Starting phenix.real_space_refine on Fri Mar 15 05:55:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/03_2024/7zrl_14918_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/03_2024/7zrl_14918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/03_2024/7zrl_14918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/03_2024/7zrl_14918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/03_2024/7zrl_14918_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/03_2024/7zrl_14918_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians K 1 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6945 2.51 5 N 1817 2.21 5 O 1957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 223": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10782 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 5003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5003 Classifications: {'peptide': 674} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1423 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 13, 'TRANS': 175} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.80, per 1000 atoms: 0.54 Number of scatterers: 10782 At special positions: 0 Unit cell: (87.032, 111.32, 164.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 1 19.00 S 61 16.00 P 1 15.00 O 1957 8.00 N 1817 7.00 C 6945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.05 Conformation dependent library (CDL) restraints added in 1.8 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 8 sheets defined 56.4% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 32 removed outlier: 3.954A pdb=" N PHE A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 21 " --> pdb=" O MET A 17 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.732A pdb=" N ARG A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 126 through 156 removed outlier: 4.104A pdb=" N LEU A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 179 through 192 removed outlier: 3.989A pdb=" N PHE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 4.337A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.384A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 295 removed outlier: 3.799A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.948A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 330 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 368 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 411 through 437 removed outlier: 4.834A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix removed outlier: 3.931A pdb=" N ALA A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 479 through 508 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 525 through 548 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 27 through 32 removed outlier: 4.184A pdb=" N TRP B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing helix chain 'B' and resid 34 through 55 Processing helix chain 'B' and resid 63 through 87 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 199 through 208 removed outlier: 4.248A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 242 removed outlier: 4.076A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 285 removed outlier: 3.968A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 4.585A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 removed outlier: 4.481A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 521 through 528 Proline residue: B 524 - end of helix removed outlier: 3.535A pdb=" N GLN B 528 " --> pdb=" O ALA B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 555 through 594 removed outlier: 4.328A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 559 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 567 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 571 " --> pdb=" O MET B 568 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 590 " --> pdb=" O TYR B 587 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 606 removed outlier: 3.702A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 635 removed outlier: 3.982A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 632 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 679 removed outlier: 4.013A pdb=" N GLY B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 4 through 19 removed outlier: 4.151A pdb=" N THR C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 134 through 148 removed outlier: 4.080A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 5 through 24 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 204 removed outlier: 3.847A pdb=" N GLN A 202 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.926A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE B 131 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 188 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU B 148 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 152 through 154 Processing sheet