Starting phenix.real_space_refine on Wed Sep 25 17:04:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/09_2024/7zrl_14918.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/09_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_14918/09_2024/7zrl_14918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/09_2024/7zrl_14918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/09_2024/7zrl_14918.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/09_2024/7zrl_14918.cif" } 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. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 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: 6.48, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.5 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... Secondary structure from input PDB file: 60 helices and 8 sheets defined 63.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 1 through 33 removed outlier: 3.747A pdb=" N GLY A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) 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 39 through 51 removed outlier: 3.557A pdb=" N GLU A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.589A pdb=" N VAL A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.569A pdb=" N GLN A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 157 Processing helix chain 'A' and resid 165 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.989A pdb=" N PHE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.812A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 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 276 through 296 removed outlier: 4.441A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.991A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 356 through 369 Proline residue: A 362 - end of helix removed outlier: 4.289A pdb=" N GLY A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 399 removed outlier: 3.764A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 438 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 440 through 445 removed outlier: 3.952A pdb=" N MET A 445 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.130A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 509 Proline residue: A 499 - end of helix removed outlier: 3.563A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 11 through 24 Processing helix chain 'B' and resid 26 through 31 removed outlier: 4.184A pdb=" N TRP B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 56 Processing helix chain 'B' and resid 62 through 88 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.510A pdb=" N GLN B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 209 removed outlier: 4.248A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 243 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 251 through 263 removed outlier: 4.015A pdb=" N ILE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 282 removed outlier: 3.574A pdb=" N GLY B 268 " --> pdb=" O PRO B 264 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 291 through 298 removed outlier: 4.021A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.848A pdb=" N THR B 311 " --> pdb=" O PHD B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 4.481A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.904A pdb=" N VAL B 439 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU B 440 " --> pdb=" O SER B 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 440' Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.244A pdb=" N ARG B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 509 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 545 removed outlier: 3.717A pdb=" N LYS B 543 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 591 removed outlier: 3.524A pdb=" N PHE B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 595 Processing helix chain 'B' and resid 599 through 607 removed outlier: 3.724A pdb=" N LEU B 602 " --> pdb=" O TYR B 599 " (cutoff:3.500A) 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) removed outlier: 3.827A pdb=" N ILE B 607 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 636 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 645 through 680 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 3 through 20 removed outlier: 4.151A pdb=" N THR C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.610A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.715A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 190 removed outlier: 4.230A pdb=" N GLU C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 25 Processing sheet with id=AA1, 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=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, 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: 7.495A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 166 removed outlier: 7.270A pdb=" N SER B 152 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 287 through 289 removed outlier: 3.528A pdb=" N ASP B 550 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N MET B 535 " --> pdb=" O MET B 515 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 512 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 303 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.609A pdb=" N GLN B 318 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 391 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id=AA7, 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) Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 132 659 hydrogen bonds defined for protein. 