Starting phenix.real_space_refine on Sun Jul 21 05:13:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/07_2024/8z9q_39867.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/07_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_39867/07_2024/8z9q_39867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/07_2024/8z9q_39867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/07_2024/8z9q_39867.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z9q_39867/07_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 Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.76, per 1000 atoms: 0.63 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 - 3.50 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 2.3 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: 1.55 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: 3.84 Time building geometry restraints manager: 5.92 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: 99.23 - 107.39: 593 107.39 - 115.54: 7771 115.54 - 123.69: 8412 123.69 - 131.85: 372 131.85 - 140.00: 36 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 2.440 nonbonded pdb=" OD2 ASP B 500 " pdb=" OH TYR B 537 " model vdw 2.134 2.440 nonbonded pdb=" O ASN C 163 " pdb=" OG SER C 166 " model vdw 2.211 2.440 nonbonded pdb=" O THR A 269 " pdb=" OG SER A 463 " model vdw 2.238 2.440 nonbonded pdb=" OD1 ASP B 172 " pdb=" NH2 ARG B 216 " model vdw 2.243 2.520 ... (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 ========== 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.200 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.100 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: 0.080 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.620 ------------------------------------------------------------------------------- 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 : 1.379 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: 1.7571 time to fit residues: 425.2181 Evaluate side-chains 174 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 307 GLN ** 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 154 GLN C 214 HIS C 252 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 12656 Z= 0.426 Angle : 0.654 7.633 17184 Z= 0.347 Chirality : 0.046 0.159 1919 Planarity : 0.006 0.057 2158 Dihedral : 9.008 84.115 1797 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.29 % Allowed : 8.95 % Favored : 88.76 % 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: 0.43 (0.22), residues: 1489 helix: 1.04 (0.20), residues: 689 sheet: 0.51 (0.48), residues: 118 loop : -0.48 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 336 HIS 0.015 0.002 HIS A 577 PHE 0.033 0.003 PHE C 41 TYR 0.020 0.002 TYR B 115 ARG 0.007 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 221 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 1.498 Fit side-chains REVERT: A 9 ASP cc_start: 0.8029 (p0) cc_final: 0.7708 (t70) REVERT: A 17 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: A 47 ASN cc_start: 0.7727 (t0) cc_final: 0.7448 (t0) REVERT: A 64 ASP cc_start: 0.7166 (t0) cc_final: 0.6919 (t0) REVERT: A 86 ASP cc_start: 0.7904 (m-30) cc_final: 0.7600 (m-30) REVERT: A 147 ARG cc_start: 0.8044 (ptm-80) cc_final: 0.7689 (ptm-80) REVERT: A 163 GLU cc_start: 0.8231 (tp30) cc_final: 0.7826 (tp30) REVERT: A 522 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 144 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7215 (tm-30) REVERT: B 283 LYS cc_start: 0.8277 (tptt) cc_final: 0.8040 (tppt) REVERT: B 672 GLN cc_start: 0.7766 (mt0) cc_final: 0.7105 (pt0) REVERT: C 18 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: C 127 ASP cc_start: 0.7303 (t0) cc_final: 0.6921 (m-30) REVERT: C 201 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7640 (tm-30) outliers start: 31 outliers final: 10 residues processed: 205 average time/residue: 1.5731 time to fit residues: 344.8856 Evaluate side-chains 188 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 429 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 500 GLN B 55 GLN B 397 ASN B 433 HIS B 506 ASN B 663 ASN C 154 GLN C 214 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12656 Z= 0.183 Angle : 0.529 6.382 17184 Z= 0.278 Chirality : 0.039 0.131 1919 Planarity : 0.004 0.049 2158 Dihedral : 8.627 78.263 1797 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.07 % Allowed : 11.09 % Favored : 86.83 % 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: 0.71 (0.22), residues: 1489 helix: 1.36 (0.21), residues: 688 sheet: 0.44 (0.47), residues: 