with id= D, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= E, first strand: chain 'B' and resid 466 through 469 removed outlier: 7.392A pdb=" N LEU B 512 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 304 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 514 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU B 306 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 516 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 531 " --> pdb=" O MET B 515 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.605A pdb=" N ARG B 391 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 428 through 432 removed outlier: 3.805A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LYS B 446 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA B 319 " --> pdb=" O LYS B 446 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.961A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1581 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: 2.83 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1763 1.31 - 1.44: 2702 1.44 - 1.57: 6405 1.57 - 1.69: 1 1.69 - 1.82: 110 Bond restraints: 10981 Sorted by residual: bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.576 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" N ILE A 145 " pdb=" CA ILE A 145 " ideal model delta sigma weight residual 1.459 1.482 -0.022 1.33e-02 5.65e+03 2.84e+00 bond pdb=" CG PHD B 307 " pdb=" OD2 PHD B 307 " ideal model delta sigma weight residual 1.218 1.185 0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C ILE A 145 " pdb=" O ILE A 145 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.32e-02 5.74e+03 2.52e+00 bond pdb=" C MET B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.51e+00 ... (remaining 10976 not shown) Histogram of bond angle deviations from ideal: 95.70 - 103.40: 137 103.40 - 111.10: 4106 111.10 - 118.80: 4833 118.80 - 126.50: 5715 126.50 - 134.19: 157 Bond angle restraints: 14948 Sorted by residual: angle pdb=" C VAL A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta sigma weight residual 121.14 111.99 9.15 1.75e+00 3.27e-01 2.74e+01 angle pdb=" CB MET A 384 " pdb=" CG MET A 384 " pdb=" SD MET A 384 " ideal model delta sigma weight residual 112.70 125.70 -13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" CB MET B 392 " pdb=" CG MET B 392 " pdb=" SD MET B 392 " ideal model delta sigma weight residual 112.70 125.58 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" C LEU C 4 " pdb=" CA LEU C 4 " pdb=" CB LEU C 4 " ideal model delta sigma weight residual 115.89 110.26 5.63 1.32e+00 5.74e-01 1.82e+01 angle pdb=" C LEU A 178 " pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta sigma weight residual 120.33 123.65 -3.32 8.00e-01 1.56e+00 1.72e+01 ... (remaining 14943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5832 17.90 - 35.80: 569 35.80 - 53.70: 108 53.70 - 71.60: 11 71.60 - 89.51: 7 Dihedral angle restraints: 6527 sinusoidal: 2430 harmonic: 4097 Sorted by residual: dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA THR A 111 " pdb=" C THR A 111 " pdb=" N ASN A 112 " pdb=" CA ASN A 112 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA MET B 206 " pdb=" C MET B 206 " pdb=" N VAL B 207 " pdb=" CA VAL B 207 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 6524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1573 0.075 - 0.150: 210 0.150 - 0.225: 18 0.225 - 0.300: 1 0.300 - 0.375: 1 Chirality restraints: 1803 Sorted by residual: chirality pdb=" CB THR A 113 " pdb=" CA THR A 113 " pdb=" OG1 THR A 113 " pdb=" CG2 THR A 113 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB ILE B 448 " pdb=" CA ILE B 448 " pdb=" CG1 ILE B 448 " pdb=" CG2 ILE B 448 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL C 121 " pdb=" CA VAL C 121 " pdb=" CG1 VAL C 121 " pdb=" CG2 VAL C 121 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1800 not shown) Planarity restraints: 1897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 37 " 0.020 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE B 37 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE B 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 37 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE B 37 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 37 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 37 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 214 " -0.039 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 215 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 62 " 0.007 2.00e-02 2.50e+03 1.62e-02 5.28e+00 pdb=" CG TYR A 62 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 62 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 62 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 62 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 62 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 62 