Starting phenix.real_space_refine on Sat Aug 23 08:57:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1r_37999/08_2025/8x1r_37999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1r_37999/08_2025/8x1r_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_37999/08_2025/8x1r_37999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1r_37999/08_2025/8x1r_37999_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x1r_37999/08_2025/8x1r_37999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1r_37999/08_2025/8x1r_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.22, per 1000 atoms: 0.20 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: 0.82 Conformation dependent library (CDL) restraints added in 426.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.30 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: 1.56 Time building geometry restraints manager: 1.05 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: 0.950 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.480 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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: 0.020 Load rotamer database and sin/cos tables:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 aren 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 covalent geometry : bond 0.00637 (11211) covalent geometry : angle 0.80526 (15229) hydrogen bonds : bond 0.14904 ( 678) hydrogen bonds : angle 5.97625 ( 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 : 0.432 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: 0.4751 time to fit residues: 80.3575 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 : 0.441 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3854 r_free = 0.3854 target = 0.155099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117086 restraints weight = 11711.567| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.89 r_work: 0.3424 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11211 Z= 0.129 Angle : 0.511 5.366 15229 Z= 0.276 Chirality : 0.042 0.152 1818 Planarity : 0.004 0.052 1900 Dihedral : 4.854 45.327 1534 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.84 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 aren not related in a simple way. whole: 0.34 (0.23), residues: 1404 helix: 0.82 (0.17), residues: 904 sheet: 1.98 (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 A 553 TYR 0.024 0.001 TYR A 9 PHE 0.016 0.001 PHE B 130 TRP 0.015 0.001 TRP A 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00293 (11211) covalent geometry : angle 0.51112 (15229) hydrogen bonds : bond 0.04269 ( 678) hydrogen bonds : angle 4.26271 ( 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 : 0.366 Fit side-chains REVERT: A 68 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6394 (mtm-85) REVERT: A 266 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7256 (mp) REVERT: A 348 MET cc_start: 0.7434 (mmp) cc_final: 0.6943 (mmt) REVERT: A 464 LYS cc_start: 0.7560 (mttt) cc_final: 0.7208 (mtpt) REVERT: A 507 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7697 (tttp) REVERT: A 558 ASP cc_start: 0.7495 (m-30) cc_final: 0.7258 (m-30) REVERT: A 579 ARG cc_start: 0.6690 (mtt180) cc_final: 0.6459 (mtt180) REVERT: A 687 ASP cc_start: 0.7669 (p0) cc_final: 0.7449 (p0) REVERT: B 68 ARG cc_start: 0.7541 (mtp180) cc_final: 0.7219 (mtp85) REVERT: B 320 ASP cc_start: 0.8132 (m-30) cc_final: 0.7873 (m-30) REVERT: B 398 SER cc_start: 0.7411 (OUTLIER) cc_final: 0.7185 (p) REVERT: B 558 ASP cc_start: 0.7695 (m-30) cc_final: 0.7314 (m-30) REVERT: B 618 GLN cc_start: 0.7619 (mt0) cc_final: 0.7076 (mm110) REVERT: B 660 ASP cc_start: 0.7842 (p0) cc_final: 0.7562 (p0) outliers start: 30 outliers final: 12 residues processed: 128 average time/residue: 0.5017 time to fit residues: 69.6495 Evaluate side-chains 109 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 136 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3880 r_free = 0.3880 target = 0.157288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119370 restraints weight = 11824.457| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.99 r_work: 0.3456 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11211 Z= 0.104 