Starting phenix.real_space_refine on Thu Sep 26 14:47:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/09_2024/8z9q_39867.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/09_2024/8z9q_39867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/09_2024/8z9q_39867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/09_2024/8z9q_39867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/09_2024/8z9q_39867.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/09_2024/8z9q_39867.cif" } resolution = 2.33 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= 0.075 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 1345 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 12 5.49 5 S 74 5.16 5 C 7803 2.51 5 N 2153 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12362 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5020 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5190 Classifications: {'peptide': 647} Link IDs: {'PTRANS': 33, 'TRANS': 613} Chain breaks: 4 Chain: "C" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1926 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain breaks: 1 Chain: "D" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 226 Unusual residues: {'ATP': 1} Classifications: {'RNA': 9, 'undetermined': 1} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 5, None: 1} Not linked: pdbres="ATP D 1 " pdbres=" G D 2 " Time building chain proxies: 7.28, per 1000 atoms: 0.59 Number of scatterers: 12362 At special positions: 0 Unit cell: (91.104, 100.74, 134.028, 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 74 16.00 P 12 15.00 O 2320 8.00 N 2153 7.00 C 7803 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2878 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 50.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.964A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 80 through 84 removed outlier: 4.024A pdb=" N THR A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' 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 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: 3.559A 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 305 through 316 removed outlier: 4.121A pdb=" N GLN A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.879A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.375A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.593A pdb=" N ASN A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 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: 4.458A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 4.052A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.527A pdb=" N THR B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' 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 95 Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.946A pdb=" N LYS B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.398A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.797A 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: 3.541A pdb=" N SER B 344 " --> pdb=" O MET B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 removed outlier: 4.315A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 3.543A pdb=" N SER B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 449 Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'B' and resid 648 through 662 Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.505A pdb=" N VAL B 669 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 694 Processing helix chain 'B' and resid 698 through 708 removed outlier: 3.559A pdb=" N ARG B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 33 through 36 removed outlier: 6.158A pdb=" N THR C 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.853A 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 126 through 135 Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.525A pdb=" N LYS C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.598A pdb=" N ILE C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.789A pdb=" N GLU C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.926A pdb=" N CYS C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 59 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 237 through 238 removed outlier: 4.255A pdb=" N ILE A 450 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 7.345A 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: 