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 62 " -0.001 2.00e-02 2.50e+03 ... (remaining 1894 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 2411 2.79 - 3.37: 12648 3.37 - 3.96: 21174 3.96 - 4.55: 28592 4.55 - 5.14: 42182 Nonbonded interactions: 107007 Sorted by model distance: nonbonded pdb=" OG1 THR A 339 " pdb=" O CYS A 344 " model vdw 2.197 2.440 nonbonded pdb=" NZ LYS B 450 " pdb=" O SER B 553 " model vdw 2.266 2.520 nonbonded pdb=" OG SER A 325 " pdb=" O ASN C 131 " model vdw 2.281 2.440 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.285 2.440 nonbonded pdb=" OE2 GLU C 119 " pdb=" OG1 THR C 133 " model vdw 2.291 2.440 ... (remaining 107002 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 group one per residue 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.680 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.380 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.005 0.240 10981 Z= 0.307 Angle : 0.909 12.997 14948 Z= 0.451 Chirality : 0.051 0.375 1803 Planarity : 0.005 0.060 1897 Dihedral : 14.303 89.506 3895 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -1.26 (0.21), residues: 1436 helix: -0.03 (0.16), residues: 841 sheet: -0.92 (0.56), residues: 91 loop : -2.13 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 31 HIS 0.003 0.001 HIS B 404 PHE 0.057 0.003 PHE B 37 TYR 0.030 0.002 TYR A 62 ARG 0.016 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.193 Fit side-chains REVERT: A 384 MET cc_start: 0.8117 (mmm) cc_final: 0.7588 (mmt) REVERT: A 414 MET cc_start: 0.6959 (tpp) cc_final: 0.6297 (mtp) REVERT: B 360 PHE cc_start: 0.7191 (t80) cc_final: 0.6826 (t80) REVERT: B 402 ARG cc_start: 0.7960 (tpp80) cc_final: 0.7408 (mmp80) REVERT: C 50 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7985 (mmm160) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1898 time to fit residues: 61.3979 Evaluate side-chains 167 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10981 Z= 0.200 Angle : 0.591 8.237 14948 Z= 0.295 Chirality : 0.041 0.145 1803 Planarity : 0.004 0.042 1897 Dihedral : 4.498 29.111 1523 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.41 % Allowed : 10.88 % Favored : 87.71 % 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: -0.50 (0.22), residues: 1436 helix: 0.64 (0.18), residues: 854 sheet: -1.01 (0.58), residues: 82 loop : -1.89 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 186 HIS 0.002 0.000 HIS A 242 PHE 0.025 0.002 PHE B 374 TYR 0.021 0.002 TYR A 381 ARG 0.005 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 1.127 Fit side-chains REVERT: A 437 MET cc_start: 0.7461 (mmm) cc_final: 0.7131 (mmm) REVERT: B 69 SER cc_start: 0.7160 (OUTLIER) cc_final: 0.6892 (p) REVERT: B 383 MET cc_start: 0.6599 (mmm) cc_final: 0.5892 (mtt) REVERT: C 50 ARG cc_start: 0.8327 (mmm-85) cc_final: 0.7962 (mmm160) REVERT: C 130 ASN cc_start: 0.7868 (t0) cc_final: 0.7568 (t0) outliers start: 16 outliers final: 13 residues processed: 189 average time/residue: 0.1966 time to fit residues: 55.5496 Evaluate side-chains 186 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 129 optimal weight: 0.0070 chunk 139 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 44 optimal weight: 0.0870 chunk 103 optimal weight: 8.9990 overall best weight: 2.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10981 Z= 0.285 Angle : 0.639 15.654 14948 Z= 0.318 Chirality : 0.043 0.217 1803 Planarity : 0.004 0.048 1897 Dihedral : 4.573 37.512 1523 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 2.21 % Allowed : 15.12 % Favored : 82.67 % 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: -0.38 (0.22), residues: 1436 helix: 0.81 (0.18), residues: 851 sheet: -1.65 (0.51), residues: 89 loop : -1.83 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 186 HIS 0.002 0.001 HIS A 242 PHE 0.024 0.002 PHE A 543 TYR 0.018 0.002 TYR A 381 ARG 0.005 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.328 Fit side-chains REVERT: B 383 MET cc_start: 0.6627 (mmm) cc_final: 0.5874 (mtt) outliers start: 25 outliers final: 20 residues processed: 183 average time/residue: 0.1918 time to fit residues: 53.1305 Evaluate side-chains 177 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 122 optimal weight: 0.0050 chunk 36 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10981 Z= 0.195 Angle : 0.577 9.951 14948 Z= 0.286 Chirality : 0.041 0.218 1803 Planarity : 0.003 0.029 1897 Dihedral : 4.414 34.051 1523 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 2.12 % Allowed : 17.68 % Favored : 80.19 % 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: -0.16 (0.22), residues: 1436 helix: 0.94 (0.18), residues: 870 sheet: -1.64 (0.52), residues: 90 loop : -1.73 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 186 HIS 0.002 0.000 HIS A 242 PHE 0.040 0.001 PHE B 360 TYR 0.018 0.001 TYR A 381 ARG 0.006 