Starting phenix.real_space_refine on Fri Aug 22 22:09:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irj_35676/08_2025/8irj_35676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irj_35676/08_2025/8irj_35676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8irj_35676/08_2025/8irj_35676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irj_35676/08_2025/8irj_35676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8irj_35676/08_2025/8irj_35676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irj_35676/08_2025/8irj_35676.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5314 2.51 5 N 1422 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8228 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4114 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 30, 'TRANS': 500} Chain breaks: 6 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Restraints were copied for chains: B Time building chain proxies: 2.93, per 1000 atoms: 0.36 Number of scatterers: 8228 At special positions: 0 Unit cell: (66.3966, 96.1899, 167.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1438 8.00 N 1422 7.00 C 5314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 356 " distance=2.04 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 366 " distance=2.04 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 390 " - pdb=" SG CYS B 390 " distance=2.04 Simple disulfide: pdb=" SG CYS A 445 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 356 " distance=2.04 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 366 " distance=2.04 Simple disulfide: pdb=" SG CYS B 363 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 445 " - pdb=" SG CYS B 537 " distance=2.03 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: 0.51 Conformation dependent library (CDL) restraints added in 393.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 50.5% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 92 through 116 removed outlier: 3.603A pdb=" N THR A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.842A pdb=" N TYR A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 378 through 402 removed outlier: 3.861A pdb=" N ALA A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS A 391 " --> pdb=" O CYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.980A pdb=" N ARG A 407 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 408' Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.559A pdb=" N PHE A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 441 through 475 removed outlier: 3.870A pdb=" N THR A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 519 Proline residue: A 500 - end of helix Processing helix chain 'A' and resid 540 through 565 removed outlier: 3.570A pdb=" N GLY A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 599 removed outlier: 3.980A pdb=" N TYR A 576 " --> pdb=" O HIS A 572 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'A' and resid 603 through 632 Proline residue: A 629 - end of helix removed outlier: 3.657A pdb=" N TRP A 632 " --> pdb=" O ILE A 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 92 through 116 removed outlier: 3.602A pdb=" N THR B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 removed outlier: 3.842A pdb=" N TYR B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 378 through 402 removed outlier: 3.862A pdb=" N ALA B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS B 391 " --> pdb=" O CYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.980A pdb=" N ARG B 407 " --> pdb=" O TYR B 403 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 408' Processing helix chain 'B' and resid 416 through 431 removed outlier: 3.559A pdb=" N PHE B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 441 through 475 removed outlier: 3.869A pdb=" N THR B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 519 Proline residue: B 500 - end of helix Processing helix chain 'B' and resid 540 through 565 removed outlier: 3.571A pdb=" N GLY B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 599 removed outlier: 3.979A pdb=" N TYR B 576 " --> pdb=" O HIS B 572 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'B' and resid 603 through 632 Proline residue: B 629 - end of helix removed outlier: 3.658A pdb=" N TRP B 632 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.910A pdb=" N TYR A 80 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.852A pdb=" N PHE A 253 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY A 266 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ARG A 265 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE A 151 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN A 267 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A 149 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 269 