6.777A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.345A 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=AA5, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.502A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 227 through 230 Processing sheet with id=AA9, first strand: chain 'B' and resid 380 through 381 Processing sheet with id=AB1, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB2, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.867A pdb=" N THR C 97 " --> pdb=" O MET C 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 143 removed outlier: 4.900A pdb=" N HIS C 252 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE C 141 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR C 250 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.605A pdb=" N LYS C 151 " --> pdb=" O LEU C 227 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3994 1.34 - 1.46: 1800 1.46 - 1.57: 6720 1.57 - 1.69: 22 1.69 - 1.81: 120 Bond restraints: 12656 Sorted by residual: bond pdb=" CB ARG B 315 " pdb=" CG ARG B 315 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" CB ILE B 452 " pdb=" CG2 ILE B 452 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CA ARG A 147 " pdb=" CB ARG A 147 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.17e+00 bond pdb=" CG1 ILE A 606 " pdb=" CD1 ILE A 606 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.14e-01 bond pdb=" N LYS B 357 " pdb=" CA LYS B 357 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.24e-02 6.50e+03 6.12e-01 ... (remaining 12651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 17027 2.28 - 4.56: 141 4.56 - 6.85: 13 6.85 - 9.13: 2 9.13 - 11.41: 1 Bond angle restraints: 17184 Sorted by residual: angle pdb=" C CYS A 146 " pdb=" N ARG A 147 " pdb=" CA ARG A 147 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" N ARG A 147 " pdb=" CA ARG A 147 " pdb=" CB ARG A 147 " ideal model delta sigma weight residual 110.49 115.74 -5.25 1.69e+00 3.50e-01 9.64e+00 angle pdb=" CA ARG A 147 " pdb=" CB ARG A 147 " pdb=" CG ARG A 147 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.63e+00 angle pdb=" CG1 ILE B 452 " pdb=" CB ILE B 452 " pdb=" CG2 ILE B 452 " ideal model delta sigma weight residual 110.70 102.97 7.73 3.00e+00 1.11e-01 6.63e+00 angle pdb=" CA LEU B 487 " pdb=" CB LEU B 487 " pdb=" CG LEU B 487 " ideal model delta sigma weight residual 116.30 124.66 -8.36 3.50e+00 8.16e-02 5.71e+00 ... (remaining 17179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7114 17.77 - 35.53: 493 35.53 - 53.30: 87 53.30 - 71.07: 25 71.07 - 88.83: 14 Dihedral angle restraints: 7733 sinusoidal: 3307 harmonic: 4426 Sorted by residual: dihedral pdb=" CA ARG A 147 " pdb=" C ARG A 147 " pdb=" N ALA A 148 " pdb=" CA ALA A 148 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LEU A 145 " pdb=" C LEU A 145 " pdb=" N CYS A 146 " pdb=" CA CYS A 146 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS C 233 " pdb=" C HIS C 233 " pdb=" N THR C 234 " pdb=" CA THR C 234 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1354 0.036 - 0.072: 417 0.072 - 0.108: 115 0.108 - 0.145: 31 0.145 - 0.181: 2 Chirality restraints: 1919 Sorted by residual: chirality pdb=" CB ILE B 452 " pdb=" CA ILE B 452 " pdb=" CG1 ILE B 452 " pdb=" CG2 ILE B 452 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CG LEU A 550 " pdb=" CB LEU A 550 " pdb=" CD1 LEU A 550 " pdb=" CD2 LEU A 550 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ARG A 147 " pdb=" N ARG A 147 " pdb=" C ARG A 147 " pdb=" CB ARG A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1916 not shown) Planarity restraints: 2158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 463 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 464 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 464 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 464 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 604 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 605 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 11 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO B 12 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 12 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 12 " -0.023 5.00e-02 4.00e+02 ... (remaining 2155 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 234 2.67 - 3.23: 11908 3.23 - 3.79: 19866 3.79 - 4.34: 28172 