Starting phenix.real_space_refine on Tue Jul 29 04:42:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1r_37999/07_2025/8x1r_37999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1r_37999/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x1r_37999/07_2025/8x1r_37999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1r_37999/07_2025/8x1r_37999.map" model { file = "/net/cci-nas-00/data/ceres_data/8x1r_37999/07_2025/8x1r_37999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1r_37999/07_2025/8x1r_37999_neut.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'HIS:plan': 1, 'ASP: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: {'HIS:plan': 1, 'ASP: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: 7.65, per 1000 atoms: 0.70 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: 2.72 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.06 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: 3.76 Time building geometry restraints manager: 3.00 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 729 or resid 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 729 or resid 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: 2.510 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.430 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- 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 : 9.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (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 TRP 0.014 0.002 TRP A 63 HIS 0.005 0.001 HIS B 220 PHE 0.019 0.002 PHE A 699 TYR 0.025 0.002 TYR B 9 ARG 0.007 0.001 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.14904 ( 678) hydrogen bonds : angle 5.97625 ( 1977) covalent geometry : bond 0.00637 (11211) covalent geometry : angle 0.80526 (15229) *********************** 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 : 1.133 Fit side-chains revert: symmetry clash REVERT: A 173 ARG cc_start: 0.6407 (ttp80) cc_final: 0.6200 (ttp80) REVERT: A 276 LYS cc_start: 0.7093 (mttt) cc_final: 0.6883 (mtmp) 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: 1.1298 time to fit residues: 191.6739 Evaluate side-chains 123 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 118 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 19 ASN A 322 ASN A 326 GLN A 495 GLN A 504 GLN A 584 GLN A 612 GLN A 714 HIS 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 B 714 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113833 restraints weight = 11712.790| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.96 r_work: 0.3402 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11211 Z= 0.179 Angle : 0.555 6.196 15229 Z= 0.299 Chirality : 0.044 0.159 1818 Planarity : 0.005 0.056 1900 Dihedral : 5.278 49.677 1534 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.07 % Allowed : 14.87 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1404 helix: 0.63 (0.17), residues: 904 sheet: 1.90 (0.85), residues: 34 loop : -1.03 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 63 HIS 0.004 0.001 HIS B 220 PHE 0.017 0.001 PHE B 130 TYR 0.022 0.002 TYR B 9 ARG 0.005 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 678) hydrogen bonds : angle 4.38804 ( 1977) covalent geometry : bond 0.00436 (11211) covalent geometry : angle 0.55471 (15229) *********************** 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 146 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 1.269 Fit side-chains REVERT: A 22 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: A 68 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6360 (mtm-85) REVERT: A 99 ASP cc_start: 0.7397 (t0) cc_final: 0.7194 (t0) REVERT: A 266 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7090 (mp) REVERT: A 451 MET cc_start: 0.7450 (mtm) cc_final: 0.7111 (mtp) REVERT: A 464 LYS cc_start: 0.7506 (mttt) cc_final: 0.7177 (mtpt) REVERT: A 507 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7669 (tttp) REVERT: A 554 ARG cc_start: 0.6557 (mtm110) cc_final: 0.6327 (mtm-85) REVERT: A 558 ASP cc_start: 0.7411 (m-30) cc_final: 0.7198 (m-30) REVERT: A 579 ARG cc_start: 0.6544 (mtt180) cc_final: 0.6311 (mtt180) REVERT: A 703 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: B 68 ARG