1929 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: 3.27 Time building geometry restraints manager: 2.88 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: 0.00 - 2.60: 14610 2.60 - 5.20: 259 5.20 - 7.80: 61 7.80 - 10.40: 14 10.40 - 13.00: 4 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: 2407 2.79 - 3.37: 12541 3.37 - 3.96: 21009 3.96 - 4.55: 28480 4.55 - 5.14: 42182 Nonbonded interactions: 106619 Sorted by model distance: nonbonded pdb=" OG1 THR A 339 " pdb=" O CYS A 344 " model vdw 2.197 3.040 nonbonded pdb=" NZ LYS B 450 " pdb=" O SER B 553 " model vdw 2.266 3.120 nonbonded pdb=" OG SER A 325 " pdb=" O ASN C 131 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.285 3.040 nonbonded pdb=" OE2 GLU C 119 " pdb=" OG1 THR C 133 " model vdw 2.291 3.040 ... (remaining 106614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.700 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: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.260 Find NCS groups from input model: 0.100 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.410 ------------------------------------------------------------------------------- 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= 0.323 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 : 1.231 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: 0.1866 time to fit residues: 60.6374 Evaluate side-chains 167 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN C 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10981 Z= 0.206 Angle : 0.610 8.223 14948 Z= 0.305 Chirality : 0.042 0.143 1803 Planarity : 0.004 0.044 1897 Dihedral : 4.568 33.504 1523 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.33 % Allowed : 11.41 % Favored : 87.27 % 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: -0.30 (0.22), residues: 1436 helix: 0.82 (0.18), residues: 854 sheet: -0.67 (0.57), residues: 80 loop : -1.88 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 115 HIS 0.002 0.000 HIS A 242 PHE 0.026 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 207 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 192 time to evaluate : 1.242 Fit side-chains REVERT: A 357 LEU cc_start: 0.9011 (mt) cc_final: 0.8365 (tp) REVERT: A 360 MET cc_start: 0.7847 (tmm) cc_final: 0.7623 (tmm) REVERT: B 69 SER cc_start: 0.7133 (m) cc_final: 0.6842 (p) REVERT: B 383 MET cc_start: 0.6670 (mmm) cc_final: 0.6079 (mtt) REVERT: C 50 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.7989 (mmm160) REVERT: C 130 ASN cc_start: 0.7859 (t0) cc_final: 0.7638 (t0) REVERT: C 162 TYR cc_start: 0.7271 (m-10) cc_final: 0.7060 (m-10) outliers start: 15 outliers final: 11 residues processed: 197 average time/residue: 0.2034 time to fit residues: 58.7102 Evaluate side-chains 186 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 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 74 ILE Chi-restraints excluded: chain B residue 270 LEU 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: 1.9990 chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 0.0020 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 0.0470 chunk 44 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 overall best weight: 1.6092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10981 Z= 0.225 Angle : 0.609 13.001 14948 Z= 0.303 Chirality : 0.042 0.222 1803 Planarity : 0.003 0.041 1897 Dihedral : 4.482 35.789 1523 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.77 % Allowed : 15.47 % Favored : 82.76 % 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: 0.07 (0.22), residues: 1436 helix: 1.14 (0.18), residues: 854 sheet: -0.68 (0.58), residues: 80 loop : -1.75 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 186 HIS 0.002 0.000 HIS A 351 PHE 0.014 0.001 PHE A 543 TYR 0.020 0.001 TYR A 381 ARG 0.004 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 202 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 252 ASN cc_start: 0.8547 (m-40) cc_final: 0.8032 (t0) REVERT: A 357 LEU cc_start: 0.9028 (mt) cc_final: 0.8414 (tp) REVERT: B 69 SER cc_start: 0.7250 (m) cc_final: 0.6949 (p) REVERT: B 383 MET cc_start: 0.6515 (mmm) cc_final: 0.6288 (mmm) REVERT: C 50 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.7928 (mmm160) REVERT: C 130 ASN cc_start: 0.7844 (t0) cc_final: 0.7619 (t0) outliers start: 20 outliers final: 16 residues processed: 192 average time/residue: 0.1945 time to fit residues: 55.4945 Evaluate side-chains 182 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 372 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 133 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 129 optimal weight: 0.0570 chunk 137 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 114 optimal weight: 0.0970 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10981 Z= 0.162 Angle : 0.577 10.423 14948 Z= 0.287 Chirality : 0.041 0.225 1803 Planarity : 0.003 0.040 1897 Dihedral : 4.328 32.722 1523 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.86 % Allowed : 17.95 % 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: 0.32 (0.23), residues: 1436 helix: 1.34 (0.18), residues: 859 sheet: -0.79 (0.59), residues: 82 loop : -1.65 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 115 HIS 0.002 0.000 HIS A 351 PHE 0.042 0.001 PHE B 360 TYR 0.020 0.001 TYR A 381 ARG 0.010 0.000 ARG B 394 *********************** 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 207 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8483 (t0) REVERT: A 252 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7887 (t0) REVERT: A 414 MET cc_start: 0.7920 (mmp) cc_final: 0.7707 (mmt) REVERT: B 69 SER cc_start: 0.7178 (m) cc_final: 0.6934 (p) REVERT: B 383 MET cc_start: 0.6397 (mmm) cc_final: 0.6019 (mtm) REVERT: C 50 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.7860 (mmm160) REVERT: C 119 GLU cc_start: 0.7777 (pm20) cc_final: 0.7563 (pm20) outliers start: 21 outliers final: 15 residues processed: 199 average time/residue: 0.1884 time to fit residues: 56.5801 Evaluate side-chains 187 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 252 ASN 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 188 