Angle : 0.463 5.140 15229 Z= 0.249 Chirality : 0.041 0.146 1818 Planarity : 0.004 0.050 1900 Dihedral : 4.009 22.798 1505 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.91 % Allowed : 14.78 % Favored : 82.31 % 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 aren not related in a simple way. whole: 1.20 (0.23), residues: 1404 helix: 1.48 (0.18), residues: 908 sheet: 2.47 (0.89), residues: 34 loop : -0.67 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 13 TYR 0.017 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 covalent geometry : bond 0.00225 (11211) covalent geometry : angle 0.46286 (15229) hydrogen bonds : bond 0.03717 ( 678) hydrogen bonds : angle 3.95121 ( 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 152 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.270 Fit side-chains REVERT: A 68 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6371 (mtm-85) REVERT: A 135 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7714 (mtm) REVERT: A 266 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7016 (mp) REVERT: A 348 MET cc_start: 0.7290 (mmp) cc_final: 0.6805 (mmt) REVERT: A 457 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6561 (mm-30) REVERT: A 464 LYS cc_start: 0.7407 (mttt) cc_final: 0.7041 (mtpt) REVERT: A 558 ASP cc_start: 0.7351 (m-30) cc_final: 0.7105 (m-30) REVERT: A 579 ARG cc_start: 0.6584 (mtt180) cc_final: 0.6361 (mtt-85) REVERT: A 687 ASP cc_start: 0.7404 (p0) cc_final: 0.7034 (p0) REVERT: A 722 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6394 (mtp) REVERT: B 68 ARG cc_start: 0.7352 (mtp180) cc_final: 0.7060 (mtp85) REVERT: B 277 GLU cc_start: 0.5300 (OUTLIER) cc_final: 0.4680 (mm-30) REVERT: B 320 ASP cc_start: 0.8100 (m-30) cc_final: 0.7830 (m-30) REVERT: B 464 LYS cc_start: 0.7115 (mttt) cc_final: 0.6838 (mttp) REVERT: B 558 ASP cc_start: 0.7607 (m-30) cc_final: 0.7228 (m-30) REVERT: B 618 GLN cc_start: 0.7629 (mt0) cc_final: 0.6909 (mm110) REVERT: B 637 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 660 ASP cc_start: 0.7632 (p0) cc_final: 0.7325 (p0) outliers start: 35 outliers final: 12 residues processed: 135 average time/residue: 0.4760 time to fit residues: 70.1884 Evaluate side-chains 119 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 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: 0.0770 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 14 optimal weight: 0.0570 chunk 100 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 overall best weight: 0.2212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN A 612 GLN B 24 ASN B 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.160917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123245 restraints weight = 11762.850| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.00 r_work: 0.3503 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1990 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= 0.090 Angle : 0.436 5.370 15229 Z= 0.234 Chirality : 0.040 0.140 1818 Planarity : 0.004 0.050 1900 Dihedral : 3.759 21.502 1504 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.82 % Allowed : 15.37 % Favored : 81.81 % 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 aren not related in a simple way. whole: 1.79 (0.23), residues: 1404 helix: 1.91 (0.18), residues: 908 sheet: 2.86 (0.90), residues: 34 loop : -0.37 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.013 0.001 TYR A 9 PHE 0.014 0.001 PHE B 130 TRP 0.014 0.001 TRP A 63 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00179 (11211) covalent geometry : angle 0.43562 (15229) hydrogen bonds : bond 0.03221 ( 678) hydrogen bonds : angle 3.74713 ( 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 157 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.294 Fit side-chains REVERT: A 135 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7774 (mtm) REVERT: A 348 MET cc_start: 0.7496 (mmp) cc_final: 0.7050 (mmt) REVERT: A 362 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7834 (p) REVERT: A 363 LEU cc_start: 0.7794 (tp) cc_final: 0.7542 (tm) REVERT: A 464 LYS cc_start: 0.7494 (mttt) cc_final: 0.7129 (mtpt) REVERT: A 474 MET cc_start: 0.8242 (mmm) cc_final: 0.7870 (mmm) REVERT: A 507 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7576 (tttp) REVERT: A 558 ASP cc_start: 0.7399 (m-30) cc_final: 0.7150 (m-30) REVERT: A 579 ARG cc_start: 0.6771 (mtt180) cc_final: 0.6565 (mtt-85) REVERT: A 612 GLN cc_start: 0.6669 (mt0) cc_final: 0.5655 (pt0) REVERT: A 634 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7767 (t70) REVERT: A 722 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6454 (mtp) REVERT: B 277 GLU cc_start: 0.5355 (OUTLIER) cc_final: 0.4766 (mm-30) REVERT: B 320 ASP cc_start: 0.8046 (m-30) cc_final: 0.7791 (m-30) REVERT: B 464 LYS cc_start: 0.7204 (mttt) cc_final: 0.6947 (mttp) REVERT: B 514 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7697 (tp) REVERT: B 618 GLN cc_start: 0.7658 (mt0) cc_final: 0.6942 (mm-40) REVERT: B 637 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7817 (mp) outliers start: 34 outliers final: 11 residues processed: 142 average time/residue: 0.4458 time to fit residues: 69.6157 Evaluate side-chains 125 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 362 SER 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 645 SER Chi-restraints excluded: chain A residue 722 MET 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 453 MET 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 637 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 93 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 719 HIS B 24 ASN B 337 GLN B 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115599 restraints weight = 11803.579| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.00 r_work: 0.3420 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1662 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= 0.157 Angle : 0.502 5.274 15229 Z= 0.268 Chirality : 0.042 0.153 1818 Planarity : 0.004 0.048 1900 Dihedral : 4.045 23.004 1504 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.91 % Allowed : 16.20 % Favored : 80.90 % 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 aren not related in a simple way. whole: 1.60 (0.23), residues: 1404 helix: 1.73 (0.18), residues: 908 sheet: 2.83 (0.88), residues: 34 loop : -0.38 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 13 TYR 0.026 0.002 TYR A 9 PHE 0.016 0.001 PHE B 130 TRP 0.013 0.001 TRP B 63 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00382 (11211) covalent geometry : angle 0.50161 (15229) hydrogen bonds : bond 0.04316 ( 678) hydrogen bonds : angle 3.95534 ( 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: 35 poor density : 110 time to evaluate : 0.426 Fit side-chains REVERT: A 22 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: A 68 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6399 (mtm-85) REVERT: A 135 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7763 (mtm) REVERT: A 146 SER cc_start: 0.7409 (OUTLIER) cc_final: 0.7152 (p) REVERT: A 198 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8299 (mt) REVERT: A 266 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7076 (mp) REVERT: A 464 LYS cc_start: 0.7467 (mttt) cc_final: 0.7115 (mtpt) REVERT: A 503 THR cc_start: 0.8374 (p) cc_final: 0.8174 (p) REVERT: A 507 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7593 (tttp) REVERT: A 558 ASP cc_start: 0.7391 (m-30) cc_final: 0.7184 (m-30) REVERT: A 579 ARG cc_start: 0.6630 (mtt180) cc_final: 0.6403 (mtt-85) REVERT: A 580 LYS cc_start: 0.7037 (ttpt) cc_final: 0.6715 (pttt) REVERT: A 634 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7653 (t70) REVERT: A 722 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6400 (mtp) REVERT: B 16 TYR cc_start: 0.8795 (m-80) cc_final: 0.8547 (m-80) REVERT: B 277 GLU cc_start: 0.5313 (OUTLIER) cc_final: 0.4702 (mm-30) REVERT: B 320 ASP cc_start: 0.8063 (m-30) cc_final: 0.7812 (m-30) REVERT: B 514 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7782 (tp) REVERT: B 618 GLN cc_start: 0.7635 (mt0) cc_final: 0.6957 (mm110) REVERT: B 637 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7882 (mp) REVERT: B 645 SER cc_start: 0.8044 (m) cc_final: 0.7829 (t) outliers start: 35 outliers final: 14 residues processed: 130 average time/residue: 0.4678 time to fit residues: 66.2676 Evaluate side-chains 