Starting phenix.real_space_refine on Sun Dec 29 23:34:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrk_14917/12_2024/7zrk_14917.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrk_14917/12_2024/7zrk_14917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zrk_14917/12_2024/7zrk_14917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrk_14917/12_2024/7zrk_14917.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrk_14917/12_2024/7zrk_14917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrk_14917/12_2024/7zrk_14917.cif" } resolution = 3.1 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= 0.009 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 12 8.98 5 P 8 5.49 5 S 62 5.16 5 C 7133 2.51 5 N 1826 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11050 Number of models: 1 Model: "" Number of chains: 6 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: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} 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: "B" Number of atoms: 5025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5025 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 211 Unusual residues: {' K': 11, 'CDL': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.30, per 1000 atoms: 0.57 Number of scatterers: 11050 At special positions: 0 Unit cell: (98.164, 116.38, 146.74, 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 12 19.00 S 62 16.00 P 8 15.00 O 2009 8.00 N 1826 7.00 C 7133 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: 2.99 Conformation dependent library (CDL) restraints added in 1.6 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: 2638 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 64.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 removed outlier: 3.860A 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 41 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.734A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.913A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.835A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.509A 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 305 removed outlier: 4.290A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 Processing helix chain 'A' and resid 410 through 437 removed outlier: 4.503A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 478 through 509 removed outlier: 4.691A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 4.386A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 550 removed outlier: 4.074A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 3 through 21 removed outlier: 3.764A pdb=" N ALA C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.997A pdb=" N SER C 82 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.661A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.732A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 149 Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.656A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 61 through 99 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 215 through 247 removed outlier: 4.011A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.692A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 285 removed outlier: 5.819A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.989A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 346 through 361 removed outlier: 3.834A pdb=" N LYS B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 413 through 426 removed outlier: 4.171A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.799A pdb=" N LYS B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 595 removed outlier: 4.017A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.971A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.337A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 680 removed outlier: 4.244A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.845A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.638A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.837A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 134 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY B 144 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.791A pdb=" N SER B 152 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289 removed outlier: 5.597A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 531 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 535 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY B 472 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 489 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.768A pdb=" N ARG B 394 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 434 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 396 