118 loop : -0.39 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.006 0.001 HIS C 233 PHE 0.023 0.002 PHE C 41 TYR 0.017 0.001 TYR B 533 ARG 0.005 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 212 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 1.467 Fit side-chains REVERT: A 9 ASP cc_start: 0.7970 (p0) cc_final: 0.7660 (t70) REVERT: A 64 ASP cc_start: 0.7195 (t0) cc_final: 0.6851 (t0) REVERT: A 86 ASP cc_start: 0.7927 (m-30) cc_final: 0.7589 (m-30) REVERT: A 122 GLU cc_start: 0.7709 (pm20) cc_final: 0.7472 (pm20) REVERT: A 139 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7459 (tm-30) REVERT: A 163 GLU cc_start: 0.8221 (tp30) cc_final: 0.7767 (tp30) REVERT: A 522 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 144 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7210 (tm-30) REVERT: B 283 LYS cc_start: 0.8293 (tptt) cc_final: 0.8018 (tppt) REVERT: B 287 LYS cc_start: 0.7807 (tmtt) cc_final: 0.7578 (tmtt) REVERT: B 576 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: C 18 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8174 (tp30) REVERT: C 127 ASP cc_start: 0.7290 (t0) cc_final: 0.6978 (m-30) REVERT: C 146 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7263 (mtt) REVERT: C 201 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 210 GLU cc_start: 0.7988 (mp0) cc_final: 0.7763 (mp0) outliers start: 28 outliers final: 8 residues processed: 200 average time/residue: 1.5051 time to fit residues: 323.2334 Evaluate side-chains 187 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 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 18 GLU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 B 397 ASN B 506 ASN B 672 GLN C 154 GLN C 163 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12656 Z= 0.177 Angle : 0.510 5.738 17184 Z= 0.268 Chirality : 0.039 0.128 1919 Planarity : 0.004 0.048 2158 Dihedral : 8.344 77.473 1797 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.14 % Allowed : 11.39 % Favored : 86.46 % 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: 1.49 (0.21), residues: 688 sheet: 0.36 (0.46), residues: 118 loop : -0.40 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.005 0.001 HIS C 233 PHE 0.022 0.002 PHE C 41 TYR 0.017 0.001 TYR B 533 ARG 0.009 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 211 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 1.511 Fit side-chains REVERT: A 9 ASP cc_start: 0.7948 (p0) cc_final: 0.7639 (t70) REVERT: A 18 THR cc_start: 0.8812 (m) cc_final: 0.8504 (p) REVERT: A 64 ASP cc_start: 0.7278 (t0) cc_final: 0.6929 (t0) REVERT: A 86 ASP cc_start: 0.7918 (m-30) cc_final: 0.7579 (m-30) REVERT: A 139 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7476 (tm-30) REVERT: A 163 GLU cc_start: 0.8223 (tp30) cc_final: 0.7771 (tp30) REVERT: A 212 MET cc_start: 0.7653 (ttp) cc_final: 0.7358 (ttm) REVERT: A 522 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 579 MET cc_start: 0.8449 (mtt) cc_final: 0.8137 (mtt) REVERT: B 43 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7043 (mpt-90) REVERT: B 144 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7203 (tm-30) REVERT: B 283 LYS cc_start: 0.8289 (tptt) cc_final: 0.8014 (tppt) REVERT: B 576 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: C 18 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8149 (tp30) REVERT: C 127 ASP cc_start: 0.7296 (t0) cc_final: 0.6996 (m-30) REVERT: C 146 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7342 (mtt) REVERT: C 201 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7653 (tm-30) outliers start: 29 outliers final: 10 residues processed: 199 average time/residue: 1.5145 time to fit residues: 323.0957 Evaluate side-chains 185 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 43 ARG 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 656 GLN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.0010 chunk 82 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.0050 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 397 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 154 GLN C 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12656 Z= 0.166 Angle : 0.503 8.318 17184 Z= 0.262 Chirality : 0.039 0.128 1919 Planarity : 0.004 0.045 2158 Dihedral : 8.195 76.806 1797 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.00 % Allowed : 11.83 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.57 (0.21), residues: 687 sheet: 0.36 (0.46), residues: 118 loop : -0.37 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.006 