4.34 - 4.90: 45310 Nonbonded interactions: 105490 Sorted by model distance: nonbonded pdb=" OG SER B 472 " pdb=" O VAL B 483 " model vdw 2.117 3.040 nonbonded pdb=" OD2 ASP B 500 " pdb=" OH TYR B 537 " model vdw 2.134 3.040 nonbonded pdb=" O ASN C 163 " pdb=" OG SER C 166 " model vdw 2.211 3.040 nonbonded pdb=" O THR A 269 " pdb=" OG SER A 463 " model vdw 2.238 3.040 nonbonded pdb=" OD1 ASP B 172 " pdb=" NH2 ARG B 216 " model vdw 2.243 3.120 ... (remaining 105485 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.420 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.003 0.036 12656 Z= 0.167 Angle : 0.534 11.412 17184 Z= 0.277 Chirality : 0.040 0.181 1919 Planarity : 0.005 0.042 2158 Dihedral : 13.208 88.832 4855 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 0.58 (0.22), residues: 1489 helix: 1.12 (0.20), residues: 688 sheet: 0.62 (0.47), residues: 124 loop : -0.35 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.006 0.001 HIS A 573 PHE 0.027 0.002 PHE A 483 TYR 0.019 0.001 TYR B 104 ARG 0.006 0.000 ARG B 686 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.435 Fit side-chains REVERT: A 86 ASP cc_start: 0.7653 (m-30) cc_final: 0.7424 (m-30) REVERT: A 139 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 163 GLU cc_start: 0.8261 (tp30) cc_final: 0.7851 (tp30) REVERT: A 307 GLN cc_start: 0.7293 (pp30) cc_final: 0.7090 (pp30) REVERT: B 30 TYR cc_start: 0.7834 (m-80) cc_final: 0.7596 (m-80) REVERT: B 243 ILE cc_start: 0.9069 (pt) cc_final: 0.8855 (pp) REVERT: B 283 LYS cc_start: 0.8272 (tptt) cc_final: 0.8033 (tppt) REVERT: B 287 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7626 (tmtt) REVERT: B 672 GLN cc_start: 0.7878 (mt0) cc_final: 0.7360 (pt0) REVERT: C 127 ASP cc_start: 0.7121 (t0) cc_final: 0.6828 (t0) REVERT: C 201 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 210 GLU cc_start: 0.7759 (pm20) cc_final: 0.7545 (mp0) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 1.7534 time to fit residues: 424.6576 Evaluate side-chains 174 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 chunk 136 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 156 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 71 ASN B 267 ASN B 302 GLN B 397 ASN B 433 HIS B 506 ASN C 214 HIS C 252 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12656 Z= 0.298 Angle : 0.601 7.628 17184 Z= 0.318 Chirality : 0.043 0.150 1919 Planarity : 0.005 0.052 2158 Dihedral : 8.769 82.122 1797 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.14 % Allowed : 8.36 % Favored : 89.50 % 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: 0.70 (0.22), residues: 1489 helix: 1.32 (0.20), residues: 683 sheet: 0.56 (0.48), residues: 118 loop : -0.36 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 336 HIS 0.011 0.002 HIS A 577 PHE 0.028 0.002 PHE C 41 TYR 0.017 0.002 TYR B 115 ARG 0.008 0.001 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 1.587 Fit side-chains REVERT: A 9 ASP cc_start: 0.7982 (p0) cc_final: 0.7686 (t70) REVERT: A 17 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7444 (tp30) REVERT: A 49 HIS cc_start: 0.7924 (m90) cc_final: 0.7720 (m90) REVERT: A 58 ASP cc_start: 0.8131 (m-30) cc_final: 0.7929 (m-30) REVERT: A 86 ASP cc_start: 0.7878 (m-30) cc_final: 0.7560 (m-30) REVERT: A 139 GLN cc_start: 0.7652 (tm-30) cc_final: 0.7148 (tm-30) REVERT: A 147 ARG cc_start: 0.7929 (ptm-80) cc_final: 0.7606 (ptm-80) REVERT: A 163 GLU cc_start: 0.8207 (tp30) cc_final: 0.7808 (tp30) REVERT: B 30 TYR cc_start: 0.7949 (m-80) cc_final: 0.7731 (m-80) REVERT: B 283 LYS cc_start: 0.8268 (tptt) cc_final: 0.8034 (tppt) REVERT: B 287 LYS cc_start: 0.7925 (tmtt) cc_final: 0.7654 (tmtt) REVERT: B 576 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: B 672 GLN cc_start: 0.7881 (mt0) cc_final: 0.7234 (pt0) REVERT: B 693 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 127 ASP cc_start: 0.7253 (t0) cc_final: 0.6877 (m-30) REVERT: C 201 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7617 (tm-30) outliers start: 29 outliers final: 8 residues processed: 205 average time/residue: 1.5716 time to fit residues: 345.5698 Evaluate side-chains 188 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 163 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 0.2980 chunk 37 optimal weight: 0.0770 chunk 136 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 