Starting phenix.real_space_refine on Sun Aug 4 18:11:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z85_39838/08_2024/8z85_39838.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z85_39838/08_2024/8z85_39838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z85_39838/08_2024/8z85_39838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z85_39838/08_2024/8z85_39838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z85_39838/08_2024/8z85_39838.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z85_39838/08_2024/8z85_39838.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1075 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 63 5.16 5 C 6585 2.51 5 N 1804 2.21 5 O 1998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10467 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4771 Classifications: {'peptide': 591} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 561} Chain breaks: 2 Chain: "B" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4702 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 31, 'TRANS': 558} Chain breaks: 2 Chain: "C" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 608 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain breaks: 1 Chain: "D" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 283 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "E" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Time building chain proxies: 5.98, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 3.70 Conformation dependent library (CDL) restraints added in 1.7 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 49.6% alpha, 11.6% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.752A pdb=" N LEU A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 155 removed outlier: 4.745A pdb=" N GLY A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N CYS A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.965A pdb=" N GLN A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.526A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.999A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.433A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.710A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 517 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.810A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 4.014A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 13 through 20 removed outlier: 4.244A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 47 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 95 through 108 removed outlier: 3.622A pdb=" N LYS B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.713A pdb=" N LYS B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.652A pdb=" N GLU B 117 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.543A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.127A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.728A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 Proline residue: B 338 - end of helix removed outlier: 3.557A pdb=" N SER B 344 " --> pdb=" O MET B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 removed outlier: 4.429A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 3.618A pdb=" N SER B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 449 removed outlier: 3.552A pdb=" N LYS B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 459 removed outlier: 3.774A pdb=" N CYS B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.674A pdb=" N TYR B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.594A pdb=" N MET B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'C' and resid 52 through 55 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.921A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.688A pdb=" N LYS C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.782A pdb=" N LEU A 117 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 removed outlier: 4.503A pdb=" N ASN B 453 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 238 removed outlier: 4.253A pdb=" N ILE A 450 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 423 through 431 current: chain 'A' and resid 463 through 469 removed outlier: 6.757A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.141A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 442 through 451 current: chain 'A' and resid 290 through 291 Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245 removed outlier: 4.587A pdb=" N THR B 228 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 469 Processing sheet with id=AB3, first strand: chain 'B' and resid 633 through 634 removed outlier: 4.697A pdb=" N THR B 633 " --> pdb=" O SER C 68 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2846 1.33 - 1.45: 1854 1.45 - 1.57: 5896 1.57 - 1.69: 33 1.69 - 1.81: 105 Bond restraints: 10734 Sorted by residual: bond pdb=" CA LYS A 170 " pdb=" CB LYS A 170 " ideal