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL 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 150 LEU Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 408 ASN C 66 HIS C 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1859 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= 0.175 Angle : 0.586 11.620 14948 Z= 0.290 Chirality : 0.041 0.214 1803 Planarity : 0.003 0.040 1897 Dihedral : 4.280 34.699 1523 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.03 % Allowed : 19.27 % Favored : 78.69 % 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: 0.44 (0.23), residues: 1436 helix: 1.42 (0.18), residues: 863 sheet: -0.86 (0.58), residues: 83 loop : -1.57 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 364 HIS 0.002 0.000 HIS A 351 PHE 0.030 0.001 PHE B 360 TYR 0.021 0.001 TYR A 381 ARG 0.005 0.000 ARG A 326 *********************** 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 203 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8492 (t0) REVERT: A 252 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.7907 (t0) REVERT: A 256 MET cc_start: 0.8011 (mtt) cc_final: 0.7758 (mtt) REVERT: B 19 LYS cc_start: 0.8300 (tppt) cc_final: 0.7820 (tttt) REVERT: B 69 SER cc_start: 0.7236 (m) cc_final: 0.6981 (p) REVERT: B 383 MET cc_start: 0.6428 (mmm) cc_final: 0.6147 (mtt) REVERT: C 50 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7809 (mmm160) REVERT: C 95 ASP cc_start: 0.8027 (m-30) cc_final: 0.7034 (t0) REVERT: C 96 LYS cc_start: 0.8786 (pttt) cc_final: 0.8565 (pttt) REVERT: C 141 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8671 (mt) outliers start: 23 outliers final: 15 residues processed: 196 average time/residue: 0.1858 time to fit residues: 55.2361 Evaluate side-chains 187 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 252 ASN 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 413 GLU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL 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 150 LEU Chi-restraints excluded: chain C residue 157 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 408 ASN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10981 Z= 0.263 Angle : 0.642 14.956 14948 Z= 0.318 Chirality : 0.042 0.200 1803 Planarity : 0.003 0.038 1897 Dihedral : 4.449 41.114 1523 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 3.09 % Allowed : 19.19 % Favored : 77.72 % 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: 0.32 (0.23), residues: 1436 helix: 1.30 (0.18), residues: 864 sheet: -0.87 (0.58), residues: 82 loop : -1.56 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 364 HIS 0.002 0.001 HIS A 242 PHE 0.025 0.002 PHE B 360 TYR 0.019 0.001 TYR A 381 ARG 0.008 0.000 ARG B 394 *********************** 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 205 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8486 (t0) REVERT: A 252 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.7983 (t0) REVERT: B 69 SER cc_start: 0.7290 (m) cc_final: 0.7071 (p) REVERT: B 383 MET cc_start: 0.6285 (mmm) cc_final: 0.6010 (mtt) REVERT: B 570 MET cc_start: 0.7581 (ttm) cc_final: 0.7319 (mtp) REVERT: C 141 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 157 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7489 (mp10) outliers start: 35 outliers final: 21 residues processed: 190 average time/residue: 0.1898 time to fit residues: 54.9187 Evaluate side-chains 189 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 ASN 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 413 GLU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 576 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 Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 408 ASN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10981 Z= 0.215 Angle : 0.633 12.236 14948 Z= 0.309 Chirality : 0.042 0.175 1803 Planarity : 0.003 0.037 1897 Dihedral : 4.411 41.304 1523 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.06 % Rotamer: Outliers : 3.18 % Allowed : 19.27 % Favored : 77.54 % 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: 0.35 (0.23), residues: 1436 helix: 1.32 (0.18), residues: 867 sheet: -0.94 (0.57), residues: 83 loop : -1.57 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 167 HIS 0.003 0.001 HIS B 411 PHE 0.023 0.001 PHE B 360 TYR 0.020 0.001 TYR A 381 ARG 0.006 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 210 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8593 (t0) REVERT: A 252 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.7899 (t0) REVERT: B 19 LYS cc_start: 0.8408 (tppt) cc_final: 0.7892 (tttm) REVERT: B 383 MET cc_start: 0.6281 (mmm) cc_final: 0.6059 (mtt) REVERT: B 392 MET cc_start: 0.6531 (ppp) cc_final: 0.6151 (ppp) REVERT: C 141 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8703 (mt) REVERT: C 157 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7413 (mp10) outliers start: 36 outliers final: 24 residues processed: 198 average time/residue: 0.1843 time to fit residues: 55.9492 Evaluate side-chains 194 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 355 THR 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 413 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 576 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 Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 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: 0.8059 moved from start: 0.2357 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= 0.191 Angle : 0.636 10.792 14948 Z= 0.308 Chirality : 0.042 0.195 1803 Planarity : 0.003 0.037 1897 Dihedral : 4.364 40.575 1523 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.94 % Favored : 94.99 % Rotamer: Outliers : 2.56 % Allowed : 20.78 % Favored : 76.66 % 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: 0.44 (0.23), residues: 1436 helix: 1.40 (0.18), residues: 860 sheet: -0.92 (0.56), residues: 83 loop : -1.48 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 167 HIS 0.003 0.001 HIS B 411 PHE 0.021 0.001 PHE B 360 TYR 0.030 0.002 TYR A 62 ARG 0.007 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 204 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 175 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8516 (t0) REVERT: A 252 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7799 (t0) REVERT: A 366 MET cc_start: 0.8047 (mmm) cc_final: 0.7776 (tpp) REVERT: A 397 MET cc_start: 0.8102 (tpp) cc_final: 0.7706 (tpp) REVERT: B 19 LYS cc_start: 0.8385 (tppt) cc_final: 0.7896 (tttt) REVERT: B 383 MET cc_start: 0.6309 (mmm) cc_final: 0.6058 (mtt) REVERT: B 392 MET cc_start: 0.6375 (ppp) cc_final: 0.6132 (ppp) REVERT: C 95 ASP cc_start: 0.7969 (m-30) cc_final: 0.7009 (t0) REVERT: C 141 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8651 (mt) outliers start: 29 outliers final: 23 residues processed: 194 average time/residue: 0.1782 time to fit residues: 53.8949 Evaluate side-chains 193 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 355 THR 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 413 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 576 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 Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** 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: 0.8040 moved from start: 0.2372 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= 0.179 Angle : 0.632 11.491 14948 Z= 0.305 Chirality : 0.042 0.187 1803 Planarity : 0.003 0.037 1897 Dihedral : 4.305 39.698 1523 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.56 % Allowed : 20.87 % Favored : 76.57 % 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: 0.49 (0.23), residues: 1436 helix: 1.45 (0.18), residues: 860 sheet: -0.87 (0.57), residues: 83 loop : -1.50 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 167 HIS 0.004 0.001 HIS B 411 PHE 0.020 0.001 PHE B 360 TYR 0.031 0.001 TYR A 62 ARG 0.007 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 206 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 252 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7810 (t0) REVERT: A 366 MET cc_start: 0.8047 (mmm) cc_final: 0.7333 (tpt) REVERT: A 397 MET cc_start: 0.8079 (tpp) cc_final: 0.7644 (tpp) REVERT: B 19 LYS cc_start: 0.8391 (tppt) cc_final: 0.7846 (tttt) REVERT: B 383 MET cc_start: 0.6402 (mmm) cc_final: 0.6052 (mtt) REVERT: C 95 ASP cc_start: 0.7934 (m-30) cc_final: 0.6971 (t0) REVERT: C 141 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8623 (mt) REVERT: C 157 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7408 (mp10) outliers start: 29 outliers final: 19 residues processed: 199 average time/residue: 0.1733 time to fit residues: 53.3021 Evaluate side-chains 189 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 355 THR 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 413 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL 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 150 LEU Chi-restraints excluded: chain C residue 157 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.0770 chunk 63 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10981 Z= 0.241 Angle : 0.677 17.826 14948 Z= 0.326 Chirality : 0.042 0.177 1803 Planarity : 0.003 0.037 1897 Dihedral : 4.397 43.399 1523 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 2.30 % Allowed : 21.57 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1436 helix: 1.41 (0.18), residues: 862 sheet: -1.15 (0.53), residues: 90 loop : -1.48 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 167 HIS 0.004 0.001 HIS B 411 PHE 0.023 0.002 PHE A 471 TYR 0.029 0.002 TYR A 62 ARG 0.007 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 188 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8257 (t0) REVERT: A 252 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7929 (t0) REVERT: A 366 MET cc_start: 0.8072 (mmm) cc_final: 0.7342 (tpt) REVERT: B 383 MET cc_start: 0.6355 (mmm) cc_final: 0.6016 (mtt) REVERT: B 392 MET cc_start: 0.6062 (ppp) cc_final: 0.5729 (ppp) REVERT: C 95 ASP cc_start: 0.8006 (m-30) cc_final: 0.6988 (t0) REVERT: C 141 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8667 (mt) outliers start: 26 outliers final: 21 residues processed: 182 average time/residue: 0.1852 time to fit residues: 52.2037 Evaluate side-chains 181 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 355 THR 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 413 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL 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 150 LEU Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 16 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 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 = 0.3306 r_free = 0.3306 target = 0.098516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.081537 restraints weight = 25160.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.083411 restraints weight = 13509.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.084665 restraints weight = 8700.465| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10981 Z= 0.213 Angle : 0.673 17.123 14948 Z= 0.321 Chirality : 0.042 0.175 1803 Planarity : 0.003 0.037 1897 Dihedral : 4.399 43.210 1523 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 2.30 % Allowed : 21.84 % Favored : 75.86 % 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: 0.44 (0.23), residues: 1436 helix: 1.42 (0.18), residues: 862 sheet: -1.17 (0.53), residues: 90 loop : -1.49 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 167 HIS 0.004 0.001 HIS B 411 PHE 0.022 0.001 PHE A 471 TYR 0.029 0.001 TYR A 62 ARG 0.007 0.000 ARG C 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2101.58 seconds wall clock time: 38 minutes 21.47 seconds (2301.47 seconds total)