507 GLN B 123 GLN B 336 ASN B 397 ASN B 433 HIS B 506 ASN C 154 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12656 Z= 0.162 Angle : 0.526 6.357 17184 Z= 0.276 Chirality : 0.039 0.133 1919 Planarity : 0.004 0.046 2158 Dihedral : 8.420 79.424 1797 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.00 % Allowed : 10.06 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1489 helix: 1.52 (0.21), residues: 684 sheet: 0.39 (0.47), residues: 118 loop : -0.34 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.007 0.001 HIS A 434 PHE 0.023 0.002 PHE C 41 TYR 0.018 0.001 TYR B 533 ARG 0.008 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.405 Fit side-chains REVERT: A 9 ASP cc_start: 0.7922 (p0) cc_final: 0.7579 (t70) REVERT: A 18 THR cc_start: 0.8770 (m) cc_final: 0.8483 (p) REVERT: A 47 ASN cc_start: 0.7879 (t0) cc_final: 0.7567 (t0) REVERT: A 49 HIS cc_start: 0.8005 (m90) cc_final: 0.7777 (m90) REVERT: A 64 ASP cc_start: 0.7128 (t0) cc_final: 0.6821 (t0) REVERT: A 86 ASP cc_start: 0.7933 (m-30) cc_final: 0.7604 (m-30) REVERT: A 139 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 163 GLU cc_start: 0.8212 (tp30) cc_final: 0.7768 (tp30) REVERT: A 212 MET cc_start: 0.7642 (ttp) cc_final: 0.7409 (ttm) REVERT: B 131 ARG cc_start: 0.8319 (ptp90) cc_final: 0.8094 (ptp-170) REVERT: B 283 LYS cc_start: 0.8266 (tptt) cc_final: 0.7993 (tppt) REVERT: B 482 ASN cc_start: 0.8449 (t0) cc_final: 0.8075 (t0) REVERT: B 672 GLN cc_start: 0.7929 (mt0) cc_final: 0.7231 (pt0) REVERT: C 127 ASP cc_start: 0.7249 (t0) cc_final: 0.6934 (m-30) REVERT: C 146 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7206 (mtt) REVERT: C 201 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7594 (tm-30) outliers start: 27 outliers final: 6 residues processed: 200 average time/residue: 1.4978 time to fit residues: 320.9972 Evaluate side-chains 183 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 146 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 307 GLN B 397 ASN C 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12656 Z= 0.195 Angle : 0.531 5.911 17184 Z= 0.279 Chirality : 0.039 0.130 1919 Planarity : 0.004 0.048 2158 Dihedral : 8.277 81.087 1797 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.92 % Allowed : 10.87 % Favored : 87.20 % 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: 0.83 (0.22), residues: 1489 helix: 1.55 (0.21), residues: 684 sheet: 0.28 (0.46), residues: 118 loop : -0.37 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.008 0.001 HIS A 434 PHE 0.024 0.002 PHE C 41 TYR 0.018 0.001 TYR B 533 ARG 0.008 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 1.274 Fit side-chains REVERT: A 9 ASP cc_start: 0.7921 (p0) cc_final: 0.7607 (t70) REVERT: A 18 THR cc_start: 0.8723 (m) cc_final: 0.8434 (p) REVERT: A 47 ASN cc_start: 0.7814 (t0) cc_final: 0.7544 (t0) REVERT: A 49 HIS cc_start: 0.8003 (m90) cc_final: 0.7735 (m90) REVERT: A 64 ASP cc_start: 0.7166 (t0) cc_final: 0.6812 (t0) REVERT: A 86 ASP cc_start: 0.7947 (m-30) cc_final: 0.7589 (m-30) REVERT: A 139 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7224 (tm-30) REVERT: A 163 GLU cc_start: 0.8224 (tp30) cc_final: 0.7777 (tp30) REVERT: A 212 MET cc_start: 0.7681 (ttp) cc_final: 0.7408 (ttm) REVERT: B 283 LYS cc_start: 0.8271 (tptt) cc_final: 0.7996 (tppt) REVERT: B 287 LYS cc_start: 0.7789 (tmtt) cc_final: 0.7556 (tmtt) REVERT: B 482 ASN cc_start: 0.8416 (t0) cc_final: 0.8147 (t0) REVERT: B 576 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: B 672 GLN cc_start: 0.7872 (mt0) cc_final: 0.7192 (pt0) REVERT: B 682 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6957 (mp0) REVERT: B 686 ARG cc_start: 0.7342 (tpm170) cc_final: 0.7077 (tpm170) REVERT: C 25 LYS cc_start: 0.8421 (ttpp) cc_final: 0.8140 (ttpp) REVERT: C 127 ASP cc_start: 0.7284 (t0) cc_final: 0.6964 (m-30) REVERT: C 146 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7290 (mtt) REVERT: C 201 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7648 (tm-30) outliers start: 26 outliers final: 11 residues processed: 199 average time/residue: 1.5246 time to fit residues: 324.7090 Evaluate side-chains 188 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 0.0270 chunk 59 optimal weight: 0.0050 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.3252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 