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 432 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1980 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: 3.45 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1785 1.32 - 1.45: 2749 1.45 - 1.57: 6576 1.57 - 1.70: 16 1.70 - 1.82: 112 Bond restraints: 11238 Sorted by residual: bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.606 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C ILE C 141 " pdb=" N PRO C 142 " ideal model delta sigma weight residual 1.335 1.383 -0.047 1.36e-02 5.41e+03 1.21e+01 bond pdb=" C51 CDL A 613 " pdb=" C52 CDL A 613 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.50e-02 4.44e+03 8.66e+00 bond pdb=" OB3 CDL A 613 " pdb=" PB2 CDL A 613 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.34e+00 bond pdb=" OA3 CDL A 612 " pdb=" PA1 CDL A 612 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.15e+00 ... (remaining 11233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 14776 1.88 - 3.77: 360 3.77 - 5.65: 82 5.65 - 7.53: 32 7.53 - 9.41: 6 Bond angle restraints: 15256 Sorted by residual: angle pdb=" N VAL A 496 " pdb=" CA VAL A 496 " pdb=" C VAL A 496 " ideal model delta sigma weight residual 112.96 107.91 5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 121.13 -7.23 1.80e+00 3.09e-01 1.61e+01 angle pdb=" C MET B 392 " pdb=" N ILE B 393 " pdb=" CA ILE B 393 " ideal model delta sigma weight residual 120.69 126.14 -5.45 1.46e+00 4.69e-01 1.40e+01 angle pdb=" C ARG B 391 " pdb=" N MET B 392 " pdb=" CA MET B 392 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C LEU A 380 " pdb=" N TYR A 381 " pdb=" CA TYR A 381 " ideal model delta sigma weight residual 121.14 115.60 5.54 1.75e+00 3.27e-01 1.00e+01 ... (remaining 15251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.31: 6373 28.31 - 56.61: 336 56.61 - 84.92: 33 84.92 - 113.23: 2 113.23 - 141.53: 2 Dihedral angle restraints: 6746 sinusoidal: 2640 harmonic: 4106 Sorted by residual: dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 63.98 -123.98 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" CA5 CDL A 612 " pdb=" CA4 CDL A 612 " pdb=" OA6 CDL A 612 " pdb=" CA6 CDL A 612 " ideal model delta sinusoidal sigma weight residual 168.24 26.71 141.53 1 3.00e+01 1.11e-03 1.90e+01 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 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 6743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1394 0.051 - 0.101: 337 0.101 - 0.152: 70 0.152 - 0.203: 10 0.203 - 0.253: 4 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CB4 CDL A 613 " pdb=" CB3 CDL A 613 " pdb=" CB6 CDL A 613 " pdb=" OB6 CDL A 613 " both_signs ideal model delta sigma weight residual False -2.57 -2.32 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA4 CDL A 612 " pdb=" CA3 CDL A 612 " pdb=" CA6 CDL A 612 " pdb=" OA6 CDL A 612 " both_signs ideal model delta sigma weight residual False -2.57 -2.34 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA4 CDL A 613 " pdb=" CA3 CDL A 613 " pdb=" CA6 CDL A 613 " pdb=" OA6 CDL A 613 " both_signs ideal model delta sigma weight residual False -2.57 -2.35 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1812 not shown) Planarity restraints: 1910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 163 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 164 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 495 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO B 496 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 58 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO B 59 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.033 5.00e-02 4.00e+02 ... (remaining 1907 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 3302 2.83 - 3.41: 12547 3.41 - 3.98: 22053 3.98 - 4.56: 31145 4.56 - 5.14: 44819 Nonbonded interactions: 113866 Sorted by model distance: nonbonded pdb=" OE2 GLU C 119 " pdb=" OG1 THR C 133 " model vdw 2.251 3.040 nonbonded pdb=" O GLY B 149 " pdb=" OG SER B 169 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR B 47 " pdb=" OG SER B 69 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 615 " pdb=" OD1 ASP B 673 " model vdw 2.322 3.040 nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.324 3.040 ... (remaining 113861 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 0.210 11238 Z= 0.302 Angle : 0.773 9.415 15256 Z= 0.390 Chirality : 0.047 0.253 1815 Planarity : 0.006 0.084 1910 Dihedral : 16.226 141.532 4108 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 (0.21), residues: 1436 helix: 0.67 (0.16), residues: 854 sheet: -0.82 (0.78), residues: 49 loop : -1.43 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 31 HIS 0.007 0.001 HIS B 563 PHE 0.021 0.002 PHE B 9 TYR 0.021 0.002 TYR A 381 