model delta sigma weight residual 1.518 1.541 -0.023 2.08e-02 2.31e+03 1.27e+00 bond pdb=" C ALA A 169 " pdb=" N LYS A 170 " ideal model delta sigma weight residual 1.325 1.338 -0.013 1.14e-02 7.69e+03 1.25e+00 bond pdb=" CA VAL B 491 " pdb=" CB VAL B 491 " ideal model delta sigma weight residual 1.546 1.538 0.009 8.80e-03 1.29e+04 9.61e-01 bond pdb=" CA ILE A 414 " pdb=" CB ILE A 414 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 8.37e-01 bond pdb=" CB MET B 526 " pdb=" CG MET B 526 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.58e-01 ... (remaining 10729 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.22: 435 106.22 - 113.18: 5849 113.18 - 120.15: 3684 120.15 - 127.12: 4474 127.12 - 134.09: 181 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.790 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10734 Z= 0.136 Angle : 0.484 6.893 14623 Z= 0.249 Chirality : 0.038 0.136 1645 Planarity : 0.004 0.044 1804 Dihedral : 13.262 85.961 4144 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1240 helix: 0.58 (0.22), residues: 543 sheet: 0.43 (0.46), residues: 123 loop : -0.55 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.006 0.001 HIS B 476 PHE 0.017 0.001 PHE A 483 TYR 0.015 0.001 TYR B 22 ARG 0.008 0.000 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 155 ASN cc_start: 0.7519 (m110) cc_final: 0.7080 (m110) REVERT: B 422 ASP cc_start: 0.7675 (p0) cc_final: 0.7249 (p0) REVERT: B 575 ASP cc_start: 0.8128 (t70) cc_final: 0.7884 (t70) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 1.4693 time to fit residues: 249.9785 Evaluate side-chains 130 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 311 GLN A 516 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 132 ASN B 148 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10734 Z= 0.230 Angle : 0.581 7.408 14623 Z= 0.299 Chirality : 0.043 0.182 1645 Planarity : 0.005 0.049 1804 Dihedral : 10.234 73.017 1629 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.61 % Allowed : 7.23 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1240 helix: 1.21 (0.22), residues: 559 sheet: -0.02 (0.45), residues: 128 loop : -0.40 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.005 0.001 HIS A 577 PHE 0.018 0.002 PHE A 483 TYR 0.018 0.002 TYR A 489 ARG 0.013 0.001 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: B 93 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7545 (mpp80) REVERT: B 332 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7615 (mmm) REVERT: C 68 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8496 (p) outliers start: 18 outliers final: 5 residues processed: 138 average time/residue: 1.4968 time to fit residues: 219.6819 Evaluate side-chains 138 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.0170 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 311 GLN A 358 ASN A 516 ASN B 148 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10734 Z= 0.222 Angle : 0.542 7.993 14623 Z= 0.280 Chirality : 0.042 0.176 1645 Planarity : 0.004 0.038 1804 Dihedral : 10.251 73.141 1629 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.41 % Allowed : 8.74 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1240 helix: 1.49 (0.22), residues: 559 sheet: -0.29 (0.43), residues: 130 loop : -0.41 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS B 475 PHE 0.017 0.001 PHE A 483 TYR 0.014 0.002 TYR B 533 ARG 0.007 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.8650 (mtm) cc_final: 0.8437 (mtt) REVERT: A 468 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8249 (mmmm) REVERT: A 489 TYR cc_start: 0.8845 (t80) cc_final: 0.8613 (t80) REVERT: A 546 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8391 (ptm) REVERT: B 17 GLU cc_start: 0.7850 (pt0) cc_final: 0.7639 (pt0) REVERT: B 131 ARG cc_start: 0.8368 (ptt90) cc_final: 0.8096 (ptt90) REVERT: B 383 ASN cc_start: 0.8649 (t0) cc_final: 0.8191 (t0) outliers start: 27 outliers final: 12 residues processed: 145 average time/residue: 1.5187 time to fit residues: 234.0821 Evaluate side-chains 142 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10734 Z= 0.230 Angle : 0.535 7.748 14623 Z= 0.275 Chirality : 0.042 0.179 1645 Planarity : 0.004 0.038 1804 Dihedral : 10.257 73.085 1629 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.50 % Allowed : 9.10 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1240 helix: 1.55 (0.22), residues: 560 sheet: -0.45 (0.43), residues: 130 loop : -0.42 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 426 HIS 0.004 0.001 HIS B 476 PHE 0.013 0.001 PHE A 483 TYR 0.016 0.002 TYR B 533 ARG 0.010 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8254 (mmmm) REVERT: A 516 ASN cc_start: 0.8857 (m-40) cc_final: 0.8226 (m110) REVERT: A 546 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8338 (ptm) REVERT: B 17 GLU cc_start: 0.7896 (pt0) cc_final: 0.7680 (pt0) REVERT: B 131 ARG cc_start: 0.8317 (ptt90) cc_final: 0.8041 (ptt90) REVERT: B 369 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8311 (mmm) REVERT: B 383 ASN cc_start: 0.8790 (t0) cc_final: 0.8388 (t0) REVERT: B 436 MET cc_start: 0.8868 (ttp) cc_final: 0.8615 (ttp) outliers start: 28 outliers final: 12 residues processed: 142 average time/residue: 1.5616 time to fit residues: 236.3168 Evaluate side-chains 146 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain 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 B residue 625 SER Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.0020 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10734 Z= 0.166 Angle : 0.502 7.196 14623 Z= 0.258 Chirality : 0.040 0.168 1645 Planarity : 0.004 0.039 1804 Dihedral : 10.189 73.228 1629 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.23 % Allowed : 9.72 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1240 helix: 1.66 (0.22), residues: 562 sheet: -0.46 (0.43), residues: 130 loop : -0.39 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS B 476 PHE 0.012 0.001 PHE B 214 TYR 0.017 0.001 TYR A 489 ARG 0.010 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8277 (mmmm) REVERT: A 546 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8261 (ptm) REVERT: B 93 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7635 (mtp85) REVERT: B 131 ARG cc_start: 0.8262 (ptt90) cc_final: 0.8022 (ptt90) REVERT: B 383 ASN cc_start: 0.8840 (t0) cc_final: 0.8454 (t0) outliers start: 25 outliers final: 10 residues processed: 147 average time/residue: 1.4842 time to fit residues: 232.4100 Evaluate side-chains 141 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 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 C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.1980 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A 577 HIS B 148 GLN B 476 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.005 0.038 10734 Z= 0.335 Angle : 0.578 8.859 14623 Z= 0.298 Chirality : 0.044 0.198 1645 Planarity : 0.005 0.047 1804 Dihedral : 10.322 73.104 1629 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.32 % Allowed : 10.44 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1240 helix: 1.43 (0.22), residues: 569 sheet: -0.46 (0.43), residues: 133 loop : -0.56 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 426 HIS 0.004 0.001 HIS B 531 PHE 0.014 0.002 PHE B 48 TYR 0.017 0.002 TYR B 533 ARG 0.011 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8251 (mmmm) REVERT: A 546 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8461 (ptm) REVERT: B 93 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7624 (mtp85) REVERT: B 131 ARG cc_start: 0.8250 (ptt90) cc_final: 0.7950 (ptt90) REVERT: C 131 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7571 (mp10) outliers start: 26 outliers final: 12 residues processed: 143 average time/residue: 1.5498 time to fit residues: 235.7647 Evaluate side-chains 140 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 93 ARG 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 B residue 625 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 131 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2265 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= 0.175 Angle : 0.514 7.215 14623 Z= 0.264 Chirality : 0.040 0.169 1645 Planarity : 0.004 0.046 1804 Dihedral : 10.201 73.249 1629 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.69 % Allowed : 11.69 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1240 helix: 1.71 (0.22), residues: 560 sheet: -0.56 (0.43), residues: 130 loop : -0.45 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 330 HIS 0.006 0.001 HIS B 475 PHE 0.011 0.001 PHE B 214 TYR 0.017 0.001 TYR B 533 ARG 0.012 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8260 (mmmm) REVERT: A 546 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8293 (ptm) REVERT: B 131 ARG cc_start: 0.8198 (ptt90) cc_final: 0.7895 (ptt90) REVERT: B 436 MET cc_start: 0.8846 (ttp) cc_final: 0.8587 (ttp) REVERT: C 131 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7561 (mp10) outliers start: 19 outliers final: 8 residues processed: 133 average time/residue: 1.5255 time to fit residues: 215.6218 Evaluate side-chains 132 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 131 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN B 476 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10734 Z= 0.179 Angle : 0.521 7.207 14623 Z= 0.266 Chirality : 0.040 0.170 1645 Planarity : 0.004 0.054 1804 Dihedral : 10.179 73.205 1629 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.61 % Allowed : 11.