Starting phenix.real_space_refine on Mon Jul 28 23:26:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrl_14918/07_2025/7zrl_14918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrl_14918/07_2025/7zrl_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/cci-nas-00/data/ceres_data/7zrl_14918/07_2025/7zrl_14918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrl_14918/07_2025/7zrl_14918.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrl_14918/07_2025/7zrl_14918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrl_14918/07_2025/7zrl_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-5711/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: 6.29, 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 - 3.00 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: 2.53 Conformation dependent library (CDL) restraints added in 1.4 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: 1.67 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: 4.49 Time building geometry restraints manager: 2.99 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.070 Find NCS groups from input model: 0.110 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.470 ------------------------------------------------------------------------------- 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= 0.225 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 Details of bonding type rmsd hydrogen bonds : bond 0.07858 ( 659) hydrogen bonds : angle 5.46792 ( 1929) covalent geometry : bond 0.00469 (10981) covalent geometry : angle 0.90932 (14948) *********************** 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 to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.122 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: 0.1940 time to fit residues: 63.0523 Evaluate side-chains 167 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN C 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.083587 restraints weight = 25096.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.085552 restraints weight = 13237.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086988 restraints weight = 8393.967| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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= 0.140 Angle : 0.610 8.224 14948 Z= 0.305 Chirality : 0.042 0.143 1803 Planarity : 0.004 0.044 1897 Dihedral : 4.568 33.506 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 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 659) hydrogen bonds : angle 4.49336 ( 1929) covalent geometry : bond 0.00316 (10981) covalent geometry : angle 0.61020 (14948) *********************** 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 to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 1.363 Fit side-chains REVERT: A 357 LEU cc_start: 0.9005 (mt) cc_final: 0.8368 (tp) REVERT: A 360 MET cc_start: 0.7911 (tmm) cc_final: 0.7664 (tmm) REVERT: B 69 SER cc_start: 0.7227 (m) cc_final: 0.6900 (p) REVERT: B 383 MET cc_start: 0.6696 (mmm) cc_final: 0.6099 (mtt) REVERT: C 50 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.8037 (mmm160) REVERT: C 119 GLU cc_start: 0.8140 (pm20) cc_final: 0.7925 (pm20) REVERT: C 130 ASN cc_start: 0.7885 (t0) cc_final: 0.7617 (t0) REVERT: C 162 TYR cc_start: 0.7352 (m-10) cc_final: 0.7134 (m-10) outliers start: 15 outliers final: 11 residues processed: 197 average time/residue: 0.2359 time to fit residues: 68.7276 Evaluate side-chains 187 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 99 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.083685 restraints weight = 25459.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085748 restraints weight = 13413.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.087010 restraints weight = 8490.883| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10981 Z= 0.116 Angle : 0.590 13.415 14948 Z= 0.292 Chirality : 0.041 0.213 1803 Planarity : 0.003 0.041 1897 Dihedral : 4.404 32.295 1523 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.59 % Allowed : 14.77 % Favored : 83.64 % 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: 0.09 (0.22), residues: 1436 helix: 1.18 (0.18), residues: 853 sheet: -0.58 (0.58), residues: 80 loop : -1.81 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 186 HIS 0.002 0.000 HIS A 351 PHE 0.014 0.001 PHE A 543 TYR 0.021 0.001 TYR A 381 ARG 0.004 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 659) hydrogen bonds : angle 4.35442 ( 1929) covalent geometry : bond 0.00256 (10981) covalent geometry : angle 0.58987 (14948) *********************** 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 209 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 1.862 Fit side-chains REVERT: A 252 ASN cc_start: 0.8577 (m-40) cc_final: 0.8161 (t0) REVERT: A 357 LEU cc_start: 0.9010 (mt) cc_final: 0.8368 (tp) REVERT: B 69 SER cc_start: 0.7253 (m) cc_final: 0.6915 (p) REVERT: B 383 MET cc_start: 0.6811 (mmm) cc_final: 0.6145 (mtt) REVERT: C 50 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.7961 (mmm160) REVERT: C 119 GLU cc_start: 0.8202 (pm20) cc_final: 0.7993 (pm20) outliers start: 18 outliers final: 13 residues processed: 200 average time/residue: 0.2646 time to fit residues: 78.9639 Evaluate side-chains 186 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 38 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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** ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN C 66 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.095646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.078451 restraints weight = 25226.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.080367 restraints weight = 13270.