Starting phenix.real_space_refine on Thu Jul 2 23:55:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1r_37999/07_2026/8x1r_37999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1r_37999/07_2026/8x1r_37999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x1r_37999/07_2026/8x1r_37999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1r_37999/07_2026/8x1r_37999_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x1r_37999/07_2026/8x1r_37999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1r_37999/07_2026/8x1r_37999.map" } resolution = 2.72 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= 0.004 sd= 0.094 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: 5 Type Number sf(0) Gaussians S 40 5.16 5 Cl 2 4.86 5 C 7203 2.51 5 N 1791 2.21 5 O 1939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10975 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5488 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 674} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5485 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 674} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 2.53, per 1000 atoms: 0.23 Number of scatterers: 10975 At special positions: 0 Unit cell: (104.272, 90.44, 127.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 40 16.00 O 1939 8.00 N 1791 7.00 C 7203 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: 0.94 Conformation dependent library (CDL) restraints added in 611.3 milliseconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 5 sheets defined 67.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 34 through 43 removed outlier: 3.864A pdb=" N CYS A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 99 removed outlier: 6.171A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.688A pdb=" N LEU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 3.904A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 148 Processing helix chain 'A' and resid 169 through 196 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 307 removed outlier: 3.514A pdb=" N ILE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 332 through 366 removed outlier: 6.119A pdb=" N GLY A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.518A pdb=" N LEU A 431 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.854A pdb=" N LEU A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N MET A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.634A pdb=" N ARG A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 503 removed outlier: 3.524A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 584 Processing helix chain 'A' and resid 612 through 618 removed outlier: 3.535A pdb=" N VAL A 615 " --> pdb=" O GLN A 612 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 618 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 Processing helix chain 'A' and resid 687 through 697 removed outlier: 3.565A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 712 through 729 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 68 through 99 removed outlier: 5.714A pdb=" N LEU B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.756A pdb=" N LEU B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.900A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 removed outlier: 3.504A pdb=" N SER B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 196 Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.546A pdb=" N LEU B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 241 through 252 Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.744A pdb=" N THR B 257 " --> pdb=" O ILE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 332 through 366 removed outlier: 5.901A pdb=" N GLY B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 removed outlier: 3.501A pdb=" N THR B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 436 through 447 removed outlier: 3.643A pdb=" N LEU B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.636A pdb=" N ARG B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 removed outlier: 3.586A pdb=" N PHE B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 503 removed outlier: 3.716A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 563 through 584 removed outlier: 3.536A pdb=" N GLN B 584 " --> pdb=" O LYS B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 618 removed outlier: 3.803A pdb=" N ASP B 617 " --> pdb=" O GLU B 614 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.961A pdb=" N ASN B 638 " --> pdb=" O LEU B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 Processing helix chain 'B' and resid 687 through 695 removed outlier: 3.583A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 709 removed outlier: 3.651A pdb=" N ILE B 708 " --> pdb=" O LYS