133 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 198 ILE 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 722 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 24 ASN B 253 GLN B 337 GLN B 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.154270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114991 restraints weight = 12001.908| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.97 r_work: 0.3400 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11211 Z= 0.202 Angle : 0.547 5.714 15229 Z= 0.292 Chirality : 0.044 0.160 1818 Planarity : 0.004 0.056 1900 Dihedral : 4.279 23.766 1504 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.16 % Allowed : 16.53 % Favored : 80.32 % 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 aren not related in a simple way. whole: 1.37 (0.23), residues: 1404 helix: 1.51 (0.17), residues: 906 sheet: 2.70 (0.86), residues: 34 loop : -0.37 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 553 TYR 0.031 0.002 TYR A 9 PHE 0.017 0.002 PHE B 130 TRP 0.015 0.002 TRP B 63 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00504 (11211) covalent geometry : angle 0.54687 (15229) hydrogen bonds : bond 0.04873 ( 678) hydrogen bonds : angle 4.14213 ( 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 145 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.432 Fit side-chains REVERT: A 68 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6494 (mtm-85) REVERT: A 146 SER cc_start: 0.7597 (OUTLIER) cc_final: 0.7330 (p) REVERT: A 198 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8306 (mp) REVERT: A 266 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7168 (mp) REVERT: A 464 LYS cc_start: 0.7616 (mttt) cc_final: 0.7276 (mtpt) REVERT: A 503 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8211 (p) REVERT: A 507 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7694 (tttp) REVERT: A 554 ARG cc_start: 0.6679 (mtm110) cc_final: 0.6421 (mtm110) REVERT: A 558 ASP cc_start: 0.7544 (m-30) cc_final: 0.7339 (m-30) REVERT: A 579 ARG cc_start: 0.6761 (mtt180) cc_final: 0.6509 (mtt-85) REVERT: A 634 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7800 (t0) REVERT: A 689 ASP cc_start: 0.6923 (m-30) cc_final: 0.6678 (m-30) REVERT: A 722 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6457 (mtp) REVERT: B 135 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7709 (mtp) REVERT: B 277 GLU cc_start: 0.5393 (OUTLIER) cc_final: 0.4767 (mm-30) REVERT: B 320 ASP cc_start: 0.8009 (m-30) cc_final: 0.7758 (m-30) REVERT: B 514 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7959 (tp) REVERT: B 558 ASP cc_start: 0.7767 (m-30) cc_final: 0.7450 (m-30) REVERT: B 618 GLN cc_start: 0.7660 (mt0) cc_final: 0.7143 (mm110) REVERT: B 637 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7937 (mp) outliers start: 38 outliers final: 16 residues processed: 131 average time/residue: 0.4940 time to fit residues: 70.0908 Evaluate side-chains 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 146 SER Chi-restraints excluded: chain A residue 198 ILE 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 30 ARG Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 135 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 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 = 0.3840 r_free = 0.3840 target = 0.154158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115449 restraints weight = 11765.294| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.99 r_work: 0.3423 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1698 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= 0.140 Angle : 0.497 5.227 15229 Z= 0.266 Chirality : 0.042 0.153 1818 Planarity : 0.004 0.053 1900 Dihedral : 4.111 23.667 1504 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.82 % Allowed : 17.19 % 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 aren not related in a simple way. whole: 1.56 (0.23), residues: 1404 helix: 1.67 (0.18), residues: 908 sheet: 2.79 (0.87), residues: 34 loop : -0.32 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 553 TYR 0.023 0.002 TYR A 9 PHE 0.016 0.001 PHE B 130 TRP 0.015 0.001 TRP A 63 HIS 0.003 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00334 (11211) covalent geometry : angle 0.49694 (15229) hydrogen bonds : bond 0.04207 ( 678) hydrogen bonds : angle 4.00227 ( 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 142 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.446 Fit side-chains REVERT: A 68 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6406 (mtm-85) REVERT: A 135 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7782 (mtm) REVERT: A 146 SER cc_start: 0.7536 (OUTLIER) cc_final: 0.7305 (p) REVERT: A 198 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8214 (mp) REVERT: A 266 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7074 (mp) REVERT: A 464 LYS cc_start: 0.7440 (mttt) cc_final: 0.7094 (mtpt) REVERT: A 503 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8097 (p) REVERT: A 507 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7589 (tttp) REVERT: A 528 ASP cc_start: 0.8415 (m-30) cc_final: 0.7536 (t0) REVERT: A 554 ARG cc_start: 0.6564 (mtm110) cc_final: 0.6291 (mtm110) REVERT: A 558 ASP cc_start: 0.7321 (m-30) cc_final: 0.7084 (m-30) REVERT: A 577 LYS cc_start: 0.6229 (ttmt) cc_final: 0.6022 (ttmt) REVERT: A 579 ARG cc_start: 0.6633 (mtt180) cc_final: 0.6384 (mtt-85) REVERT: A 634 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7649 (t70) REVERT: A 687 ASP cc_start: 0.7543 (p0) cc_final: 0.7178 (p0) REVERT: A 689 ASP cc_start: 0.6904 (m-30) cc_final: 0.6416 (m-30) REVERT: A 722 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6401 (mtp) REVERT: B 68 ARG cc_start: 0.7174 (mtm110) cc_final: 0.6867 (mtm110) REVERT: B 277 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.4771 (mm-30) REVERT: B 320 ASP cc_start: 0.8006 (m-30) cc_final: 0.7757 (m-30) REVERT: B 464 LYS cc_start: 0.7179 (mttt) cc_final: 0.6885 (mttm) REVERT: B 558 ASP cc_start: 0.7703 (m-30) cc_final: 0.7348 (m-30) REVERT: B 618 GLN cc_start: 0.7660 (mt0) cc_final: 0.6957 (mm110) REVERT: B 637 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7896 (mp) outliers start: 34 outliers final: 15 residues processed: 129 average time/residue: 0.5150 time to fit residues: 72.1224 Evaluate side-chains 131 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 146 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 198 ILE 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 514 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN B 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.156185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117835 restraints weight = 11749.302| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.99 r_work: 0.3466 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11211 Z= 0.112 Angle : 0.465 5.172 15229 Z= 0.249 Chirality : 0.041 0.147 1818 Planarity : 0.004 0.050 1900 Dihedral : 3.951 23.010 1504 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.57 % Allowed : 17.52 % 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 aren not related in a simple way. whole: 1.80 (0.23), residues: 1404 helix: 1.85 (0.18), residues: 908 sheet: 2.98 (0.88), residues: 34 loop : -0.22 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.019 0.001 TYR A 9 PHE 0.015 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 covalent geometry : bond 0.00251 (11211) covalent geometry : angle 0.46525 (15229) hydrogen bonds : bond 0.03761 ( 678) hydrogen bonds : angle 3.88041 ( 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 147 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.444 Fit side-chains REVERT: A 68 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6479 (mtm-85) REVERT: A 198 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8269 (mt) REVERT: A 348 MET cc_start: 0.7175 (mmp) cc_final: 0.6653 (mmt) REVERT: A 464 LYS cc_start: 0.7483 (mttt) cc_final: 0.7090 (mtpt) REVERT: A 503 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8122 (p) REVERT: A 528 ASP cc_start: 0.8393 (m-30) cc_final: 0.7536 (t0) REVERT: A 554 ARG cc_start: 0.6587 (mtm110) cc_final: 0.6274 (mtm110) REVERT: A 558 ASP cc_start: 0.7350 (m-30) cc_final: 0.7124 (m-30) REVERT: A 577 LYS cc_start: 0.6311 (ttmt) cc_final: 0.5996 (ttmt) REVERT: A 579 ARG cc_start: 0.6718 (mtt180) cc_final: 0.6480 (mtt-85) REVERT: A 580 LYS cc_start: 0.6936 (ttpt) cc_final: 0.6633 (pttt) REVERT: A 612 GLN cc_start: 0.6664 (mt0) cc_final: 0.5630 (pt0) REVERT: A 634 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7610 (t70) REVERT: A 689 ASP cc_start: 0.6940 (m-30) cc_final: 0.6685 (m-30) REVERT: A 722 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6421 (mtp) REVERT: B 70 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7219 (mmtt) REVERT: B 277 GLU cc_start: 0.5437 (OUTLIER) cc_final: 0.4791 (mm-30) REVERT: B 320 ASP cc_start: 0.8018 (m-30) cc_final: 0.7779 (m-30) REVERT: B 464 LYS cc_start: 0.7193 (mttt) cc_final: 0.6922 (mttm) REVERT: B 558 ASP cc_start: 0.7645 (m-30) cc_final: 0.7256 (m-30) REVERT: B 618 GLN cc_start: 0.7648 (mt0) cc_final: 0.6994 (mm110) REVERT: B 637 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7935 (mp) outliers start: 31 outliers final: 13 residues processed: 135 average time/residue: 0.4211 time to fit residues: 62.4232 Evaluate side-chains 130 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 503 THR 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 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 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: 2.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 ASN B 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.153819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114360 restraints weight = 11906.546| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.97 r_work: 0.3378 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11211 Z= 0.223 Angle : 0.567 5.945 15229 Z= 0.302 Chirality : 0.045 0.163 1818 Planarity : 0.005 0.061 1900 Dihedral : 4.291 23.350 1504 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.74 % Allowed : 17.28 % 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 aren not related in a simple way. whole: 1.39 (0.23), residues: 1404 helix: 1.50 (0.17), residues: 906 sheet: 2.72 (0.86), residues: 34 loop : -0.30 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 665 TYR 0.030 0.002 TYR A 9 PHE 0.017 0.002 PHE B 130 TRP 0.015 0.002 TRP B 63 HIS 0.005 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00562 (11211) covalent geometry : angle 0.56726 (15229) hydrogen bonds : bond 0.04999 ( 678) hydrogen bonds : angle 4.15856 ( 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 138 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.432 Fit side-chains REVERT: A 22 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: A 68 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6511 (mtm-85) REVERT: A 146 SER cc_start: 0.7619 (OUTLIER) cc_final: 0.7343 (p) REVERT: A 198 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 266 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7159 (mp) REVERT: A 464 LYS cc_start: 0.7616 (mttt) cc_final: 0.7286 (mtpt) REVERT: A 503 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8242 (p) REVERT: A 507 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7698 (tttp) REVERT: A 554 ARG cc_start: 0.6720 (mtm110) cc_final: 0.6451 (mtm110) REVERT: A 577 LYS cc_start: 0.6282 (ttmt) cc_final: 0.6068 (ttmt) REVERT: A 579 ARG cc_start: 0.6794 (mtt180) cc_final: 0.6536 (mtt-85) REVERT: A 634 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7661 (t0) REVERT: A 689 ASP cc_start: 0.6984 (m-30) cc_final: 0.6730 (m-30) REVERT: A 722 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6454 (mtp) REVERT: B 277 GLU cc_start: 0.5311 (OUTLIER) cc_final: 0.4732 (mm-30) REVERT: B 320 ASP cc_start: 0.8040 (m-30) cc_final: 0.7806 (m-30) REVERT: B 618 GLN cc_start: 0.7633 (mt0) cc_final: 0.7152 (mm-40) REVERT: B 637 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7978 (mp) outliers start: 33 outliers final: 15 residues processed: 126 average time/residue: 0.4923 time to fit residues: 67.3387 Evaluate side-chains 125 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 173 ARG Chi-restraints excluded: chain A residue 198 ILE 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 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 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 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 Chi-restraints excluded: chain