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.081635 restraints weight = 8424.298| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10981 Z= 0.216 Angle : 0.668 10.877 14948 Z= 0.337 Chirality : 0.044 0.192 1803 Planarity : 0.004 0.038 1897 Dihedral : 4.679 44.543 1523 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.74 % Allowed : 18.04 % Favored : 79.22 % 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: -0.01 (0.22), residues: 1436 helix: 1.04 (0.18), residues: 859 sheet: -0.76 (0.58), residues: 80 loop : -1.74 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 186 HIS 0.004 0.001 HIS A 242 PHE 0.044 0.002 PHE B 360 TYR 0.017 0.002 TYR A 381 ARG 0.005 0.001 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 659) hydrogen bonds : angle 4.49922 ( 1929) covalent geometry : bond 0.00496 (10981) covalent geometry : angle 0.66778 (14948) *********************** 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 202 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8540 (t0) REVERT: A 244 PHE cc_start: 0.8573 (m-10) cc_final: 0.8306 (m-10) REVERT: A 252 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8233 (t0) REVERT: B 69 SER cc_start: 0.7417 (m) cc_final: 0.7200 (p) REVERT: B 383 MET cc_start: 0.6205 (mmm) cc_final: 0.5898 (mtm) outliers start: 31 outliers final: 21 residues processed: 187 average time/residue: 0.1801 time to fit residues: 51.2376 Evaluate side-chains 190 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN 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 426 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 THR 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 D residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.080397 restraints weight = 25068.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.082354 restraints weight = 13216.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.083571 restraints weight = 8381.873| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10981 Z= 0.140 Angle : 0.609 11.272 14948 Z= 0.303 Chirality : 0.042 0.194 1803 Planarity : 0.003 0.039 1897 Dihedral : 4.522 41.239 1523 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 2.30 % Allowed : 18.57 % Favored : 79.13 % 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: 0.21 (0.22), residues: 1436 helix: 1.20 (0.18), residues: 867 sheet: -0.85 (0.56), residues: 81 loop : -1.64 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 186 HIS 0.002 0.000 HIS A 242 PHE 0.028 0.001 PHE B 360 TYR 0.020 0.001 TYR A 381 ARG 0.006 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 659) hydrogen bonds : angle 4.37771 ( 1929) covalent geometry : bond 0.00322 (10981) covalent geometry : angle 0.60928 (14948) *********************** 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 200 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7568 (mm-30) REVERT: A 244 PHE cc_start: 0.8501 (m-10) cc_final: 0.8281 (m-10) REVERT: A 245 GLU cc_start: 0.8725 (tp30) cc_final: 0.7603 (mm-30) REVERT: A 252 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8030 (t0) REVERT: A 327 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7007 (p90) REVERT: B 69 SER cc_start: 0.7462 (m) cc_final: 0.7233 (p) REVERT: B 570 MET cc_start: 0.7707 (ttm) cc_final: 0.7479 (mtp) REVERT: C 141 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8753 (mt) outliers start: 26 outliers final: 18 residues processed: 189 average time/residue: 0.2053 time to fit residues: 59.1517 Evaluate side-chains 184 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 133 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 B residue 644 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.080440 restraints weight = 25289.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.082332 restraints weight = 13513.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083425 restraints weight = 8643.793| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10981 Z= 0.140 Angle : 0.614 10.266 14948 Z= 0.302 Chirality : 0.042 0.247 1803 Planarity : 0.003 0.039 1897 Dihedral : 4.470 42.570 1523 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 2.83 % Allowed : 19.10 % Favored : 78.07 % 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: 0.29 (0.23), residues: 1436 helix: 1.31 (0.18), residues: 864 sheet: -1.06 (0.55), residues: 83 loop : -1.62 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 115 HIS 0.002 0.000 HIS B 404 PHE 0.024 0.001 PHE B 360 TYR 0.020 0.001 TYR A 381 ARG 0.006 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 659) hydrogen bonds : angle 4.35151 ( 1929) covalent geometry : bond 0.00320 (10981) covalent geometry : angle 0.61385 (14948) *********************** 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 204 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 244 PHE cc_start: 0.8554 (m-10) cc_final: 0.8277 (m-10) REVERT: A 245 GLU cc_start: 0.8835 (tp30) cc_final: 0.7963 (mm-30) REVERT: A 252 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8069 (t0) REVERT: A 327 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7029 (p90) REVERT: A 471 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7908 (m-10) REVERT: B 69 SER cc_start: 0.7451 (m) cc_final: 0.7231 (p) REVERT: B 383 MET cc_start: 0.5865 (mtm) cc_final: 0.5559 (mtt) REVERT: C 141 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8731 (mt) outliers start: 32 outliers final: 20 residues processed: 192 average time/residue: 0.2001 time to fit residues: 59.0286 Evaluate side-chains 190 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 471 PHE 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 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 644 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 34 PHE 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 176 VAL Chi-restraints excluded: chain D residue 11 LEU 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 85 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 133 optimal weight: 0.0000 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 114 ASN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.083323 restraints weight = 25404.