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA A 147 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP A 271 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A 162 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 203 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 221 removed outlier: 7.872A pdb=" N THR B 173 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A 201 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU B 175 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A 203 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B 162 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 271 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 147 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN B 269 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU B 149 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN B 267 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE B 151 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ARG B 265 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY B 266 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 253 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 304 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.764A pdb=" N PHE A 534 " --> pdb=" O GLY A 526 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.909A pdb=" N TYR B 80 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 236 through 237 Processing sheet with id=AA9, first strand: chain 'B' and resid 300 through 304 Processing sheet with id=AB1, first strand: chain 'B' and resid 526 through 527 removed outlier: 3.763A pdb=" N PHE B 534 " --> pdb=" O GLY B 526 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1230 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: 1.25 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2482 1.34 - 1.46: 1974 1.46 - 1.58: 3900 1.58 - 1.71: 2 1.71 - 1.83: 68 Bond restraints: 8426 Sorted by residual: bond pdb=" C GLN A 225 " pdb=" N GLN A 226 " ideal model delta sigma weight residual 1.335 1.411 -0.076 1.33e-02 5.65e+03 3.31e+01 bond pdb=" C GLN B 225 " pdb=" N GLN B 226 " ideal model delta sigma weight residual 1.335 1.411 -0.076 1.33e-02 5.65e+03 3.29e+01 bond pdb=" C LEU A 473 " pdb=" N PHE A 474 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.27e-02 6.20e+03 1.89e+01 bond pdb=" C LEU B 473 " pdb=" N PHE B 474 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.27e-02 6.20e+03 1.86e+01 bond pdb=" N VAL B 523 " pdb=" CA VAL B 523 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.23e-02 6.61e+03 1.25e+01 ... (remaining 8421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 10955 2.56 - 5.12: 455 5.12 - 7.68: 48 7.68 - 10.24: 4 10.24 - 12.80: 2 Bond angle restraints: 11464 Sorted by residual: angle pdb=" N PRO A 521 " pdb=" CA PRO A 521 " pdb=" C PRO A 521 " ideal model delta sigma weight residual 113.65 100.85 12.80 1.35e+00 5.49e-01 8.99e+01 angle pdb=" N PRO B 521 " pdb=" CA PRO B 521 " pdb=" C PRO B 521 " ideal model delta sigma weight residual 113.65 100.87 12.78 1.35e+00 5.49e-01 8.96e+01 angle pdb=" N ARG B 406 " pdb=" CA ARG B 406 " pdb=" C ARG B 406 " ideal model delta sigma weight residual 114.62 106.47 8.15 1.14e+00 7.69e-01 5.12e+01 angle pdb=" N ARG A 406 " pdb=" CA ARG A 406 " pdb=" C ARG A 406 " ideal model delta sigma weight residual 114.62 106.50 8.12 1.14e+00 7.69e-01 5.07e+01 angle pdb=" C ARG A 525 " pdb=" CA ARG A 525 " pdb=" CB ARG A 525 " ideal model delta sigma weight residual 110.34 118.05 -7.71 1.40e+00 5.10e-01 3.03e+01 ... (remaining 11459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4504 17.96 - 35.91: 403 35.91 - 53.87: 76 53.87 - 71.82: 12 71.82 - 89.78: 10 Dihedral angle restraints: 5005 sinusoidal: 1961 harmonic: 3044 Sorted by residual: dihedral pdb=" CA PHE B 431 " pdb=" C PHE B 431 " pdb=" N PRO B 432 " pdb=" CA PRO B 432 " ideal model delta harmonic sigma weight residual 180.00 -150.66 -29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA PHE A 431 " pdb=" C PHE A 431 " pdb=" N PRO A 432 " pdb=" CA PRO A 432 " ideal model delta harmonic sigma weight residual 180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA SER A 486 " pdb=" C SER A 486 " pdb=" N SER A 487 " pdb=" CA SER A 487 " ideal model delta harmonic sigma weight residual 180.00 154.52 25.48 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 5002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1273 0.136 - 0.271: 27 0.271 - 0.407: 6 0.407 - 0.542: 0 0.542 - 0.678: 2 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CG LEU B 428 " pdb=" CB LEU B 428 " pdb=" CD1 LEU B 428 " pdb=" CD2 LEU B 428 " both_signs ideal model delta sigma weight residual False -2.59 -1.91 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" CG LEU A 428 " pdb=" CB LEU A 428 " pdb=" CD1 LEU A 428 " pdb=" CD2 