cc_start: 0.7455 (mtp180) cc_final: 0.7107 (mtp85) REVERT: B 398 SER cc_start: 0.7423 (OUTLIER) cc_final: 0.7174 (p) REVERT: B 618 GLN cc_start: 0.7661 (mt0) cc_final: 0.7108 (mm-40) outliers start: 37 outliers final: 15 residues processed: 132 average time/residue: 1.2254 time to fit residues: 175.9831 Evaluate side-chains 116 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 592 LYS Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 398 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 96 optimal weight: 0.0040 chunk 104 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.155839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117600 restraints weight = 11744.602| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.98 r_work: 0.3435 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1429 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= 0.114 Angle : 0.478 5.381 15229 Z= 0.257 Chirality : 0.041 0.194 1818 Planarity : 0.004 0.050 1900 Dihedral : 4.162 23.157 1507 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.66 % Allowed : 15.12 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1404 helix: 1.34 (0.17), residues: 908 sheet: 2.38 (0.88), residues: 34 loop : -0.72 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 63 HIS 0.003 0.001 HIS A 220 PHE 0.015 0.001 PHE B 130 TYR 0.021 0.001 TYR A 9 ARG 0.004 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 678) hydrogen bonds : angle 4.05168 ( 1977) covalent geometry : bond 0.00252 (11211) covalent geometry : angle 0.47801 (15229) *********************** 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 145 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.126 Fit side-chains REVERT: A 22 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: A 68 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6406 (mtm-85) REVERT: A 99 ASP cc_start: 0.7315 (t0) cc_final: 0.7113 (t0) REVERT: A 266 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7007 (mp) REVERT: A 348 MET cc_start: 0.7418 (mmp) cc_final: 0.6889 (mmt) REVERT: A 464 LYS cc_start: 0.7441 (mttt) cc_final: 0.7082 (mtpt) REVERT: A 507 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7609 (tttp) REVERT: A 558 ASP cc_start: 0.7364 (m-30) cc_final: 0.7120 (m-30) REVERT: A 579 ARG cc_start: 0.6602 (mtt180) cc_final: 0.6379 (mtt180) REVERT: A 722 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6350 (mtp) REVERT: B 68 ARG cc_start: 0.7393 (mtp180) cc_final: 0.7074 (mtp85) REVERT: B 277 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.4693 (mm-30) REVERT: B 320 ASP cc_start: 0.8137 (m-30) cc_final: 0.7889 (m-30) REVERT: B 464 LYS cc_start: 0.7140 (mttt) cc_final: 0.6859 (mttp) REVERT: B 558 ASP cc_start: 0.7534 (m-30) cc_final: 0.7143 (m-30) REVERT: B 618 GLN cc_start: 0.7521 (mt0) cc_final: 0.6950 (mm110) REVERT: B 637 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7751 (mp) outliers start: 32 outliers final: 13 residues processed: 132 average time/residue: 1.1661 time to fit residues: 168.0773 Evaluate side-chains 117 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 208 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 514 ILE 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 55 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 128 optimal weight: 0.0370 chunk 106 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 127 optimal weight: 0.0270 chunk 111 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 504 GLN A 612 GLN B 24 ASN B 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.157930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120073 restraints weight = 11682.773| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.99 r_work: 0.3494 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1802 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= 0.098 Angle : 0.452 5.290 15229 Z= 0.243 Chirality : 0.040 0.146 1818 Planarity : 0.004 0.050 1900 Dihedral : 3.907 22.311 1505 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.57 % Allowed : 15.78 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.23), residues: 1404 helix: 1.77 (0.18), residues: 908 sheet: 2.73 (0.90), residues: 34 loop : -0.49 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 