0.001 HIS C 169 PHE 0.022 0.001 PHE C 41 TYR 0.017 0.001 TYR B 533 ARG 0.008 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 207 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7882 (p0) cc_final: 0.7615 (t70) REVERT: A 18 THR cc_start: 0.8762 (m) cc_final: 0.8451 (p) REVERT: A 64 ASP cc_start: 0.7296 (t0) cc_final: 0.6945 (t0) REVERT: A 86 ASP cc_start: 0.7901 (m-30) cc_final: 0.7576 (m-30) REVERT: A 139 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 163 GLU cc_start: 0.8224 (tp30) cc_final: 0.7772 (tp30) REVERT: A 212 MET cc_start: 0.7682 (ttp) cc_final: 0.7372 (ttm) REVERT: A 522 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 579 MET cc_start: 0.8407 (mtt) cc_final: 0.7957 (mtt) REVERT: B 43 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7038 (mpt-90) REVERT: B 144 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7211 (tm-30) REVERT: B 283 LYS cc_start: 0.8284 (tptt) cc_final: 0.8006 (tppt) REVERT: B 576 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: C 18 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: C 75 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7902 (pt) REVERT: C 127 ASP cc_start: 0.7275 (t0) cc_final: 0.7000 (m-30) REVERT: C 201 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7651 (tm-30) outliers start: 27 outliers final: 12 residues processed: 194 average time/residue: 1.4381 time to fit residues: 299.9508 Evaluate side-chains 185 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 532 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 43 ARG 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 656 GLN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 254 ASN 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: 0.9980 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 0.0870 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 257 GLN B 55 GLN B 397 ASN C 154 GLN C 163 ASN C 214 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12656 Z= 0.229 Angle : 0.530 5.986 17184 Z= 0.279 Chirality : 0.040 0.133 1919 Planarity : 0.004 0.048 2158 Dihedral : 8.248 80.566 1797 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.14 % Allowed : 12.57 % Favored : 85.28 % 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: 1.53 (0.21), residues: 686 sheet: 0.47 (0.46), residues: 113 loop : -0.40 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.006 0.001 HIS A 577 PHE 0.024 0.002 PHE C 41 TYR 0.019 0.001 TYR B 533 ARG 0.008 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 206 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7884 (p0) cc_final: 0.7676 (t70) REVERT: A 18 THR cc_start: 0.8802 (m) cc_final: 0.8489 (p) REVERT: A 64 ASP cc_start: 0.7290 (t0) cc_final: 0.6941 (t0) REVERT: A 86 ASP cc_start: 0.7970 (m-30) cc_final: 0.7626 (m-30) REVERT: A 139 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7509 (tm-30) REVERT: A 163 GLU cc_start: 0.8232 (tp30) cc_final: 0.7785 (tp30) REVERT: A 205 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6153 (mm-30) REVERT: B 43 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7128 (mpt-90) REVERT: B 144 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: B 283 LYS cc_start: 0.8293 (tptt) cc_final: 0.8015 (tppt) REVERT: C 18 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8158 (tp30) REVERT: C 127 ASP cc_start: 0.7346 (t0) cc_final: 0.7093 (m-30) REVERT: C 201 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7648 (tm-30) outliers start: 29 outliers final: 13 residues processed: 193 average time/residue: 1.5062 time to fit residues: 312.2182 Evaluate side-chains 185 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 166 SER 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 43 ARG Chi-restraints excluded: chain B residue 144 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 C residue 13 LEU 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 254 ASN 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: 0.9980 chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 144 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN C 154 GLN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1829 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= 0.172 Angle : 0.512 9.906 17184 Z= 0.266 Chirality : 0.039 0.142 1919 Planarity : 0.004 0.046 2158 Dihedral : 8.129 79.182 1797 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.92 % Allowed : 12.87 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.61 (0.21), residues: 687 sheet: 0.40 (0.46), residues: 115 loop : -0.37 