_work: 0.2770 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10734 Z= 0.184 Angle : 0.557 8.334 14623 Z= 0.287 Chirality : 0.043 0.199 1645 Planarity : 0.004 0.053 1804 Dihedral : 10.284 73.108 1629 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.05 % Allowed : 11.42 % Favored : 86.53 % 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: 0.66 (0.24), residues: 1240 helix: 1.56 (0.22), residues: 563 sheet: -0.55 (0.42), residues: 130 loop : -0.44 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 536 TYR 0.021 0.002 TYR A 489 PHE 0.013 0.002 PHE B 48 TRP 0.013 0.001 TRP A 426 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (10734) covalent geometry : angle 0.55682 / 0.29 (14623) hydrogen bonds : bond 0.04268 / 2.90 ( 455) hydrogen bonds : angle 4.32391 / 3.01 ( 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 : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8404 (mmmm) REVERT: A 515 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: B 17 GLU cc_start: 0.8667 (pt0) cc_final: 0.8347 (pt0) REVERT: B 93 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7965 (mtp-110) REVERT: B 383 ASN cc_start: 0.8996 (t0) cc_final: 0.8684 (t0) REVERT: C 127 ASP cc_start: 0.8335 (t0) cc_final: 0.7975 (t70) REVERT: C 131 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7889 (mp10) outliers start: 23 outliers final: 12 residues processed: 141 average time/residue: 0.7328 time to fit residues: 109.7873 Evaluate side-chains 144 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 A residue 515 GLU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain 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 131 GLN 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: 3.9990 chunk 10 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 87 optimal weight: 0.0270 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.080017 restraints weight = 13809.541| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.06 r_work: 0.2823 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10734 Z= 0.130 Angle : 0.531 7.605 14623 Z= 0.273 Chirality : 0.041 0.183 1645 Planarity : 0.004 0.054 1804 Dihedral : 10.252 73.125 1629 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.32 % Allowed : 11.51 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.73 (0.24), residues: 1240 helix: 1.64 (0.22), residues: 561 sheet: -0.58 (0.43), residues: 130 loop : -0.41 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 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 0.006 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10734) covalent geometry : angle 0.53070 / 0.27 (14623) hydrogen bonds : bond 0.03894 / 2.64 ( 455) hydrogen bonds : angle 4.27074 / 2.97 ( 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 157 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8429 (mmmm) REVERT: B 17 GLU cc_start: 0.8643 (pt0) cc_final: 0.8324 (pt0) REVERT: B 148 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: B 151 ARG cc_start: 0.8629 (mmt90) cc_final: 0.8409 (mmm160) REVERT: B 383 ASN cc_start: 0.8969 (t0) cc_final: 0.8641 (t0) REVERT: C 127 ASP cc_start: 0.8334 (t0) cc_final: 0.8010 (t70) REVERT: C 131 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7930 (mp10) outliers start: 26 outliers final: 11 residues processed: 145 average time/residue: 0.6940 time to fit residues: 106.9557 Evaluate side-chains 140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 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 A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 591 LEU 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 131 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 4.9990 chunk 21 optimal weight: 0.0170 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.080970 restraints weight = 13710.693| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.05 r_work: 0.2809 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10734 Z= 0.108 Angle : 0.527 7.705 14623 Z= 0.271 Chirality : 0.040 0.174 1645 Planarity : 0.004 0.056 1804 Dihedral : 10.224 73.189 1629 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.87 % Allowed : 12.04 % 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: 0.77 (0.24), residues: 1240 helix: 1.69 (0.22), residues: 561 sheet: -0.60 (0.43), residues: 130 loop : -0.39 (0.26), residues: 549 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 0.011 0.001 PHE B 214 TRP 0.011 0.001 TRP B 330 HIS 0.005 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10734) covalent geometry : angle 0.52713 / 0.27 (14623) hydrogen bonds : bond 0.03666 / 2.47 ( 455) hydrogen bonds : angle 4.24812 / 2.96 ( 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: 21 poor density : 126 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8415 (mmmm) REVERT: B 17 GLU cc_start: 0.8626 (pt0) cc_final: 0.8279 (pt0) REVERT: B 69 ASP cc_start: 0.8546 (t0) cc_final: 0.7855 (t0) REVERT: B 148 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: B 151 ARG cc_start: 0.8541 (mmt90) cc_final: 0.8320 (mmm160) REVERT: B 332 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8191 (mtm) REVERT: C 127 ASP cc_start: 0.8329 (t0) cc_final: 0.7999 (t70) REVERT: C 131 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7916 (mp10) outliers start: 21 outliers final: 12 residues processed: 136 average time/residue: 0.7406 time to fit residues: 106.9856 Evaluate side-chains 139 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 591 LEU 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 131 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 31 optimal weight: 0.0040 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.119996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.080691 restraints weight = 13801.456| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.04 r_work: 0.2804 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10734 Z= 0.127 Angle : 0.539 8.521 14623 Z= 0.277 Chirality : 0.041 0.184 1645 Planarity : 0.004 0.067 1804 Dihedral : 10.216 73.168 1629 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.61 % Allowed : 12.31 % 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: 0.77 (0.24), residues: 1240 helix: 1.69 (0.22), residues: 561 sheet: -0.62 (0.43), residues: 130 loop : -0.39 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 536 TYR 0.017 0.001 TYR B 533 PHE 0.012 0.001 PHE B 145 TRP 0.010 0.001 TRP A 336 HIS 0.006 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (10734) covalent geometry : angle 0.53921 / 0.28 (14623) hydrogen bonds : bond 0.03749 / 2.53 ( 455) hydrogen bonds : angle 4.25328 / 2.97 ( 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 139 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8407 (mmmm) REVERT: B 17 GLU cc_start: 0.8617 (pt0) cc_final: 0.8258 (pt0) REVERT: B 148 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: B 151 ARG cc_start: 0.8527 (mmt90) cc_final: 0.8308 (mmm160) REVERT: B 332 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8239 (mtm) REVERT: C 127 ASP cc_start: 0.8338 (t0) cc_final: 0.8008 (t70) REVERT: C 131 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7913 (mp10) outliers start: 18 outliers final: 12 residues processed: 130 average time/residue: 0.8055 time to fit residues: 111.0717 Evaluate side-chains 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 591 LEU 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 131 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.119687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.080279 restraints weight = 13909.669| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.05 r_work: 0.2832 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10734 Z= 0.142 Angle : 0.550 8.973 14623 Z= 0.282 Chirality : 0.041 0.189 1645 Planarity : 0.004 0.064 1804 Dihedral : 10.224 73.183 1629 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.96 % Allowed : 11.95 % 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: 0.76 (0.24), residues: 1240 helix: 1.70 (0.22), residues: 559 sheet: -0.63 (0.43), residues: 130 loop : -0.40 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 536 TYR 0.017 0.001 TYR B 533 PHE 0.012 0.001 PHE B 145 TRP 0.010 0.001 TRP A 336 HIS 0.006 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (10734) covalent geometry : angle 0.54978 / 0.28 (14623) hydrogen bonds : bond 0.03848 / 2.60 ( 455) hydrogen bonds : angle 4.27302 / 2.98 ( 1288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4587.43 seconds wall clock time: 78 minutes 50.04 seconds (4730.04 seconds total)