Starting phenix.real_space_refine on Sat Jul 20 11:52:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/07_2024/7zrl_14918.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/07_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_14918/07_2024/7zrl_14918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/07_2024/7zrl_14918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/07_2024/7zrl_14918.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrl_14918/07_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 Residue "A GLU 223": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 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: 6.23, per 1000 atoms: 0.58 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: 4.39 Conformation dependent library (CDL) restraints added in 2.1 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: 4.77 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: 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 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 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 ========== 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: 0.860 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- 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 : 1.222 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: 0.1890 time to fit residues: 62.2086 Evaluate side-chains 167 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** A 165 ASN C 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10981 Z= 0.240 Angle : 0.612 8.516 14948 Z= 0.305 Chirality : 0.042 0.152 1803 Planarity : 0.004 0.043 1897 Dihedral : 4.546 31.920 1523 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.86 % Allowed : 12.02 % Favored : 86.12 % 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: -0.28 (0.22), residues: 1436 helix: 0.83 (0.18), residues: 855 sheet: -0.73 (0.57), residues: 80 loop : -1.88 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 364 HIS 0.002 0.000 HIS A 242 PHE 0.027 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 205 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 1.227 Fit side-chains REVERT: B 383 MET cc_start: 0.6696 (mmm) cc_final: 0.6088 (mtt) REVERT: C 50 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7913 (mmm160) REVERT: C 130 ASN cc_start: 0.8000 (t0) cc_final: 0.7515 (t0) outliers start: 21 outliers final: 18 residues processed: 191 average time/residue: 0.1964 time to fit residues: 56.2018 Evaluate side-chains 191 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 A residue 411 VAL Chi-restraints excluded: chain A residue 426 THR 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 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 C residue 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 133 THR 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: 2.9990 chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10981 Z= 0.252 Angle : 0.611 13.973 14948 Z= 0.304 Chirality : 0.042 0.211 1803 Planarity : 0.003 0.040 1897 Dihedral : 4.492 34.713 1523 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 1.95 % Allowed : 15.56 % Favored : 82.49 % 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: 1.05 (0.18), residues: 853 sheet: -0.82 (0.57), residues: 80 loop : -1.76 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 364 HIS 0.002 0.000 HIS A 242 PHE 0.020 0.002 PHE A 543 TYR 0.020 0.002 TYR A 381 ARG 0.005 0.000 ARG B 394 *********************** 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: 22 poor density : 175 time to evaluate : 1.235 Fit side-chains REVERT: C 50 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.7989 (mmm160) REVERT: C 130 ASN cc_start: 0.8025 (t0) cc_final: 0.7639 (t0) REVERT: C 141 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8793 (mt) outliers start: 22 outliers final: 17 residues processed: 185 average time/residue: 0.1998 time to fit residues: 55.0339 Evaluate side-chains 183 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 538 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 200 LEU 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 487 VAL Chi-restraints excluded: chain B residue 489 ASP 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 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: 0.9980 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 0.0870 chunk 137 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN C 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10981 Z= 0.158 Angle : 0.564 9.796 14948 Z= 0.279 Chirality : 0.040 0.226 1803 Planarity : 0.003 0.040 1897 Dihedral : 4.271 28.955 1523 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.77 % Allowed : 18.57 % Favored : 79.66 % 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: 0.30 (0.23), residues: 1436 helix: 1.36 (0.18), residues: 855 sheet: -0.72 (0.57), residues: 81 loop : -1.72 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 115 HIS 0.001 0.000 HIS A 242 PHE 0.043 0.001 PHE B 360 TYR 0.020 0.001 TYR A 381 ARG 0.002 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 203 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7959 (mmp) cc_final: 0.7569 (tpp) REVERT: B 19 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7927 (tttt) REVERT: C 50 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.7911 (mmm160) REVERT: C 130 ASN cc_start: 0.8107 (t0) cc_final: 0.7606 (t0) outliers start: 20 outliers final: 13 residues processed: 193 average time/residue: 0.1850 time to fit residues: 54.5212 Evaluate side-chains 179 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 644 LEU 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: 4.9990 chunk 102 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10981 Z= 0.246 Angle : 0.604 8.103 14948 Z= 0.302 Chirality : 0.042 0.197 1803 Planarity : 0.003 0.038 1897 Dihedral : 4.366 35.064 1523 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 2.83 % Allowed : 18.92 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1436 helix: 1.28 (0.18), residues: 859 sheet: -1.00 (0.54), residues: 88 loop : -1.65 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 167 HIS 0.002 0.000 HIS A 242 PHE 0.028 0.002 PHE B 360 TYR 0.023 0.002 TYR A 62 ARG 0.002 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 201 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 113 THR cc_start: 0.8879 (t) cc_final: 0.8584 (m) REVERT: A 366 MET cc_start: 0.8367 (mmm) cc_final: 0.7826 (mmm) REVERT: C 130 ASN cc_start: 0.8215 (t0) cc_final: 0.7549 (t0) REVERT: C 141 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8740 (mt) outliers start: 32 outliers final: 20 residues processed: 188 average time/residue: 0.1900 time to fit residues: 54.1681 Evaluate side-chains 181 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 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 154 ASP 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 433 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 644 LEU 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 150 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: 2.9990 chunk 80 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 0.0370 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2304 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= 0.190 Angle : 0.591 8.083 14948 Z= 0.290 Chirality : 0.041 0.206 1803 Planarity : 0.003 0.039 1897 Dihedral : 4.314 32.396 1523 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.40 % Rotamer: Outliers : 2.39 % Allowed : 19.72 % Favored : 77.90 % 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 (0.23), residues: 1436 helix: 1.41 (0.18), residues: 860 sheet: -1.05 (0.54), residues: 90 loop : -1.62 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 167 HIS 0.003 0.001 HIS B 411 PHE 0.027 0.001 PHE B 360 TYR 0.020 0.001 TYR A 381 ARG 0.007 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 197 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 THR cc_start: 0.8831 (t) cc_final: 0.8561 (m) REVERT: B 489 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8029 (p0) REVERT: C 130 ASN cc_start: 0.8082 (t0) cc_final: 0.7587 (t0) REVERT: C 141 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8697 (mt) outliers start: 27 outliers final: 12 residues processed: 185 average time/residue: 0.1860 time to fit residues: 52.4404 Evaluate side-chains 175 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 B residue 41 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 489 ASP 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 Chi-restraints excluded: chain C residue 150 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 136 optimal weight: 0.0970 chunk 85 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10981 Z= 0.166 Angle : 0.579 8.172 14948 Z= 0.283 Chirality : 0.040 0.197 1803 Planarity : 0.003 0.039 1897 Dihedral : 4.212 30.509 1523 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.21 % Allowed : 21.22 % 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: 0.51 (0.23), residues: 1436 helix: 1.52 (0.18), residues: 856 sheet: -1.03 (0.53), residues: 90 loop : -1.53 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 167 HIS 0.004 0.001 HIS B 411 PHE 0.024 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 199 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 113 THR cc_start: 0.8754 (t) cc_final: 0.8477 (m) REVERT: A 216 MET cc_start: 0.7686 (mmm) cc_final: 0.7409 (mmm) REVERT: A 366 MET cc_start: 0.8353 (tpp) cc_final: 0.7639 (tpp) REVERT: B 489 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7940 (p0) REVERT: C 130 ASN cc_start: 0.8127 (t0) cc_final: 0.7663 (t0) REVERT: C 141 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8646 (mt) outliers start: 25 outliers final: 14 residues processed: 188 average time/residue: 0.1720 time to fit residues: 50.0820 Evaluate side-chains 178 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 TYR 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 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 489 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 0.0770 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10981 Z= 0.164 Angle : 0.583 8.254 14948 Z= 0.283 Chirality : 0.041 0.184 1803 Planarity : 0.003 0.039 1897 Dihedral : 4.173 29.203 1523 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.48 % Allowed : 21.40 % 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: 0.58 (0.23), residues: 1436 helix: 1.58 (0.18), residues: 856 sheet: -0.94 (0.54), residues: 90 loop : -1.52 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 167 HIS 0.004 0.001 HIS B 411 PHE 0.022 0.001 PHE B 360 TYR 0.027 0.002 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 194 