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.8468 (m-10) cc_final: 0.8189 (m-10) REVERT: A 327 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7328 (p90) REVERT: A 414 MET cc_start: 0.8068 (mmp) cc_final: 0.7851 (mmp) REVERT: A 430 MET cc_start: 0.8386 (mmm) cc_final: 0.8120 (mmt) REVERT: B 383 MET cc_start: 0.6403 (mmm) cc_final: 0.5896 (mtm) REVERT: C 130 ASN cc_start: 0.8087 (t0) cc_final: 0.7743 (t0) REVERT: C 141 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8803 (mt) outliers start: 24 outliers final: 14 residues processed: 181 average time/residue: 0.1888 time to fit residues: 51.6718 Evaluate side-chains 176 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.0270 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10981 Z= 0.291 Angle : 0.636 8.200 14948 Z= 0.315 Chirality : 0.043 0.190 1803 Planarity : 0.004 0.031 1897 Dihedral : 4.621 40.183 1523 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.57 % Favored : 94.36 % Rotamer: Outliers : 3.18 % Allowed : 19.36 % Favored : 77.45 % 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: -0.25 (0.22), residues: 1436 helix: 0.88 (0.18), residues: 859 sheet: -1.78 (0.51), residues: 90 loop : -1.70 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 167 HIS 0.003 0.001 HIS A 242 PHE 0.026 0.002 PHE B 360 TYR 0.018 0.002 TYR A 381 ARG 0.007 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7923 (tmm) cc_final: 0.7600 (tmm) REVERT: A 327 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.6845 (p90) REVERT: A 366 MET cc_start: 0.8568 (tpp) cc_final: 0.7734 (tpp) REVERT: B 463 MET cc_start: 0.7951 (ttm) cc_final: 0.7720 (ttm) REVERT: B 570 MET cc_start: 0.7485 (ttm) cc_final: 0.6995 (mtp) REVERT: C 141 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8876 (mt) outliers start: 36 outliers final: 25 residues processed: 180 average time/residue: 0.1902 time to fit residues: 51.9836 Evaluate side-chains 177 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 114 optimal weight: 0.0980 chunk 63 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10981 Z= 0.178 Angle : 0.586 9.789 14948 Z= 0.286 Chirality : 0.041 0.199 1803 Planarity : 0.003 0.029 1897 Dihedral : 4.444 34.466 1523 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 1.77 % Allowed : 21.40 % Favored : 76.83 % 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: -0.06 (0.23), residues: 1436 helix: 1.04 (0.18), residues: 874 sheet: -1.67 (0.51), residues: 90 loop : -1.74 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 167 HIS 0.002 0.000 HIS A 242 PHE 0.024 0.001 PHE B 360 TYR 0.012 0.001 TYR A 381 ARG 0.006 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.6839 (p90) REVERT: B 489 ASP cc_start: 0.8431 (p0) cc_final: 0.8147 (p0) REVERT: B 570 MET cc_start: 0.7313 (ttm) cc_final: 0.6848 (mtp) REVERT: C 141 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8757 (mt) REVERT: C 162 TYR cc_start: 0.6890 (m-10) cc_final: 0.6646 (m-10) outliers start: 20 outliers final: 10 residues processed: 176 average time/residue: 0.1818 time to fit residues: 48.6657 Evaluate side-chains 164 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 6.9990 chunk 78 optimal weight: 0.0470 chunk 100 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 136 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10981 Z= 0.157 Angle : 0.572 10.272 14948 Z= 0.278 Chirality : 0.040 0.216 1803 Planarity : 0.003 0.029 1897 Dihedral : 4.303 30.313 1523 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.21 % Allowed : 22.10 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.04 (0.23), residues: 1436 helix: 1.12 (0.18), residues: 873 sheet: -1.54 (0.52), residues: 90 loop : -1.72 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 167 HIS 0.002 0.000 HIS B 404 PHE 0.020 0.001 PHE B 360 TYR 0.022 0.001 TYR A 62 ARG 0.004 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7427 (mm-30) REVERT: A 245 GLU cc_start: 0.8655 (tp30) cc_final: 0.7387 (mm-30) REVERT: A 327 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.6862 (p90) REVERT: A 366 MET cc_start: 0.8561 (tpp) cc_final: 0.7555 (tpp) REVERT: B 489 ASP cc_start: 0.8415 (p0) cc_final: 0.8128 (p0) REVERT: B 570 MET cc_start: 0.7239 (ttm) cc_final: 0.6744 (mtp) REVERT: C 130 ASN cc_start: 0.8136 (t0) cc_final: 0.7845 (t0) REVERT: C 141 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8756 (mt) REVERT: C 162 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.6386 (m-10) REVERT: C 180 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7413 (mt-10) outliers start: 25 outliers final: 12 residues processed: 179 average time/residue: 0.1948 time to fit residues: 53.0809 Evaluate side-chains 169 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 162 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 107 optimal weight: 0.0020 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10981 