Starting phenix.real_space_refine on Fri Jul 3 03:24:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lgu_23329/07_2026/7lgu_23329.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lgu_23329/07_2026/7lgu_23329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lgu_23329/07_2026/7lgu_23329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lgu_23329/07_2026/7lgu_23329.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lgu_23329/07_2026/7lgu_23329.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lgu_23329/07_2026/7lgu_23329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lgu_23329/07_2026/7lgu_23329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lgu_23329/07_2026/7lgu_23329.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.048 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 48 5.16 5 Cl 2 4.86 5 C 7892 2.51 5 N 1690 2.21 5 O 1965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11597 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 517 Unusual residues: {' CL': 1, 'C14': 2, 'CLR': 1, 'D10': 18, 'D12': 5, 'HEX': 1, 'HP6': 2, 'OCT': 25} Classifications: {'undetermined': 55} Link IDs: {None: 54} Chain: "B" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 517 Unusual residues: {' CL': 1, 'C14': 2, 'CLR': 1, 'D10': 18, 'D12': 5, 'HEX': 1, 'HP6': 2, 'OCT': 25} Classifications: {'undetermined': 55} Link IDs: {None: 54} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Time building chain proxies: 2.59, per 1000 atoms: 0.22 Number of scatterers: 11597 At special positions: 0 Unit cell: (102.16, 119.078, 113.222, 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 48 16.00 O 1965 8.00 N 1690 7.00 C 7892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 549.2 milliseconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 5 sheets defined 71.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.642A pdb=" N ARG A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 75 through 105 removed outlier: 5.733A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.856A pdb=" N GLY A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.582A pdb=" N PHE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.681A pdb=" N PHE A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.860A pdb=" N PHE 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 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 335 through 366 removed outlier: 6.136A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.790A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 436 through 448 Processing helix chain 'A' and resid 448 through 454 removed outlier: 3.792A pdb=" N GLN A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.870A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 485 through 505 removed outlier: 4.105A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 560 removed outlier: 4.877A pdb=" N ASP A 550 " --> pdb=" O TYR A 546 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 579 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 653 through 670 removed outlier: 3.693A pdb=" N VAL A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 705 through 725 removed outlier: 3.820A pdb=" N SER A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 removed outlier: 3.642A pdb=" N ARG B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 75 through 105 removed outlier: 5.733A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.856A pdb=" N GLY B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.582A pdb=" N PHE B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.682A pdb=" N PHE B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 removed outlier: 3.861A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 366 removed outlier: 6.135A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.791A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 406 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 448 Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.790A pdb=" N GLN B 454 " --> pdb=" O GLY B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.871A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 485 through 505 removed outlier: 4.106A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 560 removed outlier: 4.877A pdb=" N ASP B 550 " --> pdb=" O TYR B 546 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 653 through 670 removed outlier: 3.693A pdb=" N VAL B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'B' and resid 705 through 725 removed outlier: 3.820A pdb=" N SER B 725 " --> pdb=" O GLU B 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 135 removed