ARG 0.008 0.000 ARG A 48 *********************** 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 161 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.127 Fit side-chains REVERT: A 6 PHE cc_start: 0.7967 (t80) cc_final: 0.7690 (t80) REVERT: A 414 MET cc_start: 0.7693 (mmm) cc_final: 0.7469 (mmp) REVERT: B 609 CYS cc_start: 0.7899 (m) cc_final: 0.7645 (m) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2283 time to fit residues: 53.2265 Evaluate side-chains 134 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 8.9990 chunk 108 optimal weight: 0.0270 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11238 Z= 0.244 Angle : 0.575 6.284 15256 Z= 0.288 Chirality : 0.041 0.171 1815 Planarity : 0.005 0.056 1910 Dihedral : 12.198 128.941 1728 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.35 % Allowed : 7.23 % Favored : 92.42 % 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: 0.46 (0.22), residues: 1436 helix: 1.39 (0.18), residues: 867 sheet: -1.09 (0.69), residues: 55 loop : -1.43 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 31 HIS 0.005 0.001 HIS B 563 PHE 0.022 0.002 PHE B 377 TYR 0.031 0.002 TYR A 381 ARG 0.002 0.000 ARG A 48 *********************** 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 144 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 1.447 Fit side-chains REVERT: A 408 LYS cc_start: 0.8172 (mptt) cc_final: 0.7865 (mptt) REVERT: A 414 MET cc_start: 0.7743 (mmm) cc_final: 0.7488 (mmp) REVERT: C 48 THR cc_start: 0.8157 (t) cc_final: 0.7809 (m) REVERT: B 279 MET cc_start: 0.7564 (mmp) cc_final: 0.7260 (mmp) REVERT: B 318 GLN cc_start: 0.6255 (pt0) cc_final: 0.5989 (mt0) REVERT: B 568 MET cc_start: 0.8182 (mtp) cc_final: 0.7967 (mtm) REVERT: B 609 CYS cc_start: 0.8082 (m) cc_final: 0.7809 (m) outliers start: 4 outliers final: 4 residues processed: 143 average time/residue: 0.2208 time to fit residues: 46.9028 Evaluate side-chains 133 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 88 optimal weight: 0.0010 chunk 35 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS D 25 ASN ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11238 Z= 0.191 Angle : 0.537 6.941 15256 Z= 0.267 Chirality : 0.039 0.169 1815 Planarity : 0.004 0.048 1910 Dihedral : 11.489 123.241 1728 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.53 % Allowed : 10.14 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1436 helix: 1.70 (0.18), residues: 868 sheet: -1.17 (0.67), residues: 55 loop : -1.30 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.004 0.001 HIS B 563 PHE 0.014 0.001 PHE B 377 TYR 0.028 0.001 TYR A 381 ARG 0.003 0.000 ARG A 153 *********************** 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 146 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 1.251 Fit side-chains REVERT: A 6 PHE cc_start: 0.8147 (t80) cc_final: 0.7882 (t80) REVERT: A 408 LYS cc_start: 0.8089 (mptt) cc_final: 0.7714 (mptt) REVERT: A 414 MET cc_start: 0.7732 (mmm) cc_final: 0.7501 (mmp) REVERT: B 58 MET cc_start: 0.5055 (OUTLIER) cc_final: 0.4609 (tpt) REVERT: B 279 MET cc_start: 0.7592 (mmp) cc_final: 0.7290 (mmp) REVERT: B 318 GLN cc_start: 0.6252 (pt0) cc_final: 0.5978 (mt0) REVERT: B 609 CYS cc_start: 0.8092 (m) cc_final: 0.7815 (m) outliers start: 6 outliers final: 4 residues processed: 144 average time/residue: 0.2200 time to fit residues: 47.2431 Evaluate side-chains 139 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 156 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 87 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN D 25 ASN B 30 GLN ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11238 Z= 0.294 Angle : 0.590 6.240 15256 Z= 0.295 Chirality : 0.042 0.179 1815 Planarity : 0.004 0.046 1910 Dihedral : 11.427 127.448 1728 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.06 % Allowed : 11.11 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1436 helix: 1.59 (0.18), residues: 867 sheet: -0.98 (0.60), residues: 68 loop : -1.29 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.005 0.001 HIS B 563 PHE 0.018 0.002 PHE A 109 TYR 0.026 0.002 TYR A 381 ARG 0.003 0.000 ARG A 44 *********************** 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 149 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.100 Fit side-chains REVERT: A 414 MET cc_start: 0.7805 (mmm) cc_final: 0.7409 (mmp) REVERT: D 1 MET cc_start: 0.5085 (ptt) cc_final: 0.4373 (ptt) REVERT: B 58 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4879 (tpt) REVERT: B 318 GLN cc_start: 0.6282 (pt0) cc_final: 0.6012 (pp30) outliers start: 12 outliers final: 10 residues processed: 143 average time/residue: 0.2196 time to fit residues: 46.8597 Evaluate side-chains 142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 