LEU A 428 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA THR B 150 " pdb=" N THR B 150 " pdb=" C THR B 150 " pdb=" CB THR B 150 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 1305 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 585 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C LEU A 585 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU A 585 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A 586 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 585 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C LEU B 585 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU B 585 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU B 586 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 405 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C CYS A 405 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS A 405 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 406 " -0.015 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1930 2.80 - 3.32: 7895 3.32 - 3.85: 12666 3.85 - 4.37: 14593 4.37 - 4.90: 24922 Nonbonded interactions: 62006 Sorted by model distance: nonbonded pdb=" CG ARG A 541 " pdb=" CE3 TRP A 542 " model vdw 2.274 3.740 nonbonded pdb=" CG ARG B 541 " pdb=" CE3 TRP B 542 " model vdw 2.274 3.740 nonbonded pdb=" CG ARG A 541 " pdb=" CZ3 TRP A 542 " model vdw 2.314 3.740 nonbonded pdb=" CG ARG B 541 " pdb=" CZ3 TRP B 542 " model vdw 2.314 3.740 nonbonded pdb=" O LEU A 133 " pdb=" OG SER A 136 " model vdw 2.368 3.040 ... (remaining 62001 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.390 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 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 : 0.007 0.076 8441 Z= 0.423 Angle : 1.099 12.798 11494 Z= 0.681 Chirality : 0.063 0.678 1308 Planarity : 0.007 0.060 1456 Dihedral : 14.433 89.775 3000 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.15 % Allowed : 1.84 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.24), residues: 1034 helix: -0.16 (0.23), residues: 452 sheet: -0.02 (0.49), residues: 122 loop : -2.58 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 525 TYR 0.028 0.002 TYR B 468 PHE 0.019 0.002 PHE B 253 TRP 0.031 0.002 TRP A 450 HIS 0.006 0.001 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00732 ( 8426) covalent geometry : angle 1.09728 (11464) SS BOND : bond 0.00523 ( 15) SS BOND : angle 1.57901 ( 30) hydrogen bonds : bond 0.18323 ( 430) hydrogen bonds : angle 7.38709 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.230 Fit side-chains REVERT: A 452 ARG cc_start: 0.7990 (tpt170) cc_final: 0.7740 (tpp80) REVERT: B 452 ARG cc_start: 0.7951 (tpt170) cc_final: 0.7724 (tpp80) outliers start: 10 outliers final: 4 residues processed: 172 average time/residue: 0.0888 time to fit residues: 20.5170 Evaluate side-chains 125 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.0980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN B 204 ASN B 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.152071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.128830 restraints weight = 15789.066| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.22 r_work: 0.3376 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8441 Z= 0.148 Angle : 0.736 12.490 11494 Z= 0.357 Chirality : 0.041 0.134 1308 Planarity : 0.006 0.063 1456 Dihedral : 4.988 33.926 1156 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.07 % Allowed : 10.23 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.25), residues: 1034 helix: 0.78 (0.23), residues: 462 sheet: -0.14 (0.43), residues: 158 loop : -2.27 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.021 0.002 TYR B 468 PHE 0.019 0.001 PHE B 434 TRP 0.020 0.002 TRP A 508 HIS 0.003 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8426) covalent geometry : angle 0.73421 (11464) SS BOND : bond 0.00381 ( 15) SS BOND : angle 1.21220 ( 30) hydrogen bonds : bond 0.04741 ( 430) hydrogen bonds : angle 4.97935 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 404 ARG cc_start: 0.6187 (tpt90) cc_final: 0.4992 (ttt180) REVERT: B 376 GLU cc_start: 0.7094 (tt0) cc_final: 0.6738 (mp0) REVERT: B 392 MET cc_start: 0.8063 (mmm) cc_final: 0.7559 (mtp) outliers start: 18 outliers final: 10 residues processed: 166 average time/residue: 0.0873 time to fit residues: 20.1814 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.151671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.130433 restraints weight = 15955.542| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.17 r_work: 0.3364 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8441 Z= 0.132 Angle : 0.685 13.253 11494 Z= 0.331 Chirality : 0.040 0.157 1308 Planarity : 0.005 0.050 1456 Dihedral : 4.492 19.300 1150 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.99 % Allowed : 16.21 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.26), residues: 1034 helix: 1.23 (0.23), residues: 454 sheet: -0.15 (0.42), residues: 162 loop : -2.11 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 240 TYR 0.018 0.001 TYR B 468 PHE 0.021 0.001 PHE B 434 TRP 0.016 0.001 TRP B 450 HIS 0.012 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8426) covalent geometry : angle 0.68384 (11464) SS BOND : bond 0.00341 ( 15) SS BOND : angle 1.13255 ( 30) hydrogen bonds : bond 0.04338 ( 430) hydrogen bonds : angle 4.74383 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 404 ARG cc_start: 0.6241 (tpt90) cc_final: 0.4999 (ttt180) REVERT: B 392 MET cc_start: 0.7992 (mmm) cc_final: 0.7529 (mtp) outliers start: 26 outliers final: 18 residues processed: 149 average time/residue: 0.0929 time to fit residues: 19.0557 Evaluate side-chains 141 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 599 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 67 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 77 optimal weight: 0.0170 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.149662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3677 r_free = 0.3677 target = 0.118666 restraints weight = 16124.461| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.90 r_work: 0.3443 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8441 Z= 0.144 Angle : 0.708 12.534 11494 Z= 0.338 Chirality : 0.041 0.188 1308 Planarity : 0.005 0.048 1456 Dihedral : 4.494 18.821 1150 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.33 % Allowed : 18.51 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.26), residues: 1034 helix: 1.19 (0.23), residues: 468 sheet: -0.29 (0.42), residues: 166 loop : -2.10 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.015 0.001 TYR B 468 PHE 0.023 0.001 PHE B 434 TRP 0.015 0.001 TRP B 450 HIS 0.001 0.000 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8426) covalent geometry : angle 0.70683 (11464) SS BOND : bond 0.00356 ( 15) SS BOND : angle 1.16644 ( 30) hydrogen bonds : bond 0.04543 ( 430) hydrogen bonds : angle 4.69343 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.221 Fit side-chains REVERT: A 112 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8358 (tp) REVERT: A 404 ARG cc_start: 0.6330 (tpt90) cc_final: 0.5066 (ttt180) REVERT: A 452 ARG cc_start: 0.7902 (tpt170) cc_final: 0.7489 (tpp80) REVERT: B 392 MET cc_start: 0.8118 (mmm) cc_final: 0.7660 (mtp) outliers start: 29 outliers final: 19 residues processed: 153 average time/residue: 0.0976 time to fit residues: 20.5162 Evaluate side-chains 149 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 599 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 3 optimal weight: 0.0070 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.153459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.128319 restraints weight = 16200.219| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.90 r_work: 0.3329 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8441 Z= 0.137 Angle : 0.707 11.911 11494 Z= 0.334 Chirality : 0.042 0.167 1308 Planarity : 0.004 0.046 1456 Dihedral : 4.375 17.870 1150 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.87 % Allowed : 20.80 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.26), residues: 1034 helix: 1.27 (0.23), residues: 468 sheet: -0.24 (0.41), residues: 166 loop : -2.12 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.010 0.001 TYR A 468 PHE 0.020 0.001 PHE B 434 TRP 0.016 0.001 TRP B 450 HIS 0.001 0.000 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8426) covalent geometry : angle 0.70538 (11464) SS BOND : bond 0.00405 ( 15) SS BOND : angle 1.22173 ( 30) hydrogen bonds : bond 0.04343 ( 430) hydrogen bonds : angle 4.61653 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8301 (tp) REVERT: A 404 ARG cc_start: 0.6393 (tpt90) cc_final: 0.5129 (ttt180) REVERT: A 450 TRP cc_start: 0.7857 (m100) cc_final: 0.7358 (m100) REVERT: A 452 ARG cc_start: 0.7728 (tpt170) cc_final: 0.7434 (tpp80) REVERT: B 392 MET cc_start: 0.8114 (mmm) cc_final: 0.7663 (mtp) REVERT: B 452 ARG cc_start: 0.7682 (tpt170) cc_final: 0.7396 (tpp80) outliers start: 25 outliers final: 20 residues processed: 146 average time/residue: 0.0933 time to fit residues: 18.7895 Evaluate side-chains 149 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 94 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 103 optimal weight: 0.0010 chunk 31 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.150202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117121 restraints weight = 16099.173| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.02 r_work: 0.3349 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8441 Z= 0.177 Angle : 0.743 12.369 11494 Z= 0.356 Chirality : 0.042 