B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 729 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.665A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 12.807A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS A 536 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP A 652 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 589 Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.375A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 12.507A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B 649 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL B 684 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 651 " --> pdb=" O VAL B 684 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1977 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: 2.00 Time building geometry restraints manager: 1.24 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: 1747 1.32 - 1.44: 2898 1.44 - 1.57: 6505 1.57 - 1.69: 1 1.69 - 1.81: 60 Bond restraints: 11211 Sorted by residual: bond pdb=" C SER A 663 " pdb=" N VAL A 664 " ideal model delta sigma weight residual 1.333 1.237 0.097 1.24e-02 6.50e+03 6.06e+01 bond pdb=" C ILE A 544 " pdb=" O ILE A 544 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.19e-02 7.06e+03 1.36e+01 bond pdb=" C PHE B 478 " pdb=" O PHE B 478 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.15e-02 7.56e+03 1.15e+01 bond pdb=" N TYR A 545 " pdb=" CA TYR A 545 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.20e-02 6.94e+03 1.14e+01 bond pdb=" C MET B 474 " pdb=" O MET B 474 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.32e-02 5.74e+03 1.10e+01 ... (remaining 11206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 14803 2.15 - 4.29: 363 4.29 - 6.44: 52 6.44 - 8.59: 7 8.59 - 10.73: 4 Bond angle restraints: 15229 Sorted by residual: angle pdb=" N ASN A 548 " pdb=" CA ASN A 548 " pdb=" C ASN A 548 " ideal model delta sigma weight residual 112.59 122.58 -9.99 1.22e+00 6.72e-01 6.70e+01 angle pdb=" N THR B 475 " pdb=" CA THR B 475 " pdb=" C THR B 475 " ideal model delta sigma weight residual 111.03 102.83 8.20 1.11e+00 8.12e-01 5.45e+01 angle pdb=" N TYR A 545 " pdb=" CA TYR A 545 " pdb=" C TYR A 545 " ideal model delta sigma weight residual 109.60 120.33 -10.73 1.53e+00 4.27e-01 4.92e+01 angle pdb=" N SER A 362 " pdb=" CA SER A 362 " pdb=" C SER A 362 " ideal model delta sigma weight residual 111.14 104.50 6.64 1.08e+00 8.57e-01 3.78e+01 angle pdb=" N THR B 475 " pdb=" CA THR B 475 " pdb=" CB THR B 475 " ideal model delta sigma weight residual 109.98 118.84 -8.86 1.45e+00 4.76e-01 3.74e+01 ... (remaining 15224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 5887 16.75 - 33.51: 597 33.51 - 50.26: 144 50.26 - 67.02: 31 67.02 - 83.77: 12 Dihedral angle restraints: 6671 sinusoidal: 2577 harmonic: 4094 Sorted by residual: dihedral pdb=" C THR B 479 " pdb=" N THR B 479 " pdb=" CA THR B 479 " pdb=" CB THR B 479 " ideal model delta harmonic sigma weight residual -122.00 -136.71 14.71 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" N TYR A 545 " pdb=" C TYR A 545 " pdb=" CA TYR A 545 " pdb=" CB TYR A 545 " ideal model delta harmonic sigma weight residual 122.80 135.15 -12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" N GLU A 703 " pdb=" C GLU A 703 " pdb=" CA GLU A 703 " pdb=" CB GLU A 703 " ideal model delta harmonic sigma weight residual 122.80 135.01 -12.21 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 6668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1732 0.109 - 0.218: 67 0.218 - 0.327: 13 0.327 - 0.436: 2 0.436 - 0.545: 4 Chirality restraints: 1818 Sorted by residual: chirality pdb=" CA THR B 479 " pdb=" N THR B 479 " pdb=" C THR B 479 " pdb=" CB THR B 479 " both_signs ideal model delta sigma weight residual False 2.53 1.98 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CA TYR A 545 " pdb=" N TYR A 545 " pdb=" C TYR A 545 " pdb=" CB TYR A 545 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" CA ASN A 548 " pdb=" N ASN A 548 " pdb=" C ASN A 548 " pdb=" CB ASN A 548 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.62e+00 ... (remaining 1815 not shown) Planarity restraints: 1900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 544 " 0.023 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C ILE A 544 " -0.081 2.00e-02 2.50e+03 pdb=" O ILE A 544 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR A 545 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 32 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C HIS B 32 " -0.055 2.00e-02 2.50e+03 pdb=" O HIS B 32 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS B 33 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 475 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C THR B 475 " 0.044 2.00e-02 2.50e+03 