63 HIS 0.003 0.000 HIS A 220 PHE 0.015 0.001 PHE A 130 TYR 0.017 0.001 TYR A 9 ARG 0.003 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 678) hydrogen bonds : angle 3.85231 ( 1977) covalent geometry : bond 0.00208 (11211) covalent geometry : angle 0.45246 (15229) *********************** 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 148 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.114 Fit side-chains REVERT: A 22 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: A 68 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6520 (mtm-85) REVERT: A 99 ASP cc_start: 0.7334 (t0) cc_final: 0.7119 (t0) REVERT: A 348 MET cc_start: 0.7427 (mmp) cc_final: 0.6919 (mmt) REVERT: A 362 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7866 (p) REVERT: A 457 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6593 (mm-30) REVERT: A 464 LYS cc_start: 0.7507 (mttt) cc_final: 0.7146 (mtpt) REVERT: A 579 ARG cc_start: 0.6670 (mtt180) cc_final: 0.6450 (mtt-85) REVERT: A 722 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6451 (mtp) REVERT: B 68 ARG cc_start: 0.7344 (mtp180) cc_final: 0.7072 (mtp85) REVERT: B 277 GLU cc_start: 0.5381 (OUTLIER) cc_final: 0.4762 (mm-30) REVERT: B 320 ASP cc_start: 0.8081 (m-30) cc_final: 0.7813 (m-30) REVERT: B 464 LYS cc_start: 0.7215 (mttt) cc_final: 0.6945 (mttp) REVERT: B 558 ASP cc_start: 0.7673 (m-30) cc_final: 0.7278 (m-30) REVERT: B 618 GLN cc_start: 0.7695 (mt0) cc_final: 0.7067 (mm110) REVERT: B 637 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7816 (mp) outliers start: 31 outliers final: 11 residues processed: 134 average time/residue: 1.0586 time to fit residues: 155.2919 Evaluate side-chains 122 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 208 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 645 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 612 GLN A 719 HIS B 24 ASN B 253 GLN B 337 GLN B 504 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112077 restraints weight = 11865.940| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.98 r_work: 0.3395 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 11211 Z= 0.259 Angle : 0.594 7.343 15229 Z= 0.314 Chirality : 0.046 0.163 1818 Planarity : 0.005 0.064 1900 Dihedral : 4.387 23.331 1504 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.24 % Allowed : 16.69 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1404 helix: 1.30 (0.17), residues: 906 sheet: 2.52 (0.86), residues: 34 loop : -0.54 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.006 0.001 HIS B 220 PHE 0.020 0.002 PHE A 699 TYR 0.036 0.002 TYR A 9 ARG 0.003 0.000 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.05341 ( 678) hydrogen bonds : angle 4.23389 ( 1977) covalent geometry : bond 0.00658 (11211) covalent geometry : angle 0.59418 (15229) *********************** 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 144 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 1.212 Fit side-chains REVERT: A 22 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: A 68 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6442 (mtm-85) REVERT: A 99 ASP cc_start: 0.7435 (t0) cc_final: 0.7222 (t0) REVERT: A 146 SER cc_start: 0.7596 (OUTLIER) cc_final: 0.7255 (p) REVERT: A 266 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7162 (mp) REVERT: A 464 LYS cc_start: 0.7571 (mttt) cc_final: 0.7230 (mtpt) REVERT: A 503 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8208 (p) REVERT: A 507 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7668 (tttp) REVERT: A 528 ASP cc_start: 0.8379 (m-30) cc_final: 0.7623 (t0) REVERT: A 554 ARG cc_start: 0.6580 (mtm110) cc_final: 0.6333 (mtm110) REVERT: A 577 LYS cc_start: 0.6340 (ttmt) cc_final: 0.6109 (ttmt) REVERT: A 579 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6459 (mtt-85) REVERT: A 689 ASP cc_start: 0.6875 (m-30) cc_final: 0.6654 (m-30) REVERT: A 722 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6539 (mtp) REVERT: B 68 ARG cc_start: 0.7502 (mtp180) cc_final: 0.7153 (mtp85) REVERT: B 135 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7933 (mmm) REVERT: B 277 GLU cc_start: 0.5316 (OUTLIER) cc_final: 0.4706 (mm-30) REVERT: B 320 ASP