0.168 1308 Planarity : 0.005 0.040 1456 Dihedral : 4.622 19.401 1150 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.91 % Allowed : 20.34 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.26), residues: 1034 helix: 1.40 (0.23), residues: 468 sheet: -0.39 (0.42), residues: 164 loop : -2.06 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 240 TYR 0.011 0.001 TYR A 80 PHE 0.021 0.002 PHE B 253 TRP 0.009 0.001 TRP B 450 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8426) covalent geometry : angle 0.73960 (11464) SS BOND : bond 0.00534 ( 15) SS BOND : angle 1.48960 ( 30) hydrogen bonds : bond 0.04971 ( 430) hydrogen bonds : angle 4.67936 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8315 (tp) REVERT: A 376 GLU cc_start: 0.7310 (tt0) cc_final: 0.7016 (mp0) REVERT: A 404 ARG cc_start: 0.6372 (tpt90) cc_final: 0.5114 (ttt180) REVERT: A 450 TRP cc_start: 0.7962 (m100) cc_final: 0.7455 (m100) REVERT: A 452 ARG cc_start: 0.7824 (tpt170) cc_final: 0.7448 (tpp80) REVERT: B 392 MET cc_start: 0.8255 (mmm) cc_final: 0.7842 (mtp) REVERT: B 450 TRP cc_start: 0.7932 (m100) cc_final: 0.7682 (m100) REVERT: B 452 ARG cc_start: 0.7747 (tpt170) cc_final: 0.7425 (tpp80) outliers start: 34 outliers final: 25 residues processed: 152 average time/residue: 0.1002 time to fit residues: 20.7473 Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 599 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 3 optimal weight: 0.0370 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.152391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127404 restraints weight = 16228.587| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.05 r_work: 0.3307 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8441 Z= 0.133 Angle : 0.712 13.088 11494 Z= 0.334 Chirality : 0.040 0.156 1308 Planarity : 0.004 0.029 1456 Dihedral : 4.425 31.220 1150 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.45 % Allowed : 21.95 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.26), residues: 1034 helix: 1.57 (0.23), residues: 476 sheet: -0.39 (0.41), residues: 170 loop : -2.15 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 240 TYR 0.010 0.001 TYR A 80 PHE 0.020 0.001 PHE A 504 TRP 0.008 0.001 TRP B 450 HIS 0.010 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8426) covalent geometry : angle 0.70868 (11464) SS BOND : bond 0.00433 ( 15) SS BOND : angle 1.47897 ( 30) hydrogen bonds : bond 0.04216 ( 430) hydrogen bonds : angle 4.51168 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8268 (tp) REVERT: A 404 ARG cc_start: 0.6477 (tpt90) cc_final: 0.5242 (ttt180) REVERT: A 450 TRP cc_start: 0.7823 (m100) cc_final: 0.7324 (m100) REVERT: A 452 ARG cc_start: 0.7784 (tpt170) cc_final: 0.7493 (tpp80) REVERT: B 392 MET cc_start: 0.8183 (mmm) cc_final: 0.7739 (mtp) outliers start: 30 outliers final: 20 residues processed: 154 average time/residue: 0.0987 time to fit residues: 20.8333 Evaluate side-chains 155 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 359 CYS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 536 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.150153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.125768 restraints weight = 16063.086| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.90 r_work: 0.3333 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8441 Z= 0.167 Angle : 0.748 14.570 11494 Z= 0.356 Chirality : 0.042 0.168 1308 Planarity : 0.005 0.032 1456 Dihedral : 4.559 29.520 1150 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.10 % Allowed : 22.41 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.26), residues: 1034 helix: 1.52 (0.23), residues: 480 sheet: -0.48 (0.40), residues: 184 loop : -2.26 (0.28), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 240 TYR 0.012 0.001 TYR A 62 PHE 0.021 0.002 PHE A 434 TRP 0.008 0.001 TRP B 450 HIS 0.002 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8426) covalent geometry : angle 0.74415 (11464) SS BOND : bond 0.00521 ( 15) SS BOND : angle 1.66133 ( 30) hydrogen bonds : bond 0.04701 ( 430) hydrogen bonds : angle 4.56450 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8308 (tp) REVERT: A 240 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7452 (mpt180) REVERT: A 404 ARG cc_start: 0.6477 (tpt90) cc_final: 0.5248 (ttt180) REVERT: A 450 TRP cc_start: 0.7802 (m100) cc_final: 0.7371 (m100) REVERT: A 452 ARG cc_start: 0.7792 (tpt170) cc_final: 0.7485 (tpp80) REVERT: B 392 MET cc_start: 0.8223 (mmm) cc_final: 0.7824 (mtp) REVERT: B 404 ARG cc_start: 0.6523 (tpt170) cc_final: 0.5364 (ttt180) REVERT: B 452 ARG cc_start: 0.7866 (tpt170) cc_final: 0.7512 (tpp80) outliers start: 27 outliers final: 19 residues processed: 151 average time/residue: 0.0980 time to fit residues: 20.3980 Evaluate side-chains 