pdb=" O THR B 475 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE B 476 " -0.015 2.00e-02 2.50e+03 ... (remaining 1897 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1088 2.74 - 3.28: 11039 3.28 - 3.82: 18243 3.82 - 4.36: 22881 4.36 - 4.90: 39072 Nonbonded interactions: 92323 Sorted by model distance: nonbonded pdb=" O VAL A 402 " pdb=" OG1 THR A 406 " model vdw 2.197 3.040 nonbonded pdb=" OD2 ASP A 76 " pdb=" OG1 THR A 410 " model vdw 2.206 3.040 nonbonded pdb=" O PHE A 119 " pdb=" CB ALA A 377 " model vdw 2.231 3.460 nonbonded pdb=" NH1 ARG B 576 " pdb=" OE1 GLU B 606 " model vdw 2.231 3.120 nonbonded pdb=" NH1 ARG A 665 " pdb=" OE1 GLU B 207 " model vdw 2.239 3.120 ... (remaining 92318 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 591 or (resid 592 and (name N or name CA or name \ C or name O or name CB )) or resid 593 through 801)) selection = (chain 'B' and (resid 7 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 801)) } 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: 1.640 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.520 Find NCS groups from input model: 0.380 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:9.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.006 0.097 11211 Z= 0.358 Angle : 0.805 10.733 15229 Z= 0.524 Chirality : 0.060 0.545 1818 Planarity : 0.005 0.048 1900 Dihedral : 14.903 83.769 4027 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.99 % Allowed : 15.61 % Favored : 81.40 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: -1.46 (0.21), residues: 1404 helix: -0.59 (0.16), residues: 900 sheet: 1.07 (0.81), residues: 34 loop : -1.64 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 13 TYR 0.025 0.002 TYR B 9 PHE 0.019 0.002 PHE A 699 TRP 0.014 0.002 TRP A 63 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.36 (11211) covalent geometry : angle 0.80526 / 0.52 (15229) hydrogen bonds : bond 0.14904 / 9.78 ( 678) hydrogen bonds : angle 5.97625 / 4.19 ( 1977) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 173 ARG cc_start: 0.6407 (ttp80) cc_final: 0.6200 (ttp80) REVERT: A 451 MET cc_start: 0.7381 (mtm) cc_final: 0.7072 (mtp) REVERT: A 464 LYS cc_start: 0.7824 (mttt) cc_final: 0.7507 (mtpt) REVERT: A 554 ARG cc_start: 0.6671 (mtm110) cc_final: 0.6449 (mtm-85) REVERT: A 579 ARG cc_start: 0.6898 (mtt180) cc_final: 0.6670 (mtt180) REVERT: A 615 VAL cc_start: 0.8420 (p) cc_final: 0.8212 (p) REVERT: A 660 ASP cc_start: 0.8215 (p0) cc_final: 0.7961 (p0) REVERT: B 68 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7545 (mtp85) REVERT: B 135 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7674 (mtp) REVERT: B 276 LYS cc_start: 0.6931 (mttt) cc_final: 0.6715 (mtpm) REVERT: B 618 GLN cc_start: 0.7646 (mt0) cc_final: 0.7306 (mm-40) outliers start: 36 outliers final: 21 residues processed: 156 average time/residue: 0.5164 time to fit residues: 87.2890 Evaluate side-chains 122 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 706 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN A 322 ASN A 326 GLN A 495 GLN A 504 GLN A 584 GLN A 612 GLN B 7 ASN B 8 GLN B 24 ASN B 337 GLN B 436 GLN B 495 GLN B 504 GLN B 588 GLN B 611 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.155037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117037 restraints weight = 11711.029| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.89 r_work: 0.3409 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11211 Z= 0.130 Angle : 0.512 5.294 15229 Z= 0.276 Chirality : 0.042 0.152 1818 Planarity : 0.004 0.052 1900 Dihedral : 4.880 45.514 1534 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.49 % Allowed : 14.53 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 0.34 (0.23), residues: 1404 helix: 0.81 (0.17), residues: 904 sheet: 1.99 (0.85), residues: 34 loop : -0.99 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 13 TYR 0.025 0.001 TYR A 9 PHE 0.016 0.001 PHE A 282 TRP 0.015 0.001 TRP A 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11211) covalent geometry : angle 0.51165 / 0.28 (15229) hydrogen bonds : bond 0.04277 / 2.80 ( 678) hydrogen bonds : angle 4.26468 / 3.01 ( 1977) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.403 Fit side-chains REVERT: A 22 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: A 68 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6368 (mtm-85) REVERT: A 266 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7214 (mp) REVERT: A 348 MET cc_start: 0.7406 (mmp) cc_final: 0.6917 (mmt) REVERT: A 464 LYS cc_start: 0.7528 (mttt) cc_final: 0.7176 (mtpt) REVERT: A 507 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7675 (tttp) REVERT: A 558 ASP cc_start: 0.7477 (m-30) cc_final: 0.7240 (m-30) REVERT: A 579 ARG cc_start: 0.6614 (mtt180) cc_final: 0.6385 (mtt180) REVERT: A 687 ASP cc_start: 0.7653 (p0) cc_final: 0.7382 (p0) REVERT: B 68 ARG cc_start: 0.7479 (mtp180) cc_final: 0.7150 (mtp85) REVERT: B 320 ASP cc_start: 0.8125 (m-30) cc_final: 0.7865 (m-30) REVERT: B 398 SER cc_start: 0.7326 (OUTLIER) cc_final: 0.7075 (p) REVERT: B 558 ASP cc_start: 0.7680 (m-30) cc_final: 0.7316 (m-30) REVERT: B 618 GLN cc_start: 0.7595 (mt0) cc_final: 0.7035 (mm110) REVERT: B 660 ASP cc_start: 0.7822 (p0) cc_final: 0.7539 (p0) outliers start: 30 outliers final: 12 residues processed: 128 average time/residue: 0.5107 time to fit residues: 71.3011 Evaluate side-chains 108 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 615 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 72 optimal weight: 0.0020 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 0.0060 chunk 136 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 GLN B 24 ASN B 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.156840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118862 restraints weight = 11814.037| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.99 r_work: 0.3455 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11211 Z= 0.105 Angle : 0.464 5.137 15229 Z= 0.250 Chirality : 0.041 0.146 1818 Planarity : 0.004 0.050 1900 Dihedral : 4.026 22.832 1505 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.99 % Allowed : 14.87 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 1.18 (0.23), residues: 1404 helix: 1.47 (0.18), residues: 908 sheet: 2.46 (0.89), residues: 34 loop : -0.68 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 13 TYR 0.018 0.001 TYR A 9 PHE 0.015 0.001 PHE B 130 TRP 0.014 0.001 TRP A 63 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (11211) covalent geometry : angle 0.46410 / 0.25 (15229) hydrogen bonds : bond 0.03748 / 2.46 ( 678) hydrogen bonds : angle 3.97020 / 2.82 ( 1977) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.441 Fit side-chains REVERT: A 22 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: A 68 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6339 (mtm-85) REVERT: A 135 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7718 (mtm) REVERT: A 266 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7020 (mp) REVERT: A 457 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6602 (mm-30) REVERT: A 464 LYS cc_start: 0.7417 (mttt) cc_final: 0.7050 (mtpt) REVERT: A 507 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7606 (tttp) REVERT: A 558 ASP cc_start: 0.7383 (m-30) cc_final: 0.7136 (m-30) REVERT: A 579 ARG cc_start: 0.6593 (mtt180) cc_final: 0.6366 (mtt-85) REVERT: A 722 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6380 (mtp) REVERT: B 68 ARG cc_start: 0.7362 (mtp180) cc_final: 0.7062 (mtp85) REVERT: B 277 GLU cc_start: 0.5301 (OUTLIER) cc_final: 0.4678 (mm-30) REVERT: B 320 ASP cc_start: 0.8131 (m-30) cc_final: 0.7868 (m-30) REVERT: B 464 LYS cc_start: 0.7129 (mttt) cc_final: 0.6849 (mttp) REVERT: B 618 GLN cc_start: 0.7513 (mt0) cc_final: 0.6911 (mm110) REVERT: B 637 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7735 (mp) REVERT: B 660 ASP cc_start: 0.7636 (p0) cc_final: 0.7331 (p0) outliers start: 36 outliers final: 12 residues processed: 131 average time/residue: 0.4709 time to fit residues: 67.4497 Evaluate side-chains 123 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 637 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 100 optimal weight: 0.0030 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN A 504 GLN A 612 GLN A 719 HIS B 24 ASN B 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.153500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114865 restraints weight = 11838.384| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.99 r_work: 0.3430 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11211 Z= 0.158 Angle : 0.511 6.086 15229 Z= 0.273 Chirality : 0.042 0.154 1818 Planarity : 0.004 0.051 1900 Dihedral : 4.155 23.037 1504 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.24 % Allowed : 15.53 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 1.28 (0.23), residues: 1404 helix: 1.50 (0.18), residues: 908 sheet: 2.61 (0.88), residues: 34 loop : -0.53 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.026 0.002 TYR A 9 PHE 0.016 0.001 PHE B 130 TRP 0.014 0.001 TRP B 63 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (11211) covalent geometry : angle 0.51137 / 0.27 (15229) hydrogen bonds : bond 0.04419 / 2.91 ( 678) hydrogen bonds : angle 4.06871 / 2.89 ( 1977) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.332 Fit side-chains REVERT: A 22 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: A 68 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6463 (mtm-85) REVERT: A 135 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7850 (mtm) REVERT: A 146 SER cc_start: 0.7471 (OUTLIER) cc_final: 0.7093 (p) REVERT: A 266 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7165 (mp) REVERT: A 348 MET cc_start: 0.7373 (mmt) cc_final: 0.6983 (mmt) REVERT: A 464 LYS cc_start: 0.7561 (mttt) cc_final: 0.7230 (mtpt) REVERT: A 507 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7696 (tttp) REVERT: A 554 ARG cc_start: 0.6610 (mtm110) cc_final: 0.6318 (mtm110) REVERT: A 558 ASP cc_start: 0.7401 (m-30) cc_final: 0.7177 (m-30) REVERT: A 579 ARG cc_start: 0.6670 (mtt180) cc_final: 0.6429 (mtt-85) REVERT: A 629 ILE cc_start: 0.7335 (mt) cc_final: 0.7081 (mt) REVERT: A 687 ASP cc_start: 0.7587 (p0) cc_final: 0.7313 (p0) REVERT: A 722 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6488 (mtp) REVERT: B 68 ARG cc_start: 0.7449 (mtp180) cc_final: 0.7132 (mtp85) REVERT: B 277 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.4780 (mm-30) REVERT: B 320 ASP cc_start: 0.8022 (m-30) cc_final: 0.7762 (m-30) REVERT: B 514 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7885 (tp) REVERT: B 558 ASP cc_start: 0.7757 (m-30) cc_final: 0.7404 (m-30) REVERT: B 618 GLN cc_start: 0.7597 (mt0) cc_final: 0.7069 (mm110) REVERT: B 637 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7809 (mp) outliers start: 39 outliers final: 18 residues processed: 133 average time/residue: 0.4490 time to fit residues: 65.2621 Evaluate side-chains 130 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 637 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 GLN B 24 ASN B 253 GLN B 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.155585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116460 restraints weight = 11932.043| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.98 r_work: 0.3398 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11211 Z= 0.156 Angle : 0.509 5.277 15229 Z= 0.272 Chirality : 0.042 0.156 1818 Planarity : 0.004 0.052 1900 Dihedral : 4.154 23.354 1504 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.41 % Allowed : 16.20 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 1.37 (0.23), residues: 1404 helix: 1.54 (0.18), residues: 908 sheet: 2.69 (0.87), residues: 34 loop : -0.44 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 553 TYR 0.025 0.002 TYR A 9 PHE 0.016 0.001 PHE B 130 TRP 0.015 0.001 TRP B 63 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (11211) covalent geometry : angle 0.50906 / 0.27 (15229) hydrogen bonds : bond 0.04374 / 2.87 ( 678) hydrogen bonds : angle 4.05641 / 2.88 ( 1977) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.298 Fit side-chains REVERT: A 22 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: A 68 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6581 (mtm-85) REVERT: A 135 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7994 (mtm) REVERT: A 198 ILE cc_start: 0.8648 (mt) cc_final: 0.8408 (mt) REVERT: A 266 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7246 (mp) REVERT: A 348 MET cc_start: 0.7560 (mmt) cc_final: 0.7167 (mmt) REVERT: A 464 LYS cc_start: 0.7674 (mttt) cc_final: 0.7345 (mtpt) REVERT: A 503 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8228 (p) REVERT: A 507 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7760 (tttp) REVERT: A 554 ARG cc_start: 0.6753 (mtm110) cc_final: 0.6466 (mtm110) REVERT: A 579 ARG cc_start: 0.6781 (mtt180) cc_final: 0.6532 (mtt-85) REVERT: A 687 ASP cc_start: 0.7654 (p0) cc_final: 0.7409 (p0) REVERT: A 689 ASP cc_start: 0.6914 (m-30) cc_final: 0.6699 (m-30) REVERT: A 692 GLU cc_start: 0.7546 (tp30) cc_final: 0.7343 (tp30) REVERT: A 722 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6546 (mtp) REVERT: B 68 ARG cc_start: 0.7528 (mtp180) cc_final: 0.7204 (mtp85) REVERT: B 277 GLU cc_start: 0.5543 (OUTLIER) cc_final: 0.4884 (mm-30) REVERT: B 320 ASP cc_start: 0.7999 (m-30) cc_final: 0.7741 (m-30) REVERT: B 514 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7970 (tp) REVERT: B 618 GLN cc_start: 0.7668 (mt0) cc_final: 0.7101 (mm110) REVERT: B 637 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7907 (mp) outliers start: 41 outliers final: 19 residues processed: 129 average time/residue: 0.5044 time to fit residues: 70.6004 Evaluate side-chains 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 640 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 GLN A 714 HIS B 24 ASN B 322 ASN B 326 GLN B 337 GLN B 454 GLN B 714 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111207 restraints weight = 11916.728| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.98 r_work: 0.3384 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 11211 Z= 0.300 Angle : 0.627 7.451 15229 Z= 0.332 Chirality : 0.048 0.177 1818 Planarity : 0.005 0.077 1900 Dihedral : 4.547 23.948 1504 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.65 % Allowed : 16.36 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 0.82 (0.23), residues: 1404 helix: 1.07 (0.17), residues: 906 sheet: 2.40 (0.85), residues: 34 loop : -0.53 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 553 TYR 0.035 0.003 TYR A 9 PHE 0.021 0.002 PHE A 699 TRP 0.018 0.002 TRP B 63 HIS 0.007 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.30 (11211) covalent geometry : angle 0.62735 / 0.33 (15229) hydrogen bonds : bond 0.05723 / 3.79 ( 678) hydrogen bonds : angle 4.36328 / 3.09 ( 1977) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.399 Fit side-chains REVERT: A 7 ASN cc_start: 0.4272 (OUTLIER) cc_final: 0.3923 (p0) REVERT: A 22 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: A 68 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6461 (mtm-85) REVERT: A 198 ILE cc_start: 0.8611 (mt) cc_final: 0.8336 (mp) REVERT: A 464 LYS cc_start: 0.7574 (mttt) cc_final: 0.7230 (mtpt) REVERT: A 507 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7712 (tttp) REVERT: A 554 ARG cc_start: 0.6608 (mtm110) cc_final: 0.6363 (mtm110) REVERT: A 579 ARG cc_start: 0.6797 (mtt180) cc_final: 0.6565 (mtt180) REVERT: A 592 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.5995 (tmtt) REVERT: A 689 ASP cc_start: 0.6917 (m-30) cc_final: 0.6646 (m-30) REVERT: A 722 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6462 (mtp) REVERT: B 68 ARG cc_start: 0.7453 (mtp180) cc_final: 0.7108 (mtp85) REVERT: B 135 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7735 (mtp) REVERT: B 277 GLU cc_start: 0.5216 (OUTLIER) cc_final: 0.4626 (mm-30) REVERT: B 320 ASP cc_start: 0.7980 (m-30) cc_final: 0.7721 (m-30) REVERT: B 514 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7971 (tp) REVERT: B 618 GLN cc_start: 0.7707 (mt0) cc_final: 0.7156 (mm-40) REVERT: B 637 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7939 (mp) outliers start: 44 outliers final: 22 residues processed: 131 average time/residue: 0.5017 time to fit residues: 71.3641 Evaluate side-chains 126 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 641 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 80 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 0.0060 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN A 326 GLN A 612 GLN B 24 ASN B 322 ASN B 326 GLN B 337 GLN B 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.155702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116662 restraints weight = 11907.666| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.97 r_work: 0.3414 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11211 Z= 0.139 Angle : 0.504 5.434 15229 Z= 0.269 Chirality : 0.042 0.175 1818 Planarity : 0.004 0.053 1900 Dihedral : 4.199 24.081 1504 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.74 % Allowed : 17.11 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 1.36 (0.23), residues: 1404 helix: 1.51 (0.17), residues: 906 sheet: 2.58 (0.87), residues: 34 loop : -0.37 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.021 0.001 TYR A 9 PHE 0.016 0.001 PHE B 130 TRP 0.016 0.001 TRP A 63 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (11211) covalent geometry : angle 0.50389 / 0.27 (15229) hydrogen bonds : bond 0.04247 / 2.78 ( 678) hydrogen bonds : angle 4.05317 / 2.88 ( 1977) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.323 Fit side-chains REVERT: A 22 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: A 68 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6480 (mtm-85) REVERT: A 135 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7878 (mtm) REVERT: A 198 ILE cc_start: 0.8579 (mt) cc_final: 0.8344 (mt) REVERT: A 348 MET cc_start: 0.7432 (mmp) cc_final: 0.6928 (mmt) REVERT: A 464 LYS cc_start: 0.7562 (mttt) cc_final: 0.7243 (mtpt) REVERT: A 507 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7688 (tttp) REVERT: A 554 ARG cc_start: 0.6572 (mtm110) cc_final: 0.6351 (mtm110) REVERT: A 579 ARG cc_start: 0.6859 (mtt180) cc_final: 0.6591 (mtt-85) REVERT: A 722 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6519 (mtp) REVERT: B 68 ARG cc_start: 0.7456 (mtp180) cc_final: 0.7091 (mtp85) REVERT: B 277 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.4754 (mm-30) REVERT: B 320 ASP cc_start: 0.7985 (m-30) cc_final: 0.7731 (m-30) REVERT: B 514 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7966 (tp) REVERT: B 558 ASP cc_start: 0.7730 (m-30) cc_final: 0.7413 (m-30) REVERT: B 614 GLU cc_start: 0.7546 (tp30) cc_final: 0.7206 (mm-30) REVERT: B 618 GLN cc_start: 0.7666 (mt0) cc_final: 0.7084 (mm110) REVERT: B 637 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7906 (mp) outliers start: 33 outliers final: 17 residues processed: 128 average time/residue: 0.5017 time to fit residues: 69.6120 Evaluate side-chains 127 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 637 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 GLN B 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.154296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115949 restraints weight = 11792.857| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.98 r_work: 0.3422 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11211 Z= 0.131 Angle : 0.495 5.577 15229 Z= 0.265 Chirality : 0.041 0.151 1818 Planarity : 0.004 0.053 1900 Dihedral : 4.081 23.333 1504 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.66 % Allowed : 17.44 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 1.59 (0.23), residues: 1404 helix: 1.69 (0.18), residues: 908 sheet: 2.82 (0.88), residues: 34 loop : -0.29 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.020 0.001 TYR A 9 PHE 0.015 0.001 PHE B 130 TRP 0.016 0.001 TRP A 63 HIS 0.003 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11211) covalent geometry : angle 0.49491 / 0.26 (15229) hydrogen bonds : bond 0.04075 / 2.67 ( 678) hydrogen bonds : angle 3.96692 / 2.82 ( 1977) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.405 Fit side-chains REVERT: A 22 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: A 68 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6379 (mtm-85) REVERT: A 135 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7735 (mtm) REVERT: A 348 MET cc_start: 0.7295 (mmp) cc_final: 0.6791 (mmt) REVERT: A 464 LYS cc_start: 0.7439 (mttt) cc_final: 0.7065 (mtpt) REVERT: A 503 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8082 (p) REVERT: A 507 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7577 (tttp) REVERT: A 528 ASP cc_start: 0.8393 (m-30) cc_final: 0.7504 (t0) REVERT: A 554 ARG cc_start: 0.6468 (mtm110) cc_final: 0.6250 (mtm110) REVERT: A 579 ARG cc_start: 0.6628 (mtt180) cc_final: 0.6378 (mtt-85) REVERT: A 634 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7750 (t0) REVERT: A 687 ASP cc_start: 0.7549 (p0) cc_final: 0.7083 (p0) REVERT: A 722 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6377 (mtp) REVERT: B 68 ARG cc_start: 0.7366 (mtp180) cc_final: 0.6996 (mtp85) REVERT: B 277 GLU cc_start: 0.5374 (OUTLIER) cc_final: 0.4735 (mm-30) REVERT: B 320 ASP cc_start: 0.8046 (m-30) cc_final: 0.7805 (m-30) REVERT: B 464 LYS cc_start: 0.7153 (mttt) cc_final: 0.6863 (mttm) REVERT: B 558 ASP cc_start: 0.7603 (m-30) cc_final: 0.7240 (m-30) REVERT: B 614 GLU cc_start: 0.7552 (tp30) cc_final: 0.7091 (mm-30) REVERT: B 618 GLN cc_start: 0.7550 (mt0) cc_final: 0.6980 (mm110) REVERT: B 637 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7940 (mp) outliers start: 32 outliers final: 18 residues processed: 135 average time/residue: 0.5077 time to fit residues: 74.5087 Evaluate side-chains 132 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 637 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117519 restraints weight = 11693.688| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.98 r_work: 0.3467 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11211 Z= 0.113 Angle : 0.473 5.217 15229 Z= 0.252 Chirality : 0.041 0.147 1818 Planarity : 0.004 0.049 1900 Dihedral : 3.960 22.835 1504 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.24 % Allowed : 18.11 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 1.79 (0.23), residues: 1404 helix: 1.84 (0.18), residues: 908 sheet: 2.94 (0.89), residues: 34 loop : -0.22 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 13 TYR 0.018 0.001 TYR A 9 PHE 0.015 0.001 PHE A 130 TRP 0.017 0.001 TRP A 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11211) covalent geometry : angle 0.47268 / 0.25 (15229) hydrogen bonds : bond 0.03775 / 2.48 ( 678) hydrogen bonds : angle 3.88182 / 2.77 ( 1977) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.416 Fit side-chains REVERT: A 68 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6452 (mtm-85) REVERT: A 135 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7754 (mtm) REVERT: A 198 ILE cc_start: 0.8564 (mt) cc_final: 0.8320 (mt) REVERT: A 348 MET cc_start: 0.7379 (mmp) cc_final: 0.6884 (mmt) REVERT: A 464 LYS cc_start: 0.7513 (mttt) cc_final: 0.7135 (mtpt) REVERT: A 503 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8223 (p) REVERT: A 528 ASP cc_start: 0.8368 (m-30) cc_final: 0.7499 (t0) REVERT: A 554 ARG cc_start: 0.6545 (mtm110) cc_final: 0.6317 (mtm110) REVERT: A 577 LYS cc_start: 0.6285 (ttmt) cc_final: 0.6065 (ttmt) REVERT: A 579 ARG cc_start: 0.6699 (mtt180) cc_final: 0.6460 (mtt-85) REVERT: A 612 GLN cc_start: 0.6665 (mt0) cc_final: 