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.084475 restraints weight = 13674.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.085314 restraints weight = 10017.681| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10981 Z= 0.115 Angle : 0.601 10.515 14948 Z= 0.294 Chirality : 0.041 0.234 1803 Planarity : 0.003 0.039 1897 Dihedral : 4.352 39.745 1523 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.48 % Allowed : 19.98 % 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: 0.42 (0.23), residues: 1436 helix: 1.42 (0.18), residues: 859 sheet: -0.97 (0.56), residues: 83 loop : -1.55 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 115 HIS 0.004 0.000 HIS B 404 PHE 0.022 0.001 PHE B 360 TYR 0.020 0.001 TYR A 381 ARG 0.005 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 659) hydrogen bonds : angle 4.29544 ( 1929) covalent geometry : bond 0.00253 (10981) covalent geometry : angle 0.60109 (14948) *********************** 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 212 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7745 (mm-30) REVERT: A 244 PHE cc_start: 0.8517 (m-10) cc_final: 0.8285 (m-80) REVERT: A 245 GLU cc_start: 0.8870 (tp30) cc_final: 0.7985 (mm-30) REVERT: A 252 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.7955 (t0) REVERT: A 327 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7108 (p90) REVERT: A 366 MET cc_start: 0.8758 (mmm) cc_final: 0.8146 (mmm) REVERT: A 367 GLN cc_start: 0.7701 (mm110) cc_final: 0.7279 (mp10) REVERT: B 69 SER cc_start: 0.7310 (m) cc_final: 0.7102 (p) REVERT: B 489 ASP cc_start: 0.8314 (p0) cc_final: 0.7775 (p0) REVERT: C 95 ASP cc_start: 0.8157 (m-30) cc_final: 0.7188 (t0) REVERT: C 96 LYS cc_start: 0.8792 (pttt) cc_final: 0.8527 (pttt) REVERT: C 141 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8665 (mt) outliers start: 28 outliers final: 15 residues processed: 200 average time/residue: 0.2375 time to fit residues: 73.6957 Evaluate side-chains 187 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 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 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 141 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 37 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 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 = 0.3298 r_free = 0.3298 target = 0.097969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.081376 restraints weight = 25265.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.083247 restraints weight = 13471.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.084487 restraints weight = 8624.542| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2438 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= 0.136 Angle : 0.622 8.812 14948 Z= 0.304 Chirality : 0.042 0.219 1803 Planarity : 0.003 0.039 1897 Dihedral : 4.344 42.319 1523 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.94 % Favored : 94.99 % Rotamer: Outliers : 2.30 % Allowed : 21.04 % 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: 1.43 (0.18), residues: 859 sheet: -0.93 (0.57), residues: 83 loop : -1.55 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 115 HIS 0.003 0.001 HIS B 411 PHE 0.020 0.001 PHE B 360 TYR 0.027 0.002 TYR A 62 ARG 0.004 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 659) hydrogen bonds : angle 4.31634 ( 1929) covalent geometry : bond 0.00310 (10981) covalent geometry : angle 0.62198 (14948) *********************** 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 196 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 245 GLU cc_start: 0.8898 (tp30) cc_final: 0.7799 (mm-30) REVERT: A 252 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8052 (t0) REVERT: A 327 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7077 (p90) REVERT: A 366 MET cc_start: 0.8785 (mmm) cc_final: 0.8040 (tpp) REVERT: B 69 SER cc_start: 0.7345 (m) cc_final: 0.7126 (p) REVERT: B 489 ASP cc_start: 0.8307 (p0) cc_final: 0.7798 (p0) REVERT: C 95 ASP cc_start: 0.8127 (m-30) cc_final: 0.7132 (t0) REVERT: C 141 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8676 (mt) outliers start: 26 outliers final: 19 residues processed: 188 average time/residue: 0.2522 time to fit residues: 73.4486 Evaluate side-chains 185 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 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 329 VAL 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 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 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 176 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 11 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 78 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 50 optimal weight: 0.0770 overall best weight: 0.8340 ------------------------------------------------------------------------------- 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** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 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 = 0.3315 r_free = 0.3315 target = 0.098994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.082059 restraints weight = 25332.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.084027 restraints weight = 13342.