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.6810 (p90) REVERT: A 471 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7614 (m-10) REVERT: B 19 LYS cc_start: 0.8472 (tppt) cc_final: 0.8013 (tttt) REVERT: B 489 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7911 (p0) REVERT: C 130 ASN cc_start: 0.7945 (t0) cc_final: 0.7707 (t0) REVERT: C 141 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8640 (mt) outliers start: 28 outliers final: 18 residues processed: 183 average time/residue: 0.1765 time to fit residues: 49.8693 Evaluate side-chains 187 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 252 ASN 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 41 ILE 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 433 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 150 LEU 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: 0.7980 chunk 131 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 83 optimal weight: 0.0060 chunk 134 optimal weight: 9.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** 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: 0.8038 moved from start: 0.2375 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= 0.165 Angle : 0.592 8.695 14948 Z= 0.286 Chirality : 0.041 0.239 1803 Planarity : 0.003 0.039 1897 Dihedral : 4.149 27.842 1523 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.21 % Allowed : 22.02 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1436 helix: 1.68 (0.18), residues: 849 sheet: -0.91 (0.55), residues: 90 loop : -1.51 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 167 HIS 0.004 0.001 HIS B 404 PHE 0.022 0.001 PHE B 360 TYR 0.023 0.001 TYR A 62 ARG 0.005 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 198 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.6865 (p90) REVERT: A 366 MET cc_start: 0.8375 (tpp) cc_final: 0.7719 (tpp) REVERT: A 471 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: B 489 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7947 (p0) REVERT: C 130 ASN cc_start: 0.7898 (t0) cc_final: 0.7660 (t0) REVERT: C 141 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8629 (mt) outliers start: 25 outliers final: 20 residues processed: 186 average time/residue: 0.1976 time to fit residues: 56.0346 Evaluate side-chains 192 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 THR 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 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 433 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 644 LEU 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 162 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** ** 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: 0.8084 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10981 Z= 0.214 Angle : 0.630 10.297 14948 Z= 0.303 Chirality : 0.042 0.217 1803 Planarity : 0.003 0.038 1897 Dihedral : 4.246 32.866 1523 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 2.39 % Allowed : 22.02 % Favored : 75.60 % 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: 0.56 (0.23), residues: 1436 helix: 1.53 (0.18), residues: 857 sheet: -0.97 (0.54), residues: 90 loop : -1.48 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 167 HIS 0.005 0.001 HIS B 404 PHE 0.021 0.001 PHE B 360 TYR 0.024 0.002 TYR A 62 ARG 0.005 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 193 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6663 (p90) REVERT: A 366 MET cc_start: 0.8510 (tpp) cc_final: 0.7759 (tpp) REVERT: A 471 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7828 (m-10) REVERT: B 489 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8032 (p0) REVERT: C 130 ASN cc_start: 0.8010 (t0) cc_final: 0.7687 (t0) REVERT: C 141 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8651 (mt) outliers start: 27 outliers final: 20 residues processed: 180 average time/residue: 0.1897 time to fit residues: 51.8669 Evaluate side-chains 188 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 124 LEU 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 327 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 THR 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 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 644 LEU 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 161 LYS 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: 9.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079700 restraints weight = 25338.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.081686 restraints weight = 13404.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.082939 restraints weight = 8560.970| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2566 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= 0.189 Angle : 0.629 13.737 14948 Z= 0.300 Chirality : 0.041 0.200 1803 Planarity : 0.003 0.037 1897 Dihedral : 4.225 31.628 1523 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.06 % Rotamer: Outliers : 2.48 % Allowed : 22.28 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1436 helix: 1.55 (0.18), residues: 857 sheet: -0.99 (0.54), residues: 90 loop : -1.48 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 167 HIS 0.004 0.001 HIS B 404 PHE 0.020 0.001 PHE B 360 TYR 0.025 0.001 TYR A 62 ARG 0.005 0.000 ARG C 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.95 seconds wall clock time: 38 minutes 41.30 seconds (2321.30 seconds total)