0.5631 (pt0) REVERT: A 722 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6438 (mtp) REVERT: B 68 ARG cc_start: 0.7437 (mtp180) cc_final: 0.7086 (mtp85) REVERT: B 277 GLU cc_start: 0.5413 (OUTLIER) cc_final: 0.4762 (mm-30) REVERT: B 320 ASP cc_start: 0.8024 (m-30) cc_final: 0.7791 (m-30) REVERT: B 464 LYS cc_start: 0.7199 (mttt) cc_final: 0.6920 (mttm) REVERT: B 558 ASP cc_start: 0.7642 (m-30) cc_final: 0.7269 (m-30) REVERT: B 618 GLN cc_start: 0.7719 (mt0) cc_final: 0.7051 (mm110) REVERT: B 637 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7952 (mp) outliers start: 27 outliers final: 15 residues processed: 136 average time/residue: 0.5042 time to fit residues: 74.5566 Evaluate side-chains 132 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 637 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 52 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 69 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.157047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118942 restraints weight = 11667.670| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.99 r_work: 0.3482 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11211 Z= 0.104 Angle : 0.469 6.754 15229 Z= 0.250 Chirality : 0.040 0.146 1818 Planarity : 0.004 0.047 1900 Dihedral : 3.868 22.314 1504 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.74 % Allowed : 18.60 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 1.95 (0.23), residues: 1404 helix: 1.97 (0.18), residues: 908 sheet: 3.03 (0.88), residues: 34 loop : -0.18 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 13 TYR 0.015 0.001 TYR A 9 PHE 0.016 0.001 PHE A 130 TRP 0.017 0.001 TRP A 63 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (11211) covalent geometry : angle 0.46889 / 0.25 (15229) hydrogen bonds : bond 0.03583 / 2.35 ( 678) hydrogen bonds : angle 3.81588 / 2.71 ( 1977) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.297 Fit side-chains REVERT: A 68 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6545 (mtm-85) REVERT: A 198 ILE cc_start: 0.8626 (mt) cc_final: 0.8408 (mt) REVERT: A 348 MET cc_start: 0.7395 (mmp) cc_final: 0.6923 (mmt) REVERT: A 464 LYS cc_start: 0.7550 (mttt) cc_final: 0.7156 (mtpt) REVERT: A 474 MET cc_start: 0.8259 (mmm) cc_final: 0.7996 (mmm) REVERT: A 503 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8241 (p) REVERT: A 528 ASP cc_start: 0.8357 (m-30) cc_final: 0.7501 (t0) REVERT: A 554 ARG cc_start: 0.6565 (mtm110) cc_final: 0.6341 (mtm110) REVERT: A 577 LYS cc_start: 0.6366 (ttmt) cc_final: 0.6046 (ttmt) REVERT: A 579 ARG cc_start: 0.6749 (mtt180) cc_final: 0.6513 (mtt-85) REVERT: A 580 LYS cc_start: 0.6976 (ttpt) cc_final: 0.6668 (pttt) REVERT: A 612 GLN cc_start: 0.6689 (mt0) cc_final: 0.5668 (pt0) REVERT: A 722 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6494 (mtp) REVERT: B 68 ARG cc_start: 0.7406 (mtp180) cc_final: 0.6685 (mtm110) REVERT: B 277 GLU cc_start: 0.5425 (OUTLIER) cc_final: 0.4794 (mm-30) REVERT: B 320 ASP cc_start: 0.8004 (m-30) cc_final: 0.7770 (m-30) REVERT: B 464 LYS cc_start: 0.7224 (mttt) cc_final: 0.6954 (mttm) REVERT: B 558 ASP cc_start: 0.7639 (m-30) cc_final: 0.7250 (m-30) REVERT: B 614 GLU cc_start: 0.7508 (tp30) cc_final: 0.7057 (mm-30) REVERT: B 618 GLN cc_start: 0.7629 (mt0) cc_final: 0.7017 (mm110) REVERT: B 637 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7975 (mp) outliers start: 21 outliers final: 14 residues processed: 130 average time/residue: 0.4934 time to fit residues: 70.0121 Evaluate side-chains 130 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 637 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 115 optimal weight: 0.5980 chunk 40 optimal weight: 0.0070 chunk 15 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118070 restraints weight = 11729.538| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.00 r_work: 0.3471 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11211 Z= 0.117 Angle : 0.480 6.197 15229 Z= 0.256 Chirality : 0.041 0.150 1818 Planarity : 0.004 0.047 1900 Dihedral : 3.902 22.330 1504 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.74 % Allowed : 18.44 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 1.91 (0.23), residues: 1404 helix: 1.93 (0.18), residues: 908 sheet: 3.03 (0.88), residues: 34 loop : -0.17 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.017 0.001 TYR A 9 PHE 0.016 0.001 PHE A 130 TRP 0.016 0.001 TRP A 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11211) covalent geometry : angle 0.48035 / 0.26 (15229) hydrogen bonds : bond 0.03786 / 2.48 ( 678) hydrogen bonds : angle 3.86083 / 2.75 ( 1977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3349.54 seconds wall clock time: 57 minutes 59.28 seconds (3479.28 seconds total)