55 GLN C 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12656 Z= 0.145 Angle : 0.506 8.105 17184 Z= 0.264 Chirality : 0.038 0.139 1919 Planarity : 0.004 0.042 2158 Dihedral : 8.016 77.869 1797 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.78 % Allowed : 11.83 % Favored : 86.39 % 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: 0.91 (0.22), residues: 1489 helix: 1.65 (0.21), residues: 685 sheet: -0.02 (0.45), residues: 122 loop : -0.31 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 330 HIS 0.007 0.001 HIS A 434 PHE 0.021 0.001 PHE C 41 TYR 0.017 0.001 TYR B 533 ARG 0.009 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 1.561 Fit side-chains REVERT: A 9 ASP cc_start: 0.7815 (p0) cc_final: 0.7543 (t70) REVERT: A 18 THR cc_start: 0.8656 (m) cc_final: 0.8360 (p) REVERT: A 49 HIS cc_start: 0.8017 (m90) cc_final: 0.7759 (m90) REVERT: A 64 ASP cc_start: 0.7260 (t0) cc_final: 0.6942 (t0) REVERT: A 86 ASP cc_start: 0.7932 (m-30) cc_final: 0.7579 (m-30) REVERT: A 139 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7219 (tm-30) REVERT: A 153 VAL cc_start: 0.8623 (t) cc_final: 0.8382 (m) REVERT: A 163 GLU cc_start: 0.8216 (tp30) cc_final: 0.7763 (tp30) REVERT: A 212 MET cc_start: 0.7587 (ttp) cc_final: 0.7378 (ttm) REVERT: B 283 LYS cc_start: 0.8264 (tptt) cc_final: 0.7995 (tppt) REVERT: B 482 ASN cc_start: 0.8308 (t0) cc_final: 0.7957 (t0) REVERT: B 576 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7181 (tt0) REVERT: B 672 GLN cc_start: 0.7892 (mt0) cc_final: 0.7238 (pt0) REVERT: B 686 ARG cc_start: 0.7240 (tpm170) cc_final: 0.7038 (tpt90) REVERT: B 693 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 127 ASP cc_start: 0.7230 (t0) cc_final: 0.6950 (m-30) REVERT: C 201 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7618 (tm-30) outliers start: 24 outliers final: 8 residues processed: 192 average time/residue: 1.5185 time to fit residues: 313.5183 Evaluate side-chains 175 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain C residue 126 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 35 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 139 optimal weight: 0.0870 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 507 GLN C 80 ASN C 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12656 Z= 0.166 Angle : 0.512 10.000 17184 Z= 0.267 Chirality : 0.038 0.130 1919 Planarity : 0.004 0.044 2158 Dihedral : 7.957 78.704 1797 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.92 % Allowed : 11.76 % Favored : 86.32 % 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: 0.88 (0.22), residues: 1489 helix: 1.62 (0.21), residues: 691 sheet: -0.10 (0.45), residues: 122 loop : -0.32 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.008 0.001 HIS A 434 PHE 0.021 0.001 PHE C 41 TYR 0.018 0.001 TYR B 533 ARG 0.005 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.380 Fit side-chains REVERT: A 9 ASP cc_start: 0.7801 (p0) cc_final: 0.7533 (t70) REVERT: A 18 THR cc_start: 0.8677 (m) cc_final: 0.8384 (p) REVERT: A 49 HIS cc_start: 0.7949 (m90) cc_final: 0.7695 (m90) REVERT: A 64 ASP cc_start: 0.7246 (t0) cc_final: 0.6888 (t0) REVERT: A 86 ASP cc_start: 0.7929 (m-30) cc_final: 0.7574 (m-30) REVERT: A 139 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 153 VAL cc_start: 0.8607 (t) cc_final: 0.8371 (m) REVERT: A 163 GLU cc_start: 0.8225 (tp30) cc_final: 0.7780 (tp30) REVERT: B 283 LYS cc_start: 0.8266 (tptt) cc_final: 0.7994 (tppt) REVERT: B 482 ASN cc_start: 0.8333 (t0) cc_final: 0.7998 (t0) REVERT: B 576 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: B 672 GLN cc_start: 0.7908 (mt0) cc_final: 0.7232 (pt0) REVERT: B 682 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6953 (mp0) REVERT: C 127 ASP cc_start: 0.7275 (t0) cc_final: 0.6995 (m-30) REVERT: C 201 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7652 (tm-30) outliers start: 26 outliers final: 10 residues processed: 197 average time/residue: 1.4488 time to fit residues: 306.8989 Evaluate side-chains 180 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 0.3980 chunk 90 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 311 GLN A 486 ASN B 55 GLN C 80 ASN C 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12656 Z= 0.169 Angle : 0.527 10.884 17184 Z= 0.272 Chirality : 0.038 0.137 1919 Planarity : 0.004 0.044 2158 Dihedral : 7.918 