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.085316 restraints weight = 8418.399| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2446 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= 0.123 Angle : 0.622 10.010 14948 Z= 0.303 Chirality : 0.042 0.206 1803 Planarity : 0.003 0.038 1897 Dihedral : 4.340 41.584 1523 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: 0.52 (0.23), residues: 1436 helix: 1.50 (0.18), residues: 860 sheet: -0.83 (0.57), residues: 83 loop : -1.54 (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 0.020 0.001 PHE A 471 TYR 0.028 0.001 TYR A 62 ARG 0.004 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 659) hydrogen bonds : angle 4.30367 ( 1929) covalent geometry : bond 0.00277 (10981) covalent geometry : angle 0.62192 (14948) *********************** 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 196 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7991 (mm-30) REVERT: A 245 GLU cc_start: 0.8880 (tp30) cc_final: 0.8509 (mm-30) REVERT: A 252 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8134 (t0) REVERT: A 282 MET cc_start: 0.8966 (tmm) cc_final: 0.8578 (tmm) REVERT: A 327 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7150 (p90) REVERT: A 366 MET cc_start: 0.8795 (mmm) cc_final: 0.7953 (tpp) REVERT: A 367 GLN cc_start: 0.7756 (mm110) cc_final: 0.7328 (mp10) REVERT: A 437 MET cc_start: 0.7636 (mmm) cc_final: 0.7366 (mtp) REVERT: B 19 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8017 (tttm) REVERT: B 489 ASP cc_start: 0.8271 (p0) cc_final: 0.7753 (p0) REVERT: C 95 ASP cc_start: 0.8132 (m-30) cc_final: 0.7108 (t0) REVERT: C 141 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8654 (mt) outliers start: 25 outliers final: 21 residues processed: 187 average time/residue: 0.1886 time to fit residues: 53.9787 Evaluate side-chains 190 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 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 365 LEU 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 48 CYS Chi-restraints excluded: chain B residue 133 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 48 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 150 LEU 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 92 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 127 optimal weight: 0.0040 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.097165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.080264 restraints weight = 25498.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.082207 restraints weight = 13203.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.083570 restraints weight = 8249.837| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2472 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= 0.121 Angle : 0.627 10.383 14948 Z= 0.303 Chirality : 0.041 0.190 1803 Planarity : 0.003 0.038 1897 Dihedral : 4.301 41.035 1523 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.95 % Allowed : 22.10 % Favored : 75.95 % 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: 0.53 (0.23), residues: 1436 helix: 1.51 (0.18), residues: 861 sheet: -1.03 (0.54), residues: 90 loop : -1.50 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 167 HIS 0.004 0.001 HIS B 411 PHE 0.020 0.001 PHE A 471 TYR 0.024 0.001 TYR A 62 ARG 0.004 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 659) hydrogen bonds : angle 4.29629 ( 1929) covalent geometry : bond 0.00273 (10981) covalent geometry : angle 0.62653 (14948) ********************** 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 189 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 MET cc_start: 0.7677 (mmm) cc_final: 0.7224 (mmm) REVERT: A 223 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 245 GLU cc_start: 0.8840 (tp30) cc_final: 0.8031 (mm-30) REVERT: A 252 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8099 (t0) REVERT: A 327 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7125 (p90) REVERT: A 366 MET cc_start: 0.8785 (mmm) cc_final: 0.7527 (tpp) REVERT: A 367 GLN cc_start: 0.7736 (mm110) cc_final: 0.7321 (mp10) REVERT: A 397 MET cc_start: 0.8257 (tpp) cc_final: 0.7993 (tpp) REVERT: A 437 MET cc_start: 0.7694 (mmm) cc_final: 0.7466 (mtp) REVERT: B 489 ASP cc_start: 0.8284 (p0) cc_final: 0.7757 (p0) REVERT: C 95 ASP cc_start: 0.8131 (m-30) cc_final: 0.7118 (t0) REVERT: C 141 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8643 (mt) outliers start: 22 outliers final: 16 residues processed: 184 average time/residue: 0.1805 time to fit residues: 51.2676 Evaluate side-chains 185 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 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 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 133 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 141 ILE Chi-restraints excluded: chain C residue 150 LEU 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 83 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 117 optimal weight: 0.0040 chunk 61 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- 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** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.098886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.081805 restraints weight = 25342.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.083680 restraints weight = 13327.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.084952 restraints weight = 8571.318| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 0.034 10981 Z= 0.133 Angle : 0.636 10.636 14948 Z= 0.308 Chirality : 0.042 0.175 1803 Planarity : 0.003 0.038 1897 Dihedral : 4.332 42.444 1523 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 2.21 % Allowed : 21.75 % Favored : 76.04 % 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: 0.54 (0.23), residues: 1436 helix: 1.51 (0.18), residues: 861 sheet: -1.06 (0.53), residues: 90 loop : -1.48 (0.28), residues: 485 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 A 471 TYR 0.026 0.001 TYR A 62 ARG 0.004 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 659) hydrogen bonds : angle 4.29890 ( 1929) covalent geometry : bond 0.00303 (10981) covalent geometry : angle 0.63563 (14948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3512.44 seconds wall clock time: 65 minutes 0.29 seconds (3900.29 seconds total)