outlier: 4.544A pdb=" N SER A 133 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.504A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N LYS A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ILE A 535 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N PHE A 703 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 676 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.544A pdb=" N SER B 133 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.505A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N LYS B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 12.325A pdb=" N ILE B 535 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N PHE B 703 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU B 676 " --> pdb=" O PHE B 703 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3236 1.34 - 1.46: 1983 1.46 - 1.57: 6323 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 11620 Sorted by residual: bond pdb=" C3 CLR A 802 " pdb=" O1 CLR A 802 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" C3 CLR B 802 " pdb=" O1 CLR B 802 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" C21 HP6 B 841 " pdb=" C22 HP6 B 841 " ideal model delta sigma weight residual 1.524 1.506 0.018 2.00e-02 2.50e+03 8.04e-01 bond pdb=" C8 D10 A 839 " pdb=" C9 D10 A 839 " ideal model delta sigma weight residual 1.524 1.506 0.018 2.00e-02 2.50e+03 7.83e-01 bond pdb=" C2 D10 B 839 " pdb=" C3 D10 B 839 " ideal model delta sigma weight residual 1.524 1.506 0.018 2.00e-02 2.50e+03 7.70e-01 ... (remaining 11615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 14049 1.02 - 2.04: 481 2.04 - 3.06: 114 3.06 - 4.08: 659 4.08 - 5.11: 89 Bond angle restraints: 15392 Sorted by residual: angle pdb=" CB GLU A 280 " pdb=" CG GLU A 280 " pdb=" CD GLU A 280 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.70e+00 3.46e-01 4.19e+00 angle pdb=" CB GLU B 280 " pdb=" CG GLU B 280 " pdb=" CD GLU B 280 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.70e+00 3.46e-01 4.08e+00 angle pdb=" CA VAL A 107 " pdb=" C VAL A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 117.33 119.26 -1.93 1.01e+00 9.80e-01 3.66e+00 angle pdb=" CA VAL B 107 " pdb=" C VAL B 107 " pdb=" N PRO B 108 " ideal model delta sigma weight residual 117.33 119.19 -1.86 1.01e+00 9.80e-01 3.39e+00 angle pdb=" C ARG B 463 " pdb=" N THR B 464 " pdb=" CA THR B 464 " ideal model delta sigma weight residual 122.60 119.32 3.28 1.88e+00 2.83e-01 3.04e+00 ... (remaining 15387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6365 17.99 - 35.98: 517 35.98 - 53.98: 92 53.98 - 71.97: 28 71.97 - 89.96: 12 Dihedral angle restraints: 7014 sinusoidal: 3090 harmonic: 3924 Sorted by residual: dihedral pdb=" CA PHE A 23 " pdb=" C PHE A 23 " pdb=" N SER A 24 " pdb=" CA SER A 24 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PHE B 23 " pdb=" C PHE B 23 " pdb=" N SER B 24 " pdb=" CA SER B 24 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASN A 548 " pdb=" C ASN A 548 " pdb=" N SER A 549 " pdb=" CA SER A 549 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 7011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 972 0.028 - 0.055: 458 0.055 - 0.083: 201 0.083 - 0.110: 93 0.110 - 0.138: 20 Chirality restraints: 1744 Sorted by residual: chirality pdb=" C17 CLR A 802 " pdb=" C13 CLR A 802 " pdb=" C16 CLR A 802 " pdb=" C20 CLR A 802 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA TYR B 526 " pdb=" N TYR B 526 " pdb=" C TYR B 526 " pdb=" CB TYR B 526 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA TYR A 526 " pdb=" N TYR A 526 " pdb=" C TYR A 526 " pdb=" CB TYR A 526 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1741 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 443 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C ILE B 443 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE B 443 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL B 444 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 443 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C ILE A 443 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE A 443 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 444 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 444 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C VAL A 444 " 0.020 2.00e-02 2.50e+03 pdb=" O VAL A 444 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 445 " -0.007 2.00e-02 2.50e+03 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 797 2.74 - 3.28: 11228 3.28 - 3.82: 19499 3.82 - 4.36: 25002 4.36 - 4.90: 40645 Nonbonded interactions: 97171 Sorted by model distance: nonbonded pdb=" O ALA A 495 " pdb=" OG1 THR A 498 " model vdw 2.197 3.040 nonbonded pdb=" O ALA B 495 " pdb=" OG1 THR B 498 " model vdw 2.198 3.040 nonbonded pdb=" OG SER A 654 " pdb=" OE2 GLU B 468 " model vdw 2.259 3.040 nonbonded pdb=" OE2 GLU A 468 " pdb=" OG SER B 654 " model vdw 2.262 3.040 nonbonded pdb=" NE ARG B 211 " pdb=" OD2 ASP B 457 " model vdw 2.271 3.120 ... (remaining 97166 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.003 0.024 11620 Z= 0.140 Angle : 0.934 5.106 15392 Z= 0.377 Chirality : 0.042 0.138 1744 Planarity : 0.003 0.027 1808 Dihedral : 14.183 89.961 4502 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.15 % Allowed : 14.02 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.23), residues: 1352 helix: 1.33 (0.17), residues: 898 sheet: 2.30 (0.71), residues: 50 loop : 0.01 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 502 TYR 0.013 0.001 TYR A 16 PHE 0.013 0.001 PHE A 278 TRP 0.008 0.001 TRP A 70 HIS 0.003 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (11620) covalent geometry : angle 0.93403 / 0.38 (15392) hydrogen bonds : bond 0.12186 / 7.40 ( 682) hydrogen bonds : angle 5.79161 / 4.16 ( 1968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.404 Fit side-chains REVERT: A 207 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: A 686 ASP cc_start: 0.7967 (m-30) cc_final: 0.7765 (m-30) outliers start: 13 outliers final: 8 residues processed: 128 average time/residue: 0.5010 time to fit residues: 70.1482 Evaluate side-chains 124 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 529 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 HIS A 454 GLN A 638 ASN B 337 HIS B 638 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.092695 restraints weight = 12225.098| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.82 r_work: 0.2925 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11620 Z= 0.161 Angle : 0.523 6.725 15392 Z= 0.274 Chirality : 0.044 0.145 1744 Planarity : 0.004 0.038 1808 Dihedral : 7.884 91.834 2145 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.65 % Allowed : 12.61 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.23), residues: 1352 helix: 1.82 (0.17), residues: 886 sheet: 3.36 (0.68), residues: 38 loop : -0.08 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 20 TYR 0.016 0.001 TYR B 16 PHE 0.017 0.001 PHE A 111 TRP 0.010 0.001 TRP A 70 HIS 0.004 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11620) covalent geometry : angle 0.52314 / 0.27 (15392) hydrogen bonds : bond 0.04992 / 3.17 ( 682) hydrogen bonds : angle 4.72260 / 3.40 ( 1968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.406 Fit side-chains REVERT: A 257 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7223 (pt) REVERT: B 257 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7201 (pt) outliers start: 30 outliers final: 17 residues processed: 132 average time/residue: 0.4783 time to fit residues: 68.7170 Evaluate side-chains 129 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 0.0570 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 454 GLN B 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.090580 restraints weight = 12261.592| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.84 r_work: 0.2877 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11620 Z= 0.165 Angle : 0.514 6.029 15392 Z= 0.270 Chirality : 0.044 0.152 1744 Planarity : 0.004 0.039 1808 Dihedral : 7.852 51.464 2136 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.65 % Allowed : 12.70 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.23), residues: 1352 helix: 1.79 (0.17), residues: 886 sheet: 3.15 (0.70), residues: 38 loop : -0.16 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.015 0.001 TYR B 16 PHE 0.017 0.002 PHE B 391 TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (11620) covalent geometry : angle 0.51428 / 0.27 (15392) hydrogen bonds : bond 0.05024 / 3.19 ( 682) hydrogen bonds : angle 4.65873 / 3.35 ( 1968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.303 Fit side-chains REVERT: A 257 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7186 (pt) REVERT: A 285 LYS cc_start: 0.7135 (mtpm) cc_final: 0.6878 (mtpp) REVERT: B 257 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7187 (pt) outliers start: 30 outliers final: 19 residues processed: 131 average time/residue: 0.4872 time to fit residues: 69.5423 Evaluate side-chains 131 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 59 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.091071 restraints weight = 12199.814| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.83 