78.857 1797 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.41 % Allowed : 13.46 % Favored : 85.13 % 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: 0.88 (0.22), residues: 1489 helix: 1.63 (0.21), residues: 691 sheet: -0.14 (0.45), residues: 122 loop : -0.32 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 330 HIS 0.007 0.001 HIS A 434 PHE 0.021 0.001 PHE C 41 TYR 0.018 0.001 TYR B 104 ARG 0.008 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 1.506 Fit side-chains REVERT: A 9 ASP cc_start: 0.7784 (p0) cc_final: 0.7527 (t70) REVERT: A 18 THR cc_start: 0.8692 (m) cc_final: 0.8395 (p) REVERT: A 49 HIS cc_start: 0.7979 (m90) cc_final: 0.7766 (m90) REVERT: A 64 ASP cc_start: 0.7190 (t0) cc_final: 0.6860 (t0) REVERT: A 86 ASP cc_start: 0.7923 (m-30) cc_final: 0.7550 (m-30) REVERT: A 139 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 153 VAL cc_start: 0.8592 (t) cc_final: 0.8365 (m) REVERT: A 163 GLU cc_start: 0.8231 (tp30) cc_final: 0.7791 (tp30) REVERT: A 212 MET cc_start: 0.7688 (ttp) cc_final: 0.7394 (ttm) REVERT: B 283 LYS cc_start: 0.8263 (tptt) cc_final: 0.7990 (tppt) REVERT: B 348 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7342 (t70) REVERT: B 482 ASN cc_start: 0.8340 (t0) cc_final: 0.7987 (t0) REVERT: B 576 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7225 (tt0) REVERT: B 672 GLN cc_start: 0.7905 (mt0) cc_final: 0.7200 (pt0) REVERT: C 127 ASP cc_start: 0.7284 (t0) cc_final: 0.7016 (m-30) REVERT: C 194 GLU cc_start: 0.7437 (tt0) cc_final: 0.7184 (tm-30) REVERT: C 201 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7638 (tm-30) outliers start: 19 outliers final: 10 residues processed: 183 average time/residue: 1.4623 time to fit residues: 288.1105 Evaluate side-chains 180 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN C 80 ASN C 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12656 Z= 0.308 Angle : 0.593 8.206 17184 Z= 0.313 Chirality : 0.042 0.144 1919 Planarity : 0.005 0.051 2158 Dihedral : 8.246 85.638 1797 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.33 % Allowed : 14.05 % Favored : 84.62 % 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: 0.74 (0.22), residues: 1489 helix: 1.45 (0.21), residues: 689 sheet: 0.02 (0.45), residues: 118 loop : -0.37 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 253 HIS 0.009 0.001 HIS A 434 PHE 0.026 0.002 PHE C 41 TYR 0.019 0.002 TYR B 115 ARG 0.006 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 1.285 Fit side-chains REVERT: A 9 ASP cc_start: 0.7851 (p0) cc_final: 0.7606 (t70) REVERT: A 18 THR cc_start: 0.8779 (m) cc_final: 0.8523 (p) REVERT: A 64 ASP cc_start: 0.7197 (t0) cc_final: 0.6872 (t0) REVERT: A 86 ASP cc_start: 0.8000 (m-30) cc_final: 0.7563 (m-30) REVERT: A 139 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 163 GLU cc_start: 0.8258 (tp30) cc_final: 0.7828 (tp30) REVERT: A 205 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6199 (mm-30) REVERT: A 212 MET cc_start: 0.7747 (ttp) cc_final: 0.7455 (ttm) REVERT: B 283 LYS cc_start: 0.8285 (tptt) cc_final: 0.8006 (tppt) REVERT: B 576 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: B 672 GLN cc_start: 0.7796 (mt0) cc_final: 0.7118 (pt0) REVERT: C 127 ASP cc_start: 0.7341 (t0) cc_final: 0.7028 (m-30) REVERT: C 201 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7631 (tm-30) outliers start: 18 outliers final: 10 residues processed: 190 average time/residue: 1.4819 time to fit residues: 301.8126 Evaluate side-chains 182 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0770 chunk 138 optimal weight: 0.0010 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 overall best weight: 0.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN C 80 ASN C 154 GLN C 214 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12656 Z= 0.161 Angle : 0.531 9.939 17184 Z= 0.278 Chirality : 0.039 0.134 1919 Planarity : 0.004 0.043 2158 Dihedral : 7.999 80.610 1797 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.26 % Allowed : 14.50 % Favored : 84.25 % 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: 0.87 (0.22), residues: 1489 helix: 1.65 (0.21), residues: 684 sheet: 0.03 (0.46), residues: 118 loop : -0.37 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 330 HIS 0.007 0.001 HIS A 434 PHE 0.023 0.001 PHE C 41 TYR 0.020 0.001 TYR B 104 ARG 0.007 