528 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11238 Z= 0.232 Angle : 0.554 6.118 15256 Z= 0.276 Chirality : 0.040 0.176 1815 Planarity : 0.004 0.046 1910 Dihedral : 11.174 125.428 1728 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.23 % Allowed : 12.96 % Favored : 85.80 % 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: 0.88 (0.22), residues: 1436 helix: 1.71 (0.18), residues: 868 sheet: -0.93 (0.61), residues: 68 loop : -1.25 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.004 0.001 HIS B 563 PHE 0.013 0.001 PHE A 373 TYR 0.026 0.001 TYR A 381 ARG 0.002 0.000 ARG A 153 *********************** 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 149 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.362 Fit side-chains REVERT: A 414 MET cc_start: 0.7736 (mmm) cc_final: 0.7441 (mmp) REVERT: A 544 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8170 (mm) REVERT: D 1 MET cc_start: 0.5101 (ptt) cc_final: 0.4491 (ptt) REVERT: B 114 TYR cc_start: 0.5250 (t80) cc_final: 0.5014 (t80) REVERT: B 318 GLN cc_start: 0.6278 (pt0) cc_final: 0.6018 (pp30) outliers start: 14 outliers final: 7 residues processed: 144 average time/residue: 0.2260 time to fit residues: 48.9984 Evaluate side-chains 140 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 477 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11238 Z= 0.245 Angle : 0.558 7.614 15256 Z= 0.278 Chirality : 0.040 0.177 1815 Planarity : 0.004 0.046 1910 Dihedral : 11.042 125.232 1728 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.23 % Allowed : 13.76 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1436 helix: 1.72 (0.17), residues: 874 sheet: -0.91 (0.62), residues: 68 loop : -1.28 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 71 HIS 0.004 0.001 HIS B 563 PHE 0.015 0.001 PHE A 373 TYR 0.026 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 *********************** 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 148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 6 PHE cc_start: 0.8239 (t80) cc_final: 0.7982 (t80) REVERT: A 414 MET cc_start: 0.7743 (mmm) cc_final: 0.7444 (mmp) REVERT: A 544 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8199 (mm) REVERT: C 93 GLU cc_start: 0.7591 (tp30) cc_final: 0.7339 (tp30) REVERT: B 114 TYR cc_start: 0.5295 (t80) cc_final: 0.5013 (t80) REVERT: B 318 GLN cc_start: 0.6308 (pt0) cc_final: 0.6021 (pp30) outliers start: 14 outliers final: 10 residues processed: 143 average time/residue: 0.2188 time to fit residues: 46.6474 Evaluate side-chains 143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 77 optimal weight: 0.2980 chunk 137 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11238 Z= 0.190 Angle : 0.543 9.254 15256 Z= 0.268 Chirality : 0.039 0.170 1815 Planarity : 0.004 0.047 1910 Dihedral : 10.778 122.008 1728 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.41 % Allowed : 14.02 % Favored : 84.57 % 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: 1.03 (0.22), residues: 1436 helix: 1.86 (0.18), residues: 874 sheet: -0.88 (0.65), residues: 63 loop : -1.26 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.003 0.001 HIS B 563 PHE 0.013 0.001 PHE A 373 TYR 0.026 0.001 TYR A 381 ARG 0.004 0.000 ARG A 44 *********************** 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 151 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.130 Fit side-chains REVERT: A 6 PHE cc_start: 0.8220 (t80) cc_final: 0.7964 (t80) REVERT: A 414 MET cc_start: 0.7703 (mmm) cc_final: 0.7434 (mmp) REVERT: A 544 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8174 (mm) REVERT: B 114 TYR cc_start: 0.5304 (t80) cc_final: 0.5012 (t80) REVERT: B 318 GLN cc_start: 0.6304 (pt0) cc_final: 0.6015 (pp30) REVERT: B 609 CYS cc_start: 0.8154 (m) cc_final: 0.7856 (m) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.2181 time to fit residues: 47.7357 Evaluate side-chains 144 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11238 Z= 0.311 Angle : 0.603 10.076 15256 Z= 0.298 Chirality : 0.042 0.175 1815 Planarity : 0.004 0.047 1910 Dihedral : 10.970 127.370 1728 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.23 % Allowed : 14.37 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1436 helix: 1.66 (0.17), residues: 871 sheet: -0.99 (0.57), residues: 80 loop : -1.29 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 115 HIS 0.005 0.001 HIS B 563 PHE 0.016 0.002 PHE A 373 TYR 0.025 0.002 TYR A 381 ARG 0.003 0.000 ARG A 44 *********************** 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 148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.144 Fit side-chains REVERT: A 413 GLU cc_start: 0.7419 (mp0) cc_final: 0.7191 (mp0) REVERT: A 414 MET cc_start: 0.7795 (mmm) cc_final: 0.7402 (mmp) REVERT: A 445 MET cc_start: 0.8779 (mtt) cc_final: 0.8470 (mtm) REVERT: A 471 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.6447 (m-10) REVERT: A 544 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8262 (mm) REVERT: B 114 TYR cc_start: 0.5366 (t80) cc_final: 0.5023 (t80) REVERT: B 318 GLN cc_start: 0.6343 (pt0) cc_final: 0.6068 (pp30) REVERT: B 667 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8520 (mp) outliers start: 14 outliers final: 10 residues processed: 144 average time/residue: 0.2205 time to fit residues: 47.1615 Evaluate side-chains 146 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 471 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 667 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11238 Z= 0.177 Angle : 0.538 10.618 15256 Z= 0.266 Chirality : 0.039 0.168 1815 Planarity : 0.004 0.046 1910 Dihedral : 10.598 121.045 1728 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.23 % Allowed : 14.81 % Favored : 83.95 % 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: 1.11 (0.22), residues: 1436 helix: 1.90 (0.18), residues: 874 sheet: -0.77 (0.62), residues: 68 loop : -1.21 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.003 0.001 HIS B 563 PHE 0.012 0.001 PHE A 494 TYR 0.025 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 *********************** 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 152 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 1.311 Fit side-chains REVERT: A 6 PHE cc_start: 0.8172 (t80) cc_final: 0.7912 (t80) REVERT: A 413 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7218 (mp0) REVERT: A 414 MET cc_start: 0.7763 (mmm) cc_final: 0.7509 (mmp) REVERT: A 445 MET cc_start: 0.8752 (mtt) cc_final: 0.8522 (mtt) REVERT: A 544 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8192 (mm) REVERT: B 114 TYR cc_start: 0.5382 (t80) cc_final: 0.5027 (t80) REVERT: B 318 GLN cc_start: 0.6326 (pt0) cc_final: 0.6057 (pp30) REVERT: B 392 MET cc_start: 0.4772 (ptt) cc_final: 0.4321 (ppp) REVERT: B 609 CYS cc_start: 0.8156 (m) cc_final: 0.7868 (m) outliers start: 14 outliers final: 11 residues processed: 148 average time/residue: 0.2263 time to fit residues: 50.3189 Evaluate side-chains 148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 142 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 69 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11238 Z= 0.185 Angle : 0.544 11.406 15256 Z= 0.269 Chirality : 0.039 0.165 1815 Planarity : 0.004 0.047 1910 Dihedral : 10.580 119.828 1728 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.15 % Allowed : 14.81 % Favored : 84.04 % 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: 1.15 (0.22), residues: 1436 helix: 1.94 (0.17), residues: 874 sheet: -0.74 (0.65), residues: 63 loop : -1.21 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.003 0.001 HIS B 563 PHE 0.013 0.001 PHE A 373 TYR 0.026 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 ********************** 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 148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.106 Fit side-chains REVERT: A 6 PHE cc_start: 0.8209 (t80) cc_final: 0.7948 (t80) REVERT: A 413 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7221 (mp0) REVERT: A 414 MET cc_start: 0.7751 (mmm) cc_final: 0.7484 (mmp) REVERT: A 544 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8222 (mm) REVERT: B 114 TYR cc_start: 0.5376 (t80) cc_final: 0.5029 (t80) REVERT: B 318 GLN cc_start: 0.6304 (pt0) cc_final: 0.6023 (pp30) REVERT: B 392 MET cc_start: 0.4652 (ptt) cc_final: 0.4237 (ppp) outliers start: 13 outliers final: 11 residues processed: 144 average time/residue: 0.2210 time to fit residues: 47.3311 Evaluate side-chains 146 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 662 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.147746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106160 restraints weight = 13030.383| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.81 r_work: 0.2965 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11238 Z= 0.162 Angle : 0.531 11.061 15256 Z= 0.262 Chirality : 0.039 0.158 1815 Planarity : 0.004 0.047 1910 Dihedral : 10.383 115.489 1728 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.88 % Allowed : 15.08 % Favored : 84.04 % 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: 1.27 (0.23), residues: 1436 helix: 2.04 (0.18), residues: 874 sheet: -0.83 (0.65), residues: 64 loop : -1.15 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.002 0.001 HIS B 563 PHE 0.012 0.001 PHE A 494 TYR 0.026 0.001 TYR A 381 ARG 0.003 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.10 seconds wall clock time: 43 minutes 32.53 seconds (2612.53 seconds total)