Starting phenix.real_space_refine on Wed Sep 17 20:27:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z85_39838/09_2025/8z85_39838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z85_39838/09_2025/8z85_39838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z85_39838/09_2025/8z85_39838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z85_39838/09_2025/8z85_39838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z85_39838/09_2025/8z85_39838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z85_39838/09_2025/8z85_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-2.0-5805/lib/python3.9/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: 2.86, per 1000 atoms: 0.27 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: 1.03 Conformation dependent library (CDL) restraints added in 392.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.34 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: 1.82 Time building geometry restraints manager: 1.33 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: 0.570 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.030 Find NCS groups from input model: 0.080 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10734 Z= 0.095 Angle : 0.484 6.893 14623 Z= 0.249 Chirality : 0.038 0.136 1645 Planarity : 0.004 0.044 1804 Dihedral : 13.262 85.961 4144 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00209 (10734) covalent geometry : angle 0.48408 (14623) hydrogen bonds : bond 0.24420 ( 455) hydrogen bonds : angle 7.23443 ( 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 : 0.447 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: 0.8048 time to fit residues: 136.3673 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 : 0.438 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 311 GLN A 516 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 132 ASN B 148 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.084306 restraints weight = 14075.587| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.10 r_work: 0.2868 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10734 Z= 0.135 Angle : 0.563 7.282 14623 Z= 0.290 Chirality : 0.041 0.161 1645 Planarity : 0.005 0.048 1804 Dihedral : 10.193 73.071 1629 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.61 % Allowed : 6.96 % 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 aren not related in a simple way. whole: 0.56 (0.24), residues: 1240 helix: 1.24 (0.22), residues: 558 sheet: -0.00 (0.45), residues: 128 loop : -0.35 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 536 TYR 0.017 0.002 TYR A 489 PHE 0.016 0.001 PHE A 483 TRP 0.010 0.001 TRP A 336 HIS 0.006 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00295 (10734) covalent geometry : angle 0.56304 (14623) hydrogen bonds : bond 0.05100 ( 455) hydrogen bonds : angle 4.89374 ( 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 146 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.8748 (m110) cc_final: 0.8537 (m110) REVERT: A 546 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8528 (ptt) REVERT: B 93 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7871 (mpp80) REVERT: B 332 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.7888 (mmm) outliers start: 18 outliers final: 5 residues processed: 133 average time/residue: 0.7929 time to fit residues: 112.0050 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 : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 546 MET 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 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: 0.0970 chunk 124 optimal weight: 4.9990 chunk 8 optimal weight: 30.0000 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 99 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 311 GLN A 358 ASN A 516 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.078129 restraints weight = 14007.298| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.07 r_work: 0.2786 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10734 Z= 0.226 Angle : 0.607 9.572 14623 Z= 0.314 Chirality : 0.045 0.202 1645 Planarity : 0.005 0.040 1804 Dihedral : 10.360 72.856 1629 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.23 % Allowed : 8.56 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.23), residues: 1240 helix: 1.32 (0.22), residues: 557 sheet: -0.29 (0.42), residues: 130 loop : -0.47 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 151 TYR 0.015 0.002 TYR B 533 PHE 0.018 0.002 PHE A 483 TRP 0.014 0.002 TRP A 426 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00527 (10734) covalent geometry : angle 0.60722 (14623) hydrogen bonds : bond 0.05108 ( 455) hydrogen bonds : angle 4.64125 ( 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 155 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASN cc_start: 0.8730 (m110) cc_final: 0.8494 (m110) REVERT: A 472 LYS cc_start: 0.8405 (mtmm) cc_final: 0.8186 (mtpp) REVERT: B 17 GLU cc_start: 0.8625 (pt0) cc_final: 0.8331 (pt0) REVERT: B 93 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7930 (mtp180) REVERT: B 332 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8012 (mmm) REVERT: B 588 GLU cc_start: 0.7902 (tp30) cc_final: 0.7426 (tp30) REVERT: C 68 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8712 (p) outliers start: 25 outliers final: 11 residues processed: 143 average time/residue: 0.7870 time to fit residues: 119.3595 Evaluate side-chains 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 93 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 0.0030 chunk 87 optimal weight: 0.5980 chunk 121 optimal weight: 0.0980 chunk 112 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN ** B 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 = 0.3606 r_free = 0.3606 target = 0.121592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.082724 restraints weight = 14097.807| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.09 r_work: 0.2863 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10734 Z= 0.098 Angle : 0.498 6.378 14623 Z= 0.256 Chirality : 0.039 0.155 1645 Planarity : 0.004 0.036 1804 Dihedral : 10.188 73.295 1629 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.87 % Allowed : 9.81 % 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 aren not related in a simple way. whole: 0.74 (0.24), residues: 1240 helix: 1.62 (0.22), residues: 558 sheet: -0.37 (0.43), residues: 130 loop : -0.41 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 536 TYR 0.016 0.001 TYR A 489 PHE 0.010 0.001 PHE B 214 TRP 0.010 0.001 TRP B 330 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00206 (10734) covalent geometry : angle 0.49799 (14623) hydrogen bonds : bond 0.03603 ( 455) hydrogen bonds : angle 4.35673 ( 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: 21 poor density : 132 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 516 ASN cc_start: 0.8779 (m-40) cc_final: 0.8247 (m110) REVERT: B 17 GLU cc_start: 0.8558 (pt0) cc_final: 0.8259 (pt0) REVERT: B 131 ARG cc_start: 0.8517 (ptt90) cc_final: 0.8278 (ptt90) REVERT: B 151 ARG cc_start: 0.8603 (mmt90) cc_final: 0.8365 (mmm160) REVERT: B 369 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8733 (mmm) outliers start: 21 outliers final: 8 residues processed: 141 average time/residue: 0.7832 time to fit residues: 117.1878 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 : 0.383 ------------------------------------------------------------------------------- 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 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 369 MET Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 HIS B 148 GLN B 476 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.077559 restraints weight = 13955.047| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.06 r_work: 0.2748 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10734 Z= 0.227 Angle : 0.588 7.387 14623 Z= 0.304 Chirality : 0.044 0.171 1645 Planarity : 0.005 0.043 1804 Dihedral : 10.345 72.963 1629 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.50 % Allowed : 9.81 % Favored : 87.69 % 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 aren not related in a simple way. whole: 0.59 (0.23), residues: 1240 helix: 1.48 (0.22), residues: 560 sheet: -0.46 (0.43), residues: 130 loop : -0.48 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 536 TYR 0.016 0.002 TYR B 533 PHE 0.015 0.002 PHE B 48 TRP 0.015 0.002 TRP A 426 HIS 0.005 0.001 HIS B 531 Details of bonding type rmsd covalent geometry : bond 0.00533 (10734) covalent geometry : angle 0.58780 (14623) hydrogen bonds : bond 0.04713 ( 455) hydrogen bonds : angle 4.44926 ( 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: 28 poor density : 127 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.8634 (pt0) cc_final: 0.8302 (pt0) REVERT: B 588 GLU cc_start: 0.7764 (tp30) cc_final: 0.7427 (tp30) REVERT: C 131 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7916 (mp10) outliers start: 28 outliers final: 10 residues processed: 139 average time/residue: 0.8264 time to fit residues: 121.6010 Evaluate side-chains 137 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 10 optimal weight: 30.0000 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN B 476 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.079722 restraints weight = 14087.067| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.09 r_work: 0.2819 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2186 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= 0.129 Angle : 0.515 5.158 14623 Z= 0.266 Chirality : 0.041 0.164 1645 Planarity : 0.004 0.042 1804 Dihedral : 10.249 73.228 1629 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.87 % Allowed : 10.62 % 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 aren not related in a simple way. whole: 0.72 (0.24), residues: 1240 helix: 1.63 (0.22), residues: 560 sheet: -0.51 (0.43), residues: 130 loop : -0.44 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 536 TYR 0.017 0.001 TYR B 533 PHE 0.012 0.001 PHE B 214 TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00294 (10734) covalent geometry : angle 0.51539 (14623) hydrogen bonds : bond 0.03851 ( 455) hydrogen bonds : angle 4.28004 ( 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 150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.8593 (pt0) cc_final: 0.8322 (pt0) REVERT: B 93 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8039 (mtp85) REVERT: B 131 ARG cc_start: 0.8434 (ptt90) cc_final: 0.8109 (ptt90) REVERT: B 588 GLU cc_start: 0.7768 (tp30) cc_final: 0.7470 (tp30) outliers start: 21 outliers final: 10 residues processed: 139 average time/residue: 0.8065 time to fit residues: 118.7141 Evaluate side-chains 137 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 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 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 49 optimal weight: 0.0670 chunk 6 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 77 optimal weight: 0.2980 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 516 ASN B 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080341 restraints weight = 13894.545| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.06 r_work: 0.2831 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10734 Z= 0.121 Angle : 0.505 5.152 14623 Z= 0.260 Chirality : 0.040 0.157 1645 Planarity : 0.004 0.047 1804 Dihedral : 10.187 73.201 1629 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.05 % Allowed : 10.88 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.24), residues: 1240 helix: 1.74 (0.22), residues: 559 sheet: -0.57 (0.43), residues: 130 loop : -0.42 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 536 TYR 0.018 0.001 TYR A 489 PHE 0.011 0.001 PHE B 214 TRP 0.011 0.001 TRP B 330 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00276 (10734) covalent geometry : angle 0.50503 (14623) hydrogen bonds : bond 0.03673 ( 455) hydrogen bonds : angle 4.21323 ( 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 149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.8581 (pt0) cc_final: 0.8268 (pt0) REVERT: B 131 ARG cc_start: 0.8386 (ptt90) cc_final: 0.8106 (ptt90) REVERT: B 332 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8296 (mtm) outliers start: 23 outliers final: 10 residues processed: 135 average time/residue: 0.8100 time to fit residues: 115.7688 Evaluate side-chains 135 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 393 MET 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: 3.9990 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 74 optimal weight: 