r_work: 0.2885 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11620 Z= 0.155 Angle : 0.504 5.731 15392 Z= 0.264 Chirality : 0.044 0.146 1744 Planarity : 0.004 0.040 1808 Dihedral : 7.908 51.998 2136 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.65 % Allowed : 13.23 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.23), residues: 1352 helix: 1.79 (0.17), residues: 888 sheet: 3.00 (0.71), residues: 38 loop : -0.26 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 689 TYR 0.014 0.001 TYR B 16 PHE 0.016 0.001 PHE B 391 TRP 0.011 0.001 TRP B 70 HIS 0.003 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (11620) covalent geometry : angle 0.50410 / 0.26 (15392) hydrogen bonds : bond 0.04801 / 3.06 ( 682) hydrogen bonds : angle 4.59417 / 3.30 ( 1968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.378 Fit side-chains REVERT: A 285 LYS cc_start: 0.7128 (mtpm) cc_final: 0.6866 (mtpp) REVERT: B 285 LYS cc_start: 0.7145 (mtpm) cc_final: 0.6890 (mtpp) REVERT: B 698 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8902 (mp) outliers start: 30 outliers final: 19 residues processed: 132 average time/residue: 0.4847 time to fit residues: 69.7169 Evaluate side-chains 128 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 81 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.090924 restraints weight = 12218.862| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.83 r_work: 0.2882 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11620 Z= 0.154 Angle : 0.503 5.426 15392 Z= 0.263 Chirality : 0.044 0.148 1744 Planarity : 0.004 0.042 1808 Dihedral : 7.986 53.532 2136 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.47 % Allowed : 13.23 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.23), residues: 1352 helix: 1.79 (0.17), residues: 888 sheet: 2.89 (0.71), residues: 38 loop : -0.28 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 689 TYR 0.014 0.001 TYR B 16 PHE 0.016 0.001 PHE B 391 TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11620) covalent geometry : angle 0.50254 / 0.26 (15392) hydrogen bonds : bond 0.04781 / 3.05 ( 682) hydrogen bonds : angle 4.57407 / 3.28 ( 1968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.460 Fit side-chains REVERT: A 257 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7181 (pt) REVERT: A 285 LYS cc_start: 0.7129 (mtpm) cc_final: 0.6869 (mtpp) REVERT: B 207 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: B 257 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7197 (pt) REVERT: B 285 LYS cc_start: 0.7149 (mtpm) cc_final: 0.6891 (mtpp) REVERT: B 615 LYS cc_start: 0.6888 (ttpt) cc_final: 0.6651 (ttpt) REVERT: B 698 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8897 (mp) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 0.4968 time to fit residues: 68.2307 Evaluate side-chains 132 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.089709 restraints weight = 12200.654| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.83 r_work: 0.2865 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11620 Z= 0.180 Angle : 0.527 5.148 15392 Z= 0.276 Chirality : 0.045 0.154 1744 Planarity : 0.005 0.044 1808 Dihedral : 8.453 58.923 2136 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.56 % Allowed : 14.29 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.23), residues: 1352 helix: 1.71 (0.17), residues: 890 sheet: 2.77 (0.72), residues: 38 loop : -0.29 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 689 TYR 0.015 0.001 TYR A 16 PHE 0.017 0.002 PHE B 391 TRP 0.011 0.001 TRP B 70 HIS 0.005 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (11620) covalent geometry : angle 0.52703 / 0.28 (15392) hydrogen bonds : bond 0.05106 / 3.26 ( 682) hydrogen bonds : angle 4.64283 / 3.32 ( 1968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.422 Fit side-chains REVERT: A 207 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: A 257 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7163 (pt) REVERT: A 285 LYS cc_start: 0.7144 (mtpm) cc_final: 0.6878 (mtpp) REVERT: A 615 LYS cc_start: 0.6872 (ttpt) cc_final: 0.6648 (ttpt) REVERT: A 698 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8917 (mp) REVERT: B 207 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: B 257 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7137 (pt) REVERT: B 285 LYS cc_start: 0.7149 (mtpm) cc_final: 0.6891 (mtpp) REVERT: B 528 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 615 LYS cc_start: 0.6890 (ttpt) cc_final: 0.6638 (ttpt) outliers start: 29 outliers final: 16 residues processed: 129 average