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 330 HIS 0.004 0.001 HIS A 434 PHE 0.022 0.001 PHE C 41 TYR 0.019 0.001 TYR B 104 ARG 0.009 0.000 ARG A 92 *********************** 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 202 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 176 time to evaluate : 1.550 Fit side-chains REVERT: A 9 ASP cc_start: 0.7842 (p0) cc_final: 0.7609 (t70) REVERT: A 18 THR cc_start: 0.8733 (m) cc_final: 0.8424 (p) REVERT: A 64 ASP cc_start: 0.7286 (t0) cc_final: 0.6909 (t0) REVERT: A 86 ASP cc_start: 0.7943 (m-30) cc_final: 0.7600 (m-30) REVERT: A 139 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7514 (tm-30) REVERT: A 153 VAL cc_start: 0.8634 (t) cc_final: 0.8407 (m) REVERT: A 163 GLU cc_start: 0.8228 (tp30) cc_final: 0.7778 (tp30) REVERT: B 43 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7097 (mpt-90) REVERT: B 144 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: B 283 LYS cc_start: 0.8291 (tptt) cc_final: 0.8014 (tppt) REVERT: B 576 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: C 18 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: C 127 ASP cc_start: 0.7305 (t0) cc_final: 0.7051 (m-30) REVERT: C 201 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7671 (tm-30) outliers start: 26 outliers final: 15 residues processed: 192 average time/residue: 1.5110 time to fit residues: 312.1968 Evaluate side-chains 186 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 144 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 13 LEU Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 397 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12656 Z= 0.180 Angle : 0.507 6.348 17184 Z= 0.265 Chirality : 0.039 0.129 1919 Planarity : 0.004 0.045 2158 Dihedral : 8.090 80.258 1797 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.00 % Allowed : 13.61 % Favored : 84.39 % 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: 0.94 (0.22), residues: 1489 helix: 1.65 (0.21), residues: 687 sheet: 0.40 (0.47), residues: 115 loop : -0.35 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS A 434 PHE 0.021 0.001 PHE C 41 TYR 0.017 0.001 TYR B 533 ARG 0.006 0.000 ARG A 92 *********************** 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 203 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 1.490 Fit side-chains REVERT: A 9 ASP cc_start: 0.7824 (p0) cc_final: 0.7607 (t70) REVERT: A 18 THR cc_start: 0.8734 (m) cc_final: 0.8422 (p) REVERT: A 64 ASP cc_start: 0.7233 (t0) cc_final: 0.6951 (t0) REVERT: A 86 ASP cc_start: 0.7940 (m-30) cc_final: 0.7580 (m-30) REVERT: A 139 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 153 VAL cc_start: 0.8619 (t) cc_final: 0.8398 (m) REVERT: A 163 GLU cc_start: 0.8230 (tp30) cc_final: 0.7780 (tp30) REVERT: A 205 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6190 (mm-30) REVERT: B 43 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7095 (mpt-90) REVERT: B 144 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: B 283 LYS cc_start: 0.8297 (tptt) cc_final: 0.8021 (tppt) REVERT: B 576 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: C 18 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8152 (tp30) REVERT: C 127 ASP cc_start: 0.7315 (t0) cc_final: 0.7087 (m-30) REVERT: C 201 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7663 (tm-30) outliers start: 27 outliers final: 13 residues processed: 190 average time/residue: 1.4988 time to fit residues: 305.6985 Evaluate side-chains 189 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 166 SER 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 43 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 VAL 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 180 THR Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0050 chunk 138 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 88 optimal weight: 0.1980 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 397 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 154 GLN C 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12656 Z= 0.164 Angle : 0.513 10.312 17184 Z= 0.265 Chirality : 0.038 0.129 1919 Planarity : 0.004 0.044 2158 Dihedral : 8.015 80.469 1797 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.78 % Allowed : 13.83 % Favored : 84.39 % 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: 0.98 (0.22), residues: 1489 helix: 1.70 (0.21), residues: 686 sheet: 0.41 (0.47), residues: 115 loop : -0.34 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 330 HIS 0.004 0.001 HIS A 434 PHE 0.021 0.001 