cc_start: 0.8015 (m-30) cc_final: 0.7768 (m-30) REVERT: B 514 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7924 (tp) REVERT: B 618 GLN cc_start: 0.7627 (mt0) cc_final: 0.7055 (mm-40) REVERT: B 637 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7906 (mp) outliers start: 39 outliers final: 19 residues processed: 132 average time/residue: 1.3502 time to fit residues: 194.4951 Evaluate side-chains 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 208 SER Chi-restraints excluded: chain A residue 238 THR 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 706 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 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 570 LYS 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 Chi-restraints excluded: chain B residue 641 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 59 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 128 optimal weight: 0.1980 chunk 100 optimal weight: 0.0060 chunk 72 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.3454 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.157218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119421 restraints weight = 11690.538| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.98 r_work: 0.3463 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11211 Z= 0.099 Angle : 0.460 5.143 15229 Z= 0.246 Chirality : 0.040 0.144 1818 Planarity : 0.004 0.048 1900 Dihedral : 3.953 22.826 1504 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.57 % Allowed : 17.03 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1404 helix: 1.82 (0.18), residues: 908 sheet: 2.80 (0.89), residues: 34 loop : -0.37 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 63 HIS 0.002 0.000 HIS A 220 PHE 0.014 0.001 PHE B 130 TYR 0.017 0.001 TYR A 9 ARG 0.003 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 678) hydrogen bonds : angle 3.86715 ( 1977) covalent geometry : bond 0.00202 (11211) covalent geometry : angle 0.45983 (15229) *********************** 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: 31 poor density : 114 time to evaluate : 1.085 Fit side-chains REVERT: A 68 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6528 (mtm-85) REVERT: A 146 SER cc_start: 0.7553 (OUTLIER) cc_final: 0.7314 (p) REVERT: A 348 MET cc_start: 0.7602 (mmp) cc_final: 0.7081 (mmt) REVERT: A 464 LYS cc_start: 0.7554 (mttt) cc_final: 0.7170 (mtpt) REVERT: A 528 ASP cc_start: 0.8243 (m-30) cc_final: 0.7421 (t0) REVERT: A 579 ARG cc_start: 0.6739 (mtt180) cc_final: 0.6505 (mtt-85) REVERT: A 612 GLN cc_start: 0.6706 (mt0) cc_final: 0.5666 (pt0) REVERT: A 634 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7726 (t70) REVERT: A 689 ASP cc_start: 0.6962 (m-30) cc_final: 0.6680 (m-30) REVERT: A 722 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6485 (mtp) REVERT: B 68 ARG cc_start: 0.7457 (mtp180) cc_final: 0.7156 (mtp85) REVERT: B 277 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.4815 (mm-30) REVERT: B 320 ASP cc_start: 0.8041 (m-30) cc_final: 0.7794 (m-30) REVERT: B 464 LYS cc_start: 0.7234 (mttt) cc_final: 0.6955 (mttm) REVERT: B 558 ASP cc_start: 0.7632 (m-30) cc_final: 0.7253 (m-30) REVERT: B 618 GLN cc_start: 0.7694 (mt0) cc_final: 0.7084 (mm110) REVERT: B 637 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7872 (mp) outliers start: 31 outliers final: 11 residues processed: 135 average time/residue: 1.0607 time to fit residues: 156.8066 Evaluate side-chains 127 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 208 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 362 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 113 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 0.0040 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.156050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117948 restraints weight = 11891.345| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.99 r_work: 0.3469 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11211 Z= 0.110 Angle : 0.464 5.159 15229 Z= 0.248 Chirality : 0.041 0.145 1818 Planarity : 0.004 0.048 1900 Dihedral : 3.912 22.424 1504 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.49 % Allowed : 17.77 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1404 