B residue 640 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 GLN B 311 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 = 0.3851 r_free = 0.3851 target = 0.155057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116289 restraints weight = 11676.720| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.99 r_work: 0.3429 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11211 Z= 0.126 Angle : 0.485 5.281 15229 Z= 0.259 Chirality : 0.041 0.151 1818 Planarity : 0.004 0.054 1900 Dihedral : 4.052 23.297 1504 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.24 % Allowed : 17.77 % 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 aren not related in a simple way. whole: 1.69 (0.23), residues: 1404 helix: 1.75 (0.18), residues: 908 sheet: 2.90 (0.87), residues: 34 loop : -0.23 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.020 0.001 TYR A 9 PHE 0.015 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 covalent geometry : bond 0.00290 (11211) covalent geometry : angle 0.48452 (15229) hydrogen bonds : bond 0.04004 ( 678) hydrogen bonds : angle 3.94933 ( 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 134 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.411 Fit side-chains REVERT: A 68 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6417 (mtm-85) REVERT: A 198 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8200 (mt) REVERT: A 348 MET cc_start: 0.7055 (mmp) cc_final: 0.6503 (mmt) REVERT: A 464 LYS cc_start: 0.7422 (mttt) cc_final: 0.7070 (mtpt) REVERT: A 503 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8130 (p) REVERT: A 507 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7536 (tttp) REVERT: A 528 ASP cc_start: 0.8400 (m-30) cc_final: 0.7521 (t0) REVERT: A 554 ARG cc_start: 0.6486 (mtm110) cc_final: 0.6243 (mtm110) REVERT: A 577 LYS cc_start: 0.6215 (ttmt) cc_final: 0.6008 (ttmt) REVERT: A 579 ARG cc_start: 0.6645 (mtt180) cc_final: 0.6393 (mtt-85) REVERT: A 612 GLN cc_start: 0.6606 (mt0) cc_final: 0.5555 (pt0) REVERT: A 634 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7607 (t70) REVERT: A 689 ASP cc_start: 0.6938 (m-30) cc_final: 0.6676 (m-30) REVERT: A 722 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.6366 (mtp) REVERT: B 277 GLU cc_start: 0.5374 (OUTLIER) cc_final: 0.4737 (mm-30) REVERT: B 320 ASP cc_start: 0.8029 (m-30) cc_final: 0.7799 (m-30) REVERT: B 464 LYS cc_start: 0.7140 (mttt) cc_final: 0.6860 (mttm) REVERT: B 558 ASP cc_start: 0.7662 (m-30) cc_final: 0.7306 (m-30) REVERT: B 618 GLN cc_start: 0.7646 (mt0) cc_final: 0.6989 (mm110) REVERT: B 637 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7944 (mp) outliers start: 27 outliers final: 14 residues processed: 124 average time/residue: 0.5039 time to fit residues: 67.7906 Evaluate side-chains 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 410 THR 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 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 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: 1.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 96 optimal weight: 0.0970 chunk 64 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115937 restraints weight = 11733.052| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.00 r_work: 0.3425 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11211 Z= 0.131 Angle : 0.491 5.354 15229 Z= 0.262 Chirality : 0.041 0.150 1818 Planarity : 0.004 0.051 1900 Dihedral : 4.026 23.014 1504 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.83 % Allowed : 18.27 % 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 aren not related in a simple way. whole: 1.76 (0.23), residues: 1404 helix: 1.81 (0.18), residues: 908 sheet: 2.96 (0.88), residues: 34 loop : -0.20 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 553 TYR 0.021 0.001 TYR A 9 PHE 0.015 0.001 PHE B 130 TRP 0.015 0.001 TRP A 63 HIS 0.004 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00308 (11211) covalent geometry : angle 0.49083 (15229) hydrogen bonds : bond 0.04046 ( 678) hydrogen bonds : angle 3.94031 ( 1977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3265.77 seconds wall clock time: 56 minutes 20.22 seconds (3380.22 seconds total)