154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 536 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.150637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125942 restraints weight = 16039.363| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.94 r_work: 0.3303 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8441 Z= 0.146 Angle : 0.736 14.922 11494 Z= 0.349 Chirality : 0.041 0.152 1308 Planarity : 0.004 0.034 1456 Dihedral : 4.432 28.606 1150 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.64 % Allowed : 23.22 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.26), residues: 1034 helix: 1.49 (0.23), residues: 482 sheet: -0.24 (0.46), residues: 142 loop : -1.91 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.012 0.001 TYR A 80 PHE 0.023 0.001 PHE A 434 TRP 0.012 0.001 TRP B 508 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8426) covalent geometry : angle 0.73208 (11464) SS BOND : bond 0.00423 ( 15) SS BOND : angle 1.71092 ( 30) hydrogen bonds : bond 0.04393 ( 430) hydrogen bonds : angle 4.51050 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8265 (tp) REVERT: A 404 ARG cc_start: 0.6460 (tpt90) cc_final: 0.5219 (ttt180) REVERT: A 452 ARG cc_start: 0.7781 (tpt170) cc_final: 0.7504 (tpp80) REVERT: B 392 MET cc_start: 0.8219 (mmm) cc_final: 0.7825 (mtp) REVERT: B 404 ARG cc_start: 0.6456 (tpt170) cc_final: 0.5309 (ttt180) REVERT: B 452 ARG cc_start: 0.7774 (tpt170) cc_final: 0.7455 (tpp80) outliers start: 23 outliers final: 19 residues processed: 145 average time/residue: 0.1015 time to fit residues: 20.0355 Evaluate side-chains 147 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 536 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.149720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.125346 restraints weight = 16063.516| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.08 r_work: 0.3320 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8441 Z= 0.156 Angle : 0.747 15.548 11494 Z= 0.354 Chirality : 0.041 0.158 1308 Planarity : 0.004 0.035 1456 Dihedral : 4.409 20.068 1150 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.87 % Allowed : 23.10 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.26), residues: 1034 helix: 1.47 (0.23), residues: 482 sheet: -0.29 (0.42), residues: 166 loop : -2.03 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.013 0.001 TYR A 80 PHE 0.026 0.002 PHE A 434 TRP 0.011 0.001 TRP B 508 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8426) covalent geometry : angle 0.74382 (11464) SS BOND : bond 0.00419 ( 15) SS BOND : angle 1.44295 ( 30) hydrogen bonds : bond 0.04580 ( 430) hydrogen bonds : angle 4.52149 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.320 Fit side-chains REVERT: A 112 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8301 (tp) REVERT: A 392 MET cc_start: 0.8090 (mmt) cc_final: 0.7754 (mmt) REVERT: A 404 ARG cc_start: 0.6498 (tpt90) cc_final: 0.5267 (ttt180) REVERT: A 450 TRP cc_start: 0.7755 (m100) cc_final: 0.7522 (m100) REVERT: A 452 ARG cc_start: 0.7811 (tpt170) cc_final: 0.7512 (tpp80) REVERT: B 392 MET cc_start: 0.8273 (mmm) cc_final: 0.7882 (mtp) REVERT: B 404 ARG cc_start: 0.6569 (tpt170) cc_final: 0.5426 (ttt180) REVERT: B 452 ARG cc_start: 0.7806 (tpt170) cc_final: 0.7518 (tpp80) outliers start: 25 outliers final: 22 residues processed: 150 average time/residue: 0.1030 time to fit residues: 20.9410 Evaluate side-chains 157 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 198 LYS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 581 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 0.0070 chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 96 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.151142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.126733 restraints weight = 16098.985| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.93 r_work: 0.3357 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8441 Z= 0.135 Angle : 0.732 15.501 11494 Z= 0.344 Chirality : 0.040 0.147 1308 Planarity : 0.004 0.035 1456 Dihedral : 4.261 20.121 1150 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.76 % Allowed : 23.68 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.25), residues: 1034 helix: 1.48 (0.23), residues: 484 sheet: 0.07 (0.44), residues: 146 loop : -2.08 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.011 0.001 TYR A 80 PHE 0.029 0.001 PHE B 434 TRP 0.010 0.001 TRP B 508 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8426) covalent geometry : angle 0.73002 (11464) SS BOND : bond 0.00359 ( 15) SS BOND : angle 1.34245 ( 30) hydrogen bonds : bond 0.04182 ( 430) hydrogen bonds : angle 4.44225 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2163.67 seconds wall clock time: 37 minutes 49.34 seconds (2269.34 seconds total)