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 1.512 Fit side-chains REVERT: A 9 ASP cc_start: 0.7812 (p0) cc_final: 0.7599 (t70) REVERT: A 18 THR cc_start: 0.8759 (m) cc_final: 0.8475 (p) REVERT: A 64 ASP cc_start: 0.7149 (t0) cc_final: 0.6822 (t0) REVERT: A 86 ASP cc_start: 0.7975 (m-30) cc_final: 0.7486 (m-30) REVERT: A 139 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 153 VAL cc_start: 0.8603 (t) cc_final: 0.8365 (m) REVERT: A 163 GLU cc_start: 0.8243 (tp30) cc_final: 0.7806 (tp30) REVERT: A 212 MET cc_start: 0.7688 (ttp) cc_final: 0.7346 (ttm) REVERT: B 283 LYS cc_start: 0.8272 (tptt) cc_final: 0.7999 (tppt) REVERT: B 672 GLN cc_start: 0.7781 (mt0) cc_final: 0.7112 (pt0) REVERT: B 682 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6535 (mt-10) REVERT: B 693 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7460 (tm-30) REVERT: C 127 ASP cc_start: 0.7247 (t0) cc_final: 0.7020 (m-30) REVERT: C 201 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7651 (tm-30) outliers start: 17 outliers final: 9 residues processed: 183 average time/residue: 1.5322 time to fit residues: 301.7498 Evaluate side-chains 180 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.2980 chunk 99 optimal weight: 0.0870 chunk 149 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 118 optimal weight: 0.0370 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 131 GLN C 154 GLN C 214 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12656 Z= 0.166 Angle : 0.528 7.046 17184 Z= 0.277 Chirality : 0.039 0.138 1919 Planarity : 0.004 0.044 2158 Dihedral : 7.909 80.388 1797 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.18 % Allowed : 14.79 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1489 helix: 1.69 (0.21), residues: 685 sheet: -0.02 (0.45), residues: 118 loop : -0.37 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 330 HIS 0.007 0.001 HIS A 434 PHE 0.021 0.001 PHE C 41 TYR 0.017 0.001 TYR B 533 ARG 0.012 0.000 ARG A 582 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 1.430 Fit side-chains REVERT: A 9 ASP cc_start: 0.7776 (p0) cc_final: 0.7543 (t70) REVERT: A 18 THR cc_start: 0.8732 (m) cc_final: 0.8431 (p) REVERT: A 64 ASP cc_start: 0.7124 (t0) cc_final: 0.6767 (t0) REVERT: A 86 ASP cc_start: 0.7957 (m-30) cc_final: 0.7496 (m-30) REVERT: A 139 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 153 VAL cc_start: 0.8596 (t) cc_final: 0.8390 (m) REVERT: A 163 GLU cc_start: 0.8245 (tp30) cc_final: 0.7811 (tp30) REVERT: A 212 MET cc_start: 0.7670 (ttp) cc_final: 0.7328 (ttm) REVERT: B 283 LYS cc_start: 0.8275 (tptt) cc_final: 0.7981 (tppt) REVERT: B 576 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: B 672 GLN cc_start: 0.7844 (mt0) cc_final: 0.7110 (pt0) REVERT: B 682 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: B 693 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7442 (tm-30) REVERT: C 127 ASP cc_start: 0.7249 (t0) cc_final: 0.7020 (m-30) REVERT: C 201 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7634 (tm-30) outliers start: 16 outliers final: 9 residues processed: 177 average time/residue: 1.4687 time to fit residues: 279.5200 Evaluate side-chains 177 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 49 optimal weight: 0.0770 chunk 122 optimal weight: 0.0770 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.9298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 232 HIS ** B 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 131 GLN C 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.101242 restraints weight = 15072.216| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.13 r_work: 0.3163 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12656 Z= 0.212 Angle : 0.555 9.642 17184 Z= 0.290 Chirality : 0.040 0.137 1919 Planarity : 0.005 0.047 2158 Dihedral : 7.989 83.169 1797 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.11 % Allowed : 14.87 % Favored : 84.02 % 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 (0.22), residues: 1489 helix: 1.58 (0.21), residues: 691 sheet: -0.01 (0.45), residues: 118 loop : -0.45 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 253 HIS 0.008 0.001 HIS A 434 PHE 0.023 0.002 PHE C 41 TYR 0.018 0.001 TYR B 533 ARG 0.017 0.001 ARG A 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5669.27 seconds wall clock time: 99 minutes 37.40 seconds (5977.40 seconds total)