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1240 helix: 1.76 (0.22), residues: 559 sheet: -0.56 (0.43), residues: 130 loop : -0.41 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.006 0.001 HIS B 475 PHE 0.011 0.001 PHE B 214 TYR 0.019 0.001 TYR A 489 ARG 0.013 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8269 (mmmm) REVERT: A 546 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8278 (ptm) REVERT: B 131 ARG cc_start: 0.8203 (ptt90) cc_final: 0.7981 (ptt90) REVERT: C 131 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7583 (mp10) outliers start: 18 outliers final: 9 residues processed: 132 average time/residue: 1.5011 time to fit residues: 211.0202 Evaluate side-chains 132 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 131 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2336 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= 0.202 Angle : 0.533 7.510 14623 Z= 0.272 Chirality : 0.041 0.174 1645 Planarity : 0.004 0.058 1804 Dihedral : 10.185 73.167 1629 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.78 % Allowed : 11.86 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1240 helix: 1.74 (0.22), residues: 559 sheet: -0.58 (0.43), residues: 130 loop : -0.42 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.006 0.001 HIS B 475 PHE 0.011 0.001 PHE B 214 TYR 0.016 0.001 TYR B 533 ARG 0.013 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8260 (mmmm) REVERT: A 546 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8316 (ptm) REVERT: B 131 ARG cc_start: 0.8214 (ptt90) cc_final: 0.7993 (ptt90) REVERT: C 68 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8532 (p) REVERT: C 72 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.8736 (p) REVERT: C 98 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.8050 (mtm-85) REVERT: C 131 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7608 (mp10) outliers start: 20 outliers final: 9 residues processed: 132 average time/residue: 1.6143 time to fit residues: 226.3557 Evaluate side-chains 135 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER 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 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.0570 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN B 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2409 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= 0.170 Angle : 0.518 7.015 14623 Z= 0.264 Chirality : 0.040 0.166 1645 Planarity : 0.004 0.060 1804 Dihedral : 10.142 73.211 1629 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.69 % Allowed : 11.95 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.24), residues: 1240 helix: 1.82 (0.22), residues: 554 sheet: -0.54 (0.44), residues: 133 loop : -0.38 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 330 HIS 0.005 0.001 HIS B 475 PHE 0.011 0.001 PHE B 214 TYR 0.016 0.001 TYR B 533 ARG 0.014 0.000 ARG A 536 ********************** REFINEMENT MACRO_CYCLE 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 140 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8260 (mmmm) REVERT: A 546 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8268 (ptm) REVERT: B 131 ARG cc_start: 0.8196 (ptt90) cc_final: 0.7912 (ptt90) REVERT: C 68 SER cc_start: 0.8887 (OUTLIER) cc_final: 0.8530 (p) REVERT: C 72 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8764 (p) REVERT: C 98 ARG cc_start: 0.8281 (ptm-80) cc_final: 0.8046 (mtm-85) REVERT: C 131 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7598 (mp10) outliers start: 19 outliers final: 8 residues processed: 132 average time/residue: 1.5563 time to fit residues: 218.6522 Evaluate side-chains 134 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 131 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.0040 chunk 92 optimal weight: 0.0670 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 102 optimal weight: 0.0270 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 overall best weight: 0.2588 ------------------------------------------------------------------------------- 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 531 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 = 0.3630 r_free = 0.3630 target = 0.122984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.084462 restraints weight = 13781.938| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.05 r_work: 0.2875 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2452 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= 0.125 Angle : 0.495 6.564 14623 Z= 0.252 Chirality : 0.039 0.147 1645 Planarity : 0.004 0.056 1804 Dihedral : 10.011 73.366 1629 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.07 % Allowed : 12.49 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1240 helix: 1.92 (0.22), residues: 557 sheet: -0.52 (0.44), residues: 133 loop : -0.35 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 330 HIS 0.005 0.001 HIS B 475 PHE 0.010 0.001 PHE B 214 TYR 0.016 0.001 TYR B 533 ARG 0.015 0.000 ARG A 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.41 seconds wall clock time: 79 minutes 19.57 seconds (4759.57 seconds total)