PHE C 41 TYR 0.019 0.001 TYR B 30 ARG 0.006 0.000 ARG A 147 *********************** 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 204 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 1.607 Fit side-chains REVERT: A 9 ASP cc_start: 0.7782 (p0) cc_final: 0.7575 (t70) REVERT: A 18 THR cc_start: 0.8682 (m) cc_final: 0.8394 (p) REVERT: A 64 ASP cc_start: 0.7262 (t0) cc_final: 0.6911 (t0) REVERT: A 86 ASP cc_start: 0.7938 (m-30) cc_final: 0.7575 (m-30) REVERT: A 139 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7537 (tm-30) REVERT: A 153 VAL cc_start: 0.8598 (t) cc_final: 0.8386 (m) REVERT: A 163 GLU cc_start: 0.8241 (tp30) cc_final: 0.7790 (tp30) REVERT: A 212 MET cc_start: 0.7727 (ttp) cc_final: 0.7386 (ttm) REVERT: B 43 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7111 (mpt-90) REVERT: B 144 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: B 283 LYS cc_start: 0.8289 (tptt) cc_final: 0.8013 (tppt) REVERT: B 550 GLU cc_start: 0.7814 (tp30) cc_final: 0.7612 (tt0) REVERT: B 576 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: C 18 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: C 127 ASP cc_start: 0.7247 (t0) cc_final: 0.7018 (m-30) REVERT: C 201 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7637 (tm-30) outliers start: 24 outliers final: 13 residues processed: 191 average time/residue: 1.4732 time to fit residues: 302.6253 Evaluate side-chains 185 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 166 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 576 GLU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 18 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 Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 486 ASN B 397 ASN C 154 GLN C 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12656 Z= 0.290 Angle : 0.573 7.049 17184 Z= 0.300 Chirality : 0.041 0.137 1919 Planarity : 0.005 0.049 2158 Dihedral : 8.282 87.354 1797 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.85 % Allowed : 13.98 % Favored : 84.17 % 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: 0.75 (0.22), residues: 1489 helix: 1.49 (0.21), residues: 688 sheet: 0.37 (0.47), residues: 118 loop : -0.46 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 336 HIS 0.007 0.001 HIS A 577 PHE 0.024 0.002 PHE C 41 TYR 0.024 0.002 TYR B 104 ARG 0.007 0.000 ARG A 147 ********************** 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 195 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.473 Fit side-chains REVERT: A 9 ASP cc_start: 0.7803 (p0) cc_final: 0.7598 (t70) REVERT: A 18 THR cc_start: 0.8889 (m) cc_final: 0.8601 (p) REVERT: A 47 ASN cc_start: 0.8079 (t0) cc_final: 0.7564 (t0) REVERT: A 64 ASP cc_start: 0.7310 (t0) cc_final: 0.6946 (t0) REVERT: A 86 ASP cc_start: 0.7961 (m-30) cc_final: 0.7586 (m-30) REVERT: A 139 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 163 GLU cc_start: 0.8253 (tp30) cc_final: 0.7811 (tp30) REVERT: A 205 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.6180 (mm-30) REVERT: B 283 LYS cc_start: 0.8304 (tptt) cc_final: 0.8026 (tppt) REVERT: C 18 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: C 127 ASP cc_start: 0.7370 (t0) cc_final: 0.7119 (m-30) REVERT: C 201 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7624 (tm-30) outliers start: 25 outliers final: 13 residues processed: 183 average time/residue: 1.5294 time to fit residues: 300.2950 Evaluate side-chains 180 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 166 SER 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 9 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 254 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 123 GLN C 154 GLN C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099450 restraints weight = 15012.119| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.12 r_work: 0.3128 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12656 Z= 0.214 Angle : 0.548 12.061 17184 Z= 0.284 Chirality : 0.040 0.132 1919 Planarity : 0.004 0.046 2158 Dihedral : 8.210 87.094 1797 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.41 % Allowed : 14.57 % 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: 0.82 (0.22), residues: 1489 helix: 1.56 (0.21), residues: 686 sheet: 0.37 (0.47), residues: 115 loop : -0.43 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS A 434 PHE 0.024 0.002 PHE C 41 TYR 0.018 0.001 TYR B 533 ARG 0.007 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5692.70 seconds wall clock time: 99 minutes 46.07 seconds (5986.07 seconds total)