helix: 1.92 (0.18), residues: 908 sheet: 2.91 (0.89), residues: 34 loop : -0.28 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 63 HIS 0.003 0.001 HIS B 220 PHE 0.015 0.001 PHE B 130 TYR 0.019 0.001 TYR A 9 ARG 0.003 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 678) hydrogen bonds : angle 3.84200 ( 1977) covalent geometry : bond 0.00244 (11211) covalent geometry : angle 0.46439 (15229) *********************** 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 145 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.263 Fit side-chains REVERT: A 7 ASN cc_start: 0.4215 (OUTLIER) cc_final: 0.4001 (p0) REVERT: A 58 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: A 68 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6526 (mtm-85) REVERT: A 348 MET cc_start: 0.7236 (mmp) cc_final: 0.6727 (mmt) REVERT: A 464 LYS cc_start: 0.7551 (mttt) cc_final: 0.7183 (mtpt) REVERT: A 507 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7597 (tttp) REVERT: A 528 ASP cc_start: 0.8313 (m-30) cc_final: 0.7616 (t0) REVERT: A 533 GLU cc_start: 0.7947 (tp30) cc_final: 0.7656 (mm-30) REVERT: A 577 LYS cc_start: 0.6445 (ttmt) cc_final: 0.6121 (ttmt) REVERT: A 579 ARG cc_start: 0.6800 (mtt180) cc_final: 0.6568 (mtt-85) REVERT: A 580 LYS cc_start: 0.7105 (ttpt) cc_final: 0.6779 (pttt) REVERT: A 612 GLN cc_start: 0.6697 (mt0) cc_final: 0.5679 (pt0) REVERT: A 634 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7663 (t70) REVERT: A 689 ASP cc_start: 0.6902 (m-30) cc_final: 0.6670 (m-30) REVERT: A 722 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6500 (mtp) REVERT: B 68 ARG cc_start: 0.7437 (mtp180) cc_final: 0.6695 (mtm110) REVERT: B 277 GLU cc_start: 0.5441 (OUTLIER) cc_final: 0.4808 (mm-30) REVERT: B 320 ASP cc_start: 0.8091 (m-30) cc_final: 0.7860 (m-30) REVERT: B 453 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8120 (mtm) REVERT: B 464 LYS cc_start: 0.7245 (mttt) cc_final: 0.6977 (mttp) REVERT: B 558 ASP cc_start: 0.7635 (m-30) cc_final: 0.7256 (m-30) REVERT: B 618 GLN cc_start: 0.7699 (mt0) cc_final: 0.7123 (mm110) REVERT: B 637 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7952 (mp) outliers start: 30 outliers final: 12 residues processed: 133 average time/residue: 1.1879 time to fit residues: 172.0156 Evaluate side-chains 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 451 MET 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 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 406 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 453 MET 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 109 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.156198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118045 restraints weight = 11709.838| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.98 r_work: 0.3445 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1894 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= 0.114 Angle : 0.472 5.328 15229 Z= 0.252 Chirality : 0.041 0.146 1818 Planarity : 0.004 0.048 1900 Dihedral : 3.900 22.367 1504 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.33 % Allowed : 18.27 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.23), residues: 1404 helix: 1.93 (0.18), residues: 908 sheet: 2.96 (0.89), residues: 34 loop : -0.22 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 63 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE B 130 TYR 0.020 0.001 TYR A 9 ARG 0.002 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 678) hydrogen bonds : angle 3.84112 ( 1977) covalent geometry : bond 0.00258 (11211) covalent geometry : angle 0.47249 (15229) *********************** 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 140 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.576 Fit side-chains REVERT: A 7 ASN cc_start: 0.4237 (OUTLIER) cc_final: 0.4027 (p0) REVERT: A 58 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: A 68 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6437 (mtm-85) REVERT: A 348 MET cc_start: 0.7068 (mmp) cc_final: 0.6552 (mmt) REVERT: A 457 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6582 (mm-30) REVERT: A 464 LYS cc_start: 0.7410 (mttt) cc_final: 0.7030 (mtpt) REVERT: A 528 ASP cc_start: 0.8398 (m-30) cc_final: 0.7549 (t0) REVERT: A 533 GLU cc_start: 0.7905 (tp30) cc_final: 0.7630 (mm-30) REVERT: A 554 ARG cc_start: 0.6439 (mtm110) cc_final: 0.6210 (mtm110) REVERT: A 577 LYS cc_start: 0.6239 (ttmt) cc_final: 0.5925 (ttmt) REVERT: A 579 ARG cc_start: 0.6649 (mtt180) cc_final: 0.6423 (mtt-85) REVERT: A 580 LYS cc_start: 0.6858 (ttpt) cc_final: 0.6569 (pttt) REVERT: A 612 GLN cc_start: 0.6516 (mt0) cc_final: 0.5485 (pt0) REVERT: A 634 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7612 (t70) REVERT: A 689 ASP cc_start: 0.6821 (m-30) cc_final: 0.6559 (m-30) REVERT: A 722 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6363 (mtp) REVERT: B 68 ARG cc_start: 0.7255 (mtp180) cc_final: 0.6521 (mtm110) REVERT: B 277 GLU cc_start: 0.5321 (OUTLIER) cc_final: 0.4688 (mm-30) REVERT: B 320 ASP cc_start: 0.8080 (m-30) cc_final: 0.7851 (m-30) REVERT: B 464 LYS cc_start: 0.7131 (mttt) cc_final: 0.6839 (mttm) REVERT: B 558 ASP cc_start: 0.7571 (m-30) cc_final: 0.7186 (m-30) REVERT: B 618 GLN cc_start: 0.7590 (mt0) cc_final: 0.6977 (mm110) REVERT: B 637 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7935 (mp) outliers start: 28 outliers final: 13 residues processed: 127 average time/residue: 1.1508 time to fit residues: 159.4580 Evaluate side-chains 129 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 634 ASP Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain B residue 30 ARG 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 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 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 26 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.155815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116770 restraints weight = 11983.605| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.98 r_work: 0.3402 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11211 Z= 0.154 Angle : 0.513 8.916 15229 Z= 0.272 Chirality : 0.042 0.191 1818 Planarity : 0.004 0.050 1900 Dihedral : 4.070 22.896 1504 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.08 % Allowed : 18.36 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1404 helix: 1.78 (0.18), residues: 908 sheet: 2.88 (0.88), residues: 34 loop : -0.26 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE B 130 TYR 0.026 0.002 TYR A 9 ARG 0.003 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 678) hydrogen bonds : angle 3.97037 ( 1977) covalent geometry : bond 0.00374 (11211) covalent geometry : angle 0.51308 (15229) *********************** 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 140 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.153 Fit side-chains REVERT: A 68 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6568 (mtm-85) REVERT: A 464 LYS cc_start: 0.7616 (mttt) cc_final: 0.7273 (mtpt) REVERT: A 503 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8255 (p) REVERT: A 528 ASP cc_start: 0.8323 (m-30) cc_final: 0.7506 (t0) REVERT: A 533 GLU cc_start: 0.7981 (tp30) cc_final: 0.7702 (mm-30) REVERT: A 554 ARG cc_start: 0.6685 (mtm110) cc_final: 0.6468 (mtm110) REVERT: A 577 LYS cc_start: 0.6413 (ttmt) cc_final: 0.6195 (ttmt) REVERT: A 579 ARG cc_start: 0.6784 (mtt180) cc_final: 0.6544 (mtt-85) REVERT: A 612 GLN cc_start: 0.6765 (mt0) cc_final: 0.5767 (pt0) REVERT: A 634 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7626 (t70) REVERT: A 689 ASP cc_start: 0.6950 (m-30) cc_final: 0.6695 (m-30) REVERT: A 722 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6549 (mtp) REVERT: B 68 ARG cc_start: 0.7495 (mtp180) cc_final: 0.7139 (mtp85) REVERT: B 277 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.4868 (mm-30) REVERT: B 320 ASP cc_start: 0.8055 (m-30) cc_final: 0.7820 (m-30) REVERT: B 558 ASP cc_start: 0.7801 (m-30) cc_final: 0.7437 (m-30) REVERT: B 618 GLN cc_start: 0.7746 (mt0) cc_final: 0.7162 (mm110) REVERT: B 637 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7978 (mp) outliers start: 25 outliers final: 13 residues processed: 130 average time/residue: 1.2352 time to fit residues: 173.8901 Evaluate side-chains 127 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 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 722 