time/residue: 0.4888 time to fit residues: 69.0641 Evaluate side-chains 131 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 363 ASN B 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.089742 restraints weight = 12205.367| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.82 r_work: 0.2866 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11620 Z= 0.185 Angle : 0.531 5.153 15392 Z= 0.278 Chirality : 0.045 0.155 1744 Planarity : 0.005 0.044 1808 Dihedral : 8.663 57.902 2134 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.47 % Allowed : 14.11 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.23), residues: 1352 helix: 1.69 (0.17), residues: 888 sheet: 2.74 (0.76), residues: 36 loop : -0.27 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 689 TYR 0.015 0.001 TYR B 16 PHE 0.017 0.002 PHE B 391 TRP 0.011 0.002 TRP B 70 HIS 0.004 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (11620) covalent geometry : angle 0.53119 / 0.28 (15392) hydrogen bonds : bond 0.05124 / 3.27 ( 682) hydrogen bonds : angle 4.66345 / 3.34 ( 1968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.337 Fit side-chains REVERT: A 207 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: A 257 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7136 (pt) REVERT: A 285 LYS cc_start: 0.7139 (mtpm) cc_final: 0.6871 (mtpp) REVERT: A 308 ASN cc_start: 0.7998 (t0) cc_final: 0.7520 (t0) REVERT: A 615 LYS cc_start: 0.6873 (ttpt) cc_final: 0.6633 (ttpt) REVERT: A 698 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8906 (mp) REVERT: B 207 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: B 257 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7134 (pt) REVERT: B 285 LYS cc_start: 0.7144 (mtpm) cc_final: 0.6876 (mtpp) REVERT: B 308 ASN cc_start: 0.8024 (t0) cc_final: 0.7534 (t0) REVERT: B 615 LYS cc_start: 0.6849 (ttpt) cc_final: 0.6578 (ttpt) REVERT: B 698 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8910 (mp) outliers start: 28 outliers final: 18 residues processed: 125 average time/residue: 0.4937 time to fit residues: 67.1874 Evaluate side-chains 132 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 99 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.088467 restraints weight = 12191.931| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.81 r_work: 0.2844 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11620 Z= 0.230 Angle : 0.574 5.224 15392 Z= 0.300 Chirality : 0.047 0.165 1744 Planarity : 0.005 0.050 1808 Dihedral : 9.254 54.647 2134 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.29 % Allowed : 14.11 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.22), residues: 1352 helix: 1.59 (0.17), residues: 886 sheet: 2.67 (0.76), residues: 36 loop : -0.26 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 31 TYR 0.017 0.002 TYR B 16 PHE 0.018 0.002 PHE B 391 TRP 0.011 0.002 TRP B 70 HIS 0.006 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (11620) covalent geometry : angle 0.57430 / 0.30 (15392) hydrogen bonds : bond 0.05586 / 3.56 ( 682) hydrogen bonds : angle 4.73552 / 3.38 ( 1968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.339 Fit side-chains REVERT: A 207 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: A 257 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7140 (pt) REVERT: A 285 LYS cc_start: 0.7183 (mtpm) cc_final: 0.6915 (mtpp) REVERT: A 308 ASN cc_start: 0.8012 (t0) cc_final: 0.7506 (t0) REVERT: A 615 LYS cc_start: 0.6847 (ttpt) cc_final: 0.6584 (ttpt) REVERT: A 691 ARG cc_start: 0.7173 (mtt180) cc_final: 0.6482 (mtm-85) REVERT: A 698 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8909 (mp) REVERT: B 207 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: B 257 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7141 (pt) REVERT: B 285 LYS cc_start: 0.7164 (mtpm) cc_final: 0.6896 (mtpp) REVERT: B 308 ASN cc_start: 0.8008 (t0) cc_final: 0.7480 (t0) REVERT: B 615 LYS cc_start: 0.6862 (ttpt) cc_final: 0.6580 (ttpt) REVERT: B 691 ARG cc_start: 0.7173 (mtt180) cc_final: 0.6486 (mtm-85) REVERT: B 698 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8905 (mp) outliers start: 26 outliers final: 19 residues processed: 128 average time/residue: 0.5283 time to fit residues: 73.1887 Evaluate side-chains 135 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.089842 restraints weight = 12120.039| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.81 r_work: 0.2868 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11620 Z= 0.174 Angle : 0.531 5.434 15392 Z= 0.278 Chirality : 0.045 0.152 1744 Planarity : 0.005 0.043 1808 Dihedral : 8.918 54.363 2134 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.29 % Allowed : 13.93 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.23), residues: 1352 helix: 1.67 (0.17), residues: 888 sheet: 2.70 (0.76), residues: 36 loop : -0.24 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 689 TYR 0.015 0.001 TYR A 16 PHE 0.016 0.002 PHE B 391 TRP 0.012 0.002 TRP B 70 HIS 0.004 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (11620) covalent geometry : angle 0.53125 / 0.28 (15392) hydrogen bonds : bond 0.05062 / 3.22 ( 682) hydrogen bonds : angle 4.66582 / 3.33 ( 1968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.520 Fit side-chains REVERT: A 207 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: A 257 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7155 (pt) REVERT: A 285 LYS cc_start: 0.7145 (mtpm) cc_final: 0.6838 (mtpp) REVERT: A 308 ASN cc_start: 0.7990 (t0) cc_final: 0.7524 (t0) REVERT: A 615 LYS cc_start: 0.6863 (ttpt) cc_final: 0.6598 (ttpt) REVERT: A 698 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8906 (mp) REVERT: B 207 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: B 257 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7165 (pt) REVERT: B 285 LYS cc_start: 0.7135 (mtpm) cc_final: 0.6829 (mtpp) REVERT: B 308 ASN cc_start: 0.8011 (t0) cc_final: 0.7518 (t0) REVERT: B 528 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: B 615 LYS cc_start: 0.6911 (ttpt) cc_final: 0.6614 (ttpt) REVERT: B 698 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8913 (mp) outliers start: 26 outliers final: 19 residues processed: 125 average time/residue: 0.5621 time to fit residues: 76.4863 Evaluate side-chains 135 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 527 GLU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 713 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.091798 restraints weight = 12254.652| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.83 r_work: 0.2900 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11620 Z= 0.136 Angle : 0.494 5.964 15392 Z= 0.257 Chirality : 0.043 0.144 1744 Planarity : 0.004 0.041 1808 Dihedral : 8.201 54.698 2134 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.85 % Allowed : 14.46 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.23), residues: 1352 helix: 1.79 (0.17), residues: 890 sheet: 2.78 (0.74), residues: 36 loop : -0.18 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 689 TYR 0.013 0.001 TYR A 16 PHE 0.013 0.001 PHE A 391 TRP 0.013 0.002 TRP B 70 HIS 0.003 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (11620) covalent geometry : angle 0.49396 / 0.26 (15392) hydrogen bonds : bond 0.04491 / 2.85 ( 682) hydrogen bonds : angle 4.55879 / 3.26 ( 1968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.402 Fit side-chains REVERT: A 207 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: A 308 ASN cc_start: 0.7978 (t0) cc_final: 0.7507 (t0) REVERT: A 615 LYS cc_start: 0.6927 (ttpt) cc_final: 0.6663 (ttpt) REVERT: B 207 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: B 257 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7161 (pt) REVERT: B 308 ASN cc_start: 0.7981 (t0) cc_final: 0.7467 (t0) REVERT: B 615 LYS cc_start: 0.6966 (ttpt) cc_final: 0.6666 (ttpt) outliers start: 21 outliers final: 12 residues processed: 120 average time/residue: 0.5638 time to fit residues: 73.6129 Evaluate side-chains 120 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 253 ASN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 638 ASN B 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.088910 restraints weight = 12278.857| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.80 r_work: 0.2846 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11620 Z= 0.242 Angle : 0.584 5.795 15392 Z= 0.306 Chirality : 0.048 0.165 1744 Planarity : 0.005 0.051 1808 Dihedral : 9.162 56.250 2132 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.68 % Allowed : 14.81 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.22), residues: 1352 helix: 1.55 (0.17), residues: 888 sheet: 2.70 (0.76), residues: 36 loop : -0.28 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 689 TYR 0.017 0.002 TYR A 16 PHE 0.018 0.002 PHE A 111 TRP 0.011 0.002 TRP B 70 HIS 0.006 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 (11620) covalent geometry : angle 0.58381 / 0.31 (15392) hydrogen bonds : bond 0.05670 / 3.62 ( 682) hydrogen bonds : angle 4.71463 / 3.36 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4525.86 seconds wall clock time: 77 minutes 42.11 seconds (4662.11 seconds total)