Z= 0.164 Angle : 0.581 10.288 14948 Z= 0.283 Chirality : 0.040 0.219 1803 Planarity : 0.003 0.029 1897 Dihedral : 4.223 28.744 1523 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.30 % Allowed : 22.72 % Favored : 74.98 % 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: 0.10 (0.23), residues: 1436 helix: 1.18 (0.18), residues: 871 sheet: -1.40 (0.52), residues: 90 loop : -1.72 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 167 HIS 0.003 0.000 HIS B 404 PHE 0.018 0.001 PHE B 360 TYR 0.030 0.001 TYR A 62 ARG 0.005 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7945 (mm-30) REVERT: A 245 GLU cc_start: 0.8717 (tp30) cc_final: 0.7814 (mm-30) REVERT: A 327 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.6964 (p90) REVERT: A 366 MET cc_start: 0.8542 (tpp) cc_final: 0.7487 (tpp) REVERT: A 471 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7509 (m-10) REVERT: B 267 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8075 (mt) REVERT: B 489 ASP cc_start: 0.8438 (p0) cc_final: 0.8154 (p0) REVERT: C 130 ASN cc_start: 0.8184 (t0) cc_final: 0.7885 (t0) REVERT: C 141 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8709 (mt) REVERT: C 180 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7420 (mt-10) outliers start: 26 outliers final: 14 residues processed: 177 average time/residue: 0.1848 time to fit residues: 49.9278 Evaluate side-chains 176 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10981 Z= 0.196 Angle : 0.603 9.299 14948 Z= 0.291 Chirality : 0.041 0.211 1803 Planarity : 0.003 0.029 1897 Dihedral : 4.288 30.234 1523 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.03 % Allowed : 23.70 % Favored : 74.27 % 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: 0.08 (0.23), residues: 1436 helix: 1.15 (0.18), residues: 872 sheet: -1.42 (0.52), residues: 90 loop : -1.70 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 167 HIS 0.002 0.000 HIS B 404 PHE 0.019 0.001 PHE B 360 TYR 0.024 0.002 TYR A 62 ARG 0.004 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.8270 (mtt) cc_final: 0.8065 (mtt) REVERT: A 327 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.6866 (p90) REVERT: A 366 MET cc_start: 0.8548 (tpp) cc_final: 0.7463 (tpp) REVERT: A 471 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: B 267 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 489 ASP cc_start: 0.8486 (p0) cc_final: 0.8216 (p0) REVERT: C 141 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8720 (mt) outliers start: 23 outliers final: 14 residues processed: 166 average time/residue: 0.1893 time to fit residues: 48.1930 Evaluate side-chains 166 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10981 Z= 0.257 Angle : 0.637 10.399 14948 Z= 0.310 Chirality : 0.042 0.165 1803 Planarity : 0.003 0.028 1897 Dihedral : 4.494 35.906 1523 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 2.03 % Allowed : 23.78 % Favored : 74.18 % 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: -0.03 (0.22), residues: 1436 helix: 1.06 (0.18), residues: 869 sheet: -1.51 (0.51), residues: 90 loop : -1.70 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 167 HIS 0.003 0.001 HIS B 404 PHE 0.018 0.002 PHE B 360 TYR 0.029 0.002 TYR B 587 ARG 0.004 0.000 ARG C 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.6761 (p90) REVERT: A 471 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7881 (m-10) REVERT: B 267 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8264 (mt) REVERT: B 463 MET cc_start: 0.7940 (ttm) cc_final: 0.7634 (ttm) REVERT: B 489 ASP cc_start: 0.8557 (p0) cc_final: 0.8296 (p0) REVERT: C 141 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8761 (mt) outliers start: 23 outliers final: 14 residues processed: 167 average time/residue: 0.1829 time to fit residues: 46.4348 Evaluate side-chains 167 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.081487 restraints weight = 25036.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.082726 restraints weight = 14206.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084647 restraints weight = 8855.330| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10981 Z= 0.179 Angle : 0.618 10.638 14948 Z= 0.296 Chirality : 0.041 0.172 1803 Planarity : 0.003 0.029 1897 Dihedral : 4.418 32.423 1523 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.06 % Rotamer: Outliers : 1.95 % Allowed : 24.05 % Favored : 74.01 % 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: 0.11 (0.23), residues: 1436 helix: 1.14 (0.18), residues: 864 sheet: -1.45 (0.52), residues: 90 loop : -1.56 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 167 HIS 0.003 0.001 HIS A 85 PHE 0.019 0.001 PHE B 360 TYR 0.032 0.002 TYR B 587 ARG 0.004 0.000 ARG C 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2076.92 seconds wall clock time: 38 minutes 24.28 seconds (2304.28 seconds total)