MET Chi-restraints excluded: chain B residue 30 ARG 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 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 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 120 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.117042 restraints weight = 11711.960| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.98 r_work: 0.3456 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11211 Z= 0.126 Angle : 0.488 6.760 15229 Z= 0.261 Chirality : 0.041 0.149 1818 Planarity : 0.004 0.050 1900 Dihedral : 3.971 22.793 1504 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.74 % Allowed : 18.69 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.23), residues: 1404 helix: 1.86 (0.17), residues: 908 sheet: 2.94 (0.88), residues: 34 loop : -0.23 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 63 HIS 0.005 0.001 HIS A 220 PHE 0.016 0.001 PHE B 130 TYR 0.021 0.001 TYR A 9 ARG 0.003 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 678) hydrogen bonds : angle 3.90382 ( 1977) covalent geometry : bond 0.00292 (11211) covalent geometry : angle 0.48769 (15229) ********************** 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: 21 poor density : 113 time to evaluate : 1.222 Fit side-chains REVERT: A 68 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6512 (mtm-85) REVERT: A 348 MET cc_start: 0.7202 (mmp) cc_final: 0.6638 (mmt) REVERT: A 464 LYS cc_start: 0.7537 (mttt) cc_final: 0.7164 (mtpt) REVERT: A 528 ASP cc_start: 0.8331 (m-30) cc_final: 0.7501 (t0) REVERT: A 533 GLU cc_start: 0.7921 (tp30) cc_final: 0.7654 (mm-30) REVERT: A 554 ARG cc_start: 0.6602 (mtm110) cc_final: 0.6381 (mtm110) REVERT: A 577 LYS cc_start: 0.6343 (ttmt) cc_final: 0.6042 (ttmt) REVERT: A 579 ARG cc_start: 0.6734 (mtt180) cc_final: 0.6490 (mtt-85) REVERT: A 580 LYS cc_start: 0.6895 (ttpt) cc_final: 0.6608 (pttt) REVERT: A 612 GLN cc_start: 0.6664 (mt0) cc_final: 0.5688 (pt0) REVERT: A 634 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7595 (t70) REVERT: A 689 ASP cc_start: 0.7005 (m-30) cc_final: 0.6724 (m-30) REVERT: A 722 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6505 (mtp) REVERT: B 68 ARG cc_start: 0.7434 (mtp180) cc_final: 0.6701 (mtm110) REVERT: B 277 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.4795 (mm-30) REVERT: B 320 ASP cc_start: 0.8034 (m-30) cc_final: 0.7794 (m-30) REVERT: B 464 LYS cc_start: 0.7286 (mttt) cc_final: 0.6995 (mttm) REVERT: B 558 ASP cc_start: 0.7680 (m-30) cc_final: 0.7305 (m-30) REVERT: B 618 GLN cc_start: 0.7612 (mt0) cc_final: 0.7053 (mm110) REVERT: B 637 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7975 (mp) outliers start: 21 outliers final: 13 residues processed: 125 average time/residue: 1.1797 time to fit residues: 160.4386 Evaluate side-chains 131 residues out of total 1218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 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 722 MET Chi-restraints excluded: chain B residue 30 ARG 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 406 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 23 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.153873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115223 restraints weight = 11757.650| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.98 r_work: 0.3414 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11211 Z= 0.156 Angle : 0.510 5.241 15229 Z= 0.273 Chirality : 0.042 0.154 1818 Planarity : 0.004 0.051 1900 Dihedral : 4.078 23.060 1504 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.74 % Allowed : 18.85 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.23), residues: 1404 helix: 1.76 (0.17), residues: 908 sheet: 2.87 (0.88), residues: 34 loop : -0.26 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 63 HIS 0.006 0.001 HIS A 220 PHE 0.018 0.001 PHE B 58 TYR 0.026 0.002 TYR A 9 ARG 0.004 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 678) hydrogen bonds : angle 3.97710 ( 1977) covalent geometry : bond 0.00376 (11211) covalent geometry : angle 0.51049 (15229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7824.21 seconds wall clock time: 135 minutes 54.56 seconds (8154.56 seconds total)