0.0770 chunk 110 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN B 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.077317 restraints weight = 13811.836| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.06 r_work: 0.2779 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10734 Z= 0.220 Angle : 0.579 5.959 14623 Z= 0.299 Chirality : 0.044 0.173 1645 Planarity : 0.005 0.053 1804 Dihedral : 10.322 72.973 1629 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.14 % Allowed : 11.24 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.23), residues: 1240 helix: 1.42 (0.22), residues: 571 sheet: -0.55 (0.43), residues: 129 loop : -0.58 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 536 TYR 0.017 0.002 TYR B 533 PHE 0.013 0.002 PHE B 214 TRP 0.014 0.002 TRP A 426 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00523 (10734) covalent geometry : angle 0.57891 (14623) hydrogen bonds : bond 0.04505 ( 455) hydrogen bonds : angle 4.33522 ( 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: 24 poor density : 122 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.8652 (pt0) cc_final: 0.8324 (pt0) REVERT: B 93 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8074 (mtp85) REVERT: B 131 ARG cc_start: 0.8418 (ptt90) cc_final: 0.8162 (ptt90) REVERT: C 68 SER cc_start: 0.9036 (OUTLIER) cc_final: 0.8709 (p) outliers start: 24 outliers final: 10 residues processed: 134 average time/residue: 0.7639 time to fit residues: 108.5733 Evaluate side-chains 134 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 546 MET 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 108 SER 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: 0.0980 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3597 r_free = 0.3597 target = 0.120623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.081372 restraints weight = 13800.932| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.05 r_work: 0.2850 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10734 Z= 0.103 Angle : 0.507 6.952 14623 Z= 0.260 Chirality : 0.040 0.157 1645 Planarity : 0.004 0.053 1804 Dihedral : 10.154 73.308 1629 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.61 % Allowed : 11.95 % 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 aren not related in a simple way. whole: 0.83 (0.24), residues: 1240 helix: 1.78 (0.22), residues: 560 sheet: -0.59 (0.43), residues: 130 loop : -0.41 (0.26), residues: 550 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 0.010 0.001 PHE B 214 TRP 0.011 0.001 TRP B 330 HIS 0.003 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00228 (10734) covalent geometry : angle 0.50684 (14623) hydrogen bonds : bond 0.03398 ( 455) hydrogen bonds : angle 4.13244 ( 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 141 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.8608 (pt0) cc_final: 0.8280 (pt0) REVERT: B 131 ARG cc_start: 0.8350 (ptt90) cc_final: 0.8083 (ptt90) outliers start: 18 outliers final: 8 residues processed: 131 average time/residue: 0.7692 time to fit residues: 106.8304 Evaluate side-chains 130 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 6.9990 chunk 116 optimal weight: 0.0000 chunk 31 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 98 optimal weight: 0.3980 chunk 117 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN B 475 HIS B 567 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.082134 restraints weight = 13794.781| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.05 r_work: 0.2833 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2402 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= 0.102 Angle : 0.506 7.013 14623 Z= 0.258 Chirality : 0.039 0.144 1645 Planarity : 0.004 0.059 1804 Dihedral : 10.093 73.262 1629 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.16 % Allowed : 12.58 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.24), residues: 1240 helix: 1.87 (0.22), residues: 557 sheet: -0.54 (0.43), residues: 133 loop : -0.36 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 536 TYR 0.016 0.001 TYR B 533 PHE 0.011 0.001 PHE B 214 TRP 0.012 0.001 TRP B 330 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00227 (10734) covalent geometry : angle 0.50555 (14623) hydrogen bonds : bond 0.03338 ( 455) hydrogen bonds : angle 4.10359 ( 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 136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.8647 (pt0) cc_final: 0.8289 (pt0) REVERT: B 131 ARG cc_start: 0.8390 (ptt90) cc_final: 0.8143 (ptt90) REVERT: B 148 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: B 151 ARG cc_start: 0.8391 (mmt90) cc_final: 0.8118 (mmm160) REVERT: C 67 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8690 (pt) outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 0.8436 time to fit residues: 114.2582 Evaluate side-chains 132 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 546 MET 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 68 SER Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 110 optimal weight: 0.0770 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN B 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.121510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.082296 restraints weight = 13960.374| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.08 r_work: 0.2868 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2432 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= 0.101 Angle : 0.498 6.398 14623 Z= 0.254 Chirality : 0.039 0.144 1645 Planarity : 0.004 0.061 1804 Dihedral : 10.076 73.259 1629 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.34 % Allowed : 12.13 % 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 aren not related in a simple way. whole: 0.98 (0.24), residues: 1240 helix: 1.95 (0.22), residues: 553 sheet: -0.57 (0.43), residues: 133 loop : -0.32 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 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 0.003 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00225 (10734) covalent geometry : angle 0.49823 (14623) hydrogen bonds : bond 0.03311 ( 455) hydrogen bonds : angle 4.07371 ( 1288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5382.56 seconds wall clock time: 92 minutes 10.83 seconds (5530.83 seconds total)