Starting phenix.real_space_refine on Wed Mar 4 07:28:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lgu_23329/03_2026/7lgu_23329.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lgu_23329/03_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_23329/03_2026/7lgu_23329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lgu_23329/03_2026/7lgu_23329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lgu_23329/03_2026/7lgu_23329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lgu_23329/03_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-5986/lib/python3.9/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: 2.97, per 1000 atoms: 0.26 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: 1.10 Conformation dependent library (CDL) restraints added in 615.5 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: 0.42 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: 1.95 Time building geometry restraints manager: 1.46 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: 6475 17.99 - 35.98: 519 35.98 - 53.98: 92 53.98 - 71.97: 28 71.97 - 89.96: 12 Dihedral angle restraints: 7126 sinusoidal: 3202 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 7123 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.510 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.710 Find NCS groups from input model: 0.090 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 14.032 89.961 4614 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 covalent geometry : bond 0.00291 (11620) covalent geometry : angle 0.93403 (15392) hydrogen bonds : bond 0.12186 ( 682) hydrogen bonds : angle 5.79161 ( 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 : 0.477 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: 0.5666 time to fit residues: 78.8827 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 : 0.418 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 337 HIS A 454 GLN A 638 ASN B 337 HIS B 454 GLN B 638 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.131735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091368 restraints weight = 12220.038| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.83 r_work: 0.2892 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0735 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= 0.160 Angle : 0.525 6.683 15392 Z= 0.275 Chirality : 0.044 0.144 1744 Planarity : 0.004 0.038 1808 Dihedral : 8.105 89.955 2257 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.82 % Allowed : 12.43 % 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: 1.87 (0.23), residues: 1352 helix: 1.81 (0.17), residues: 886 sheet: 3.34 (0.68), residues: 38 loop : -0.11 (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 0.011 0.001 TRP A 70 HIS 0.004 0.001 HIS B 640 Details of bonding type rmsd covalent geometry : bond 0.00362 (11620) covalent geometry : angle 0.52473 (15392) hydrogen bonds : bond 0.04958 ( 682) hydrogen bonds : angle 4.70965 ( 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 145 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.520 Fit side-chains REVERT: A 257 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7214 (pt) REVERT: B 257 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7191 (pt) outliers start: 32 outliers final: 20 residues processed: 133 average time/residue: 0.6068 time to fit residues: 87.5240 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 : 0.519 ------------------------------------------------------------------------------- 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 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 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 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 527 GLU 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: 2.9990 chunk 80 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3509 r_free = 0.3509 target = 0.129421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.088699 restraints weight = 12236.784| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.82 r_work: 0.2847 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11620 Z= 0.223 Angle : 0.565 5.912 15392 Z= 0.296 Chirality : 0.047 0.165 1744 Planarity : 0.005 0.048 1808 Dihedral : 8.814 55.045 2248 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.47 % Allowed : 13.05 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.22), residues: 1352 helix: 1.62 (0.17), residues: 886 sheet: 2.89 (0.70), residues: 38 loop : -0.23 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 20 TYR 0.017 0.002 TYR B 16 PHE 0.018 0.002 PHE A 391 TRP 0.010 0.002 TRP B 70 HIS 0.005 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00527 (11620) covalent geometry : angle 0.56515 (15392) hydrogen bonds : bond 0.05626 ( 682) hydrogen bonds : angle 4.77223 ( 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 136 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.415 Fit side-chains REVERT: A 257 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7154 (pt) REVERT: A 285 LYS cc_start: 0.7155 (mtpm) cc_final: 0.6861 (mtpp) REVERT: B 257 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7155 (pt) REVERT: B 285 LYS cc_start: 0.7165 (mtpm) cc_final: 0.6878 (mtpp) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 0.5514 time to fit residues: 75.5966 Evaluate side-chains 129 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 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: 0.9990 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: 2.9990 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3527 r_free = 0.3527 target = 0.130926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.090473 restraints weight = 12211.584| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.83 r_work: 0.2876 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11620 Z= 0.154 Angle : 0.508 5.816 15392 Z= 0.266 Chirality : 0.044 0.148 1744 Planarity : 0.004 0.040 1808 Dihedral : 8.617 59.719 2248 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.56 % Allowed : 13.58 % Favored : 83.86 % 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: 1.66 (0.23), residues: 1352 helix: 1.70 (0.17), residues: 888 sheet: 2.78 (0.71), residues: 38 loop : -0.27 (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 0.015 0.001 PHE A 391 TRP 0.012 0.001 TRP A 70 HIS 0.003 0.001 HIS B 640 Details of bonding type rmsd covalent geometry : bond 0.00348 (11620) covalent geometry : angle 0.50757 (15392) hydrogen bonds : bond 0.04891 ( 682) hydrogen bonds : angle 4.63859 ( 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 143 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.388 Fit side-chains REVERT: A 285 LYS cc_start: 0.7129 (mtpm) cc_final: 0.6866 (mtpp) REVERT: B 285 LYS cc_start: 0.7153 (mtpm) cc_final: 0.6894 (mtpp) outliers start: 29 outliers final: 16 residues processed: 129 average time/residue: 0.5537 time to fit residues: 77.5155 Evaluate side-chains 123 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 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 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 529 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 81 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3508 r_free = 0.3508 target = 0.129398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.088686 restraints weight = 12215.659| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.82 r_work: 0.2847 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11620 Z= 0.213 Angle : 0.559 5.603 15392 Z= 0.292 Chirality : 0.046 0.161 1744 Planarity : 0.005 0.048 1808 Dihedral : 9.232 59.157 2248 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.47 % Allowed : 13.84 % 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: 1.54 (0.22), residues: 1352 helix: 1.58 (0.17), residues: 886 sheet: 2.68 (0.76), residues: 36 loop : -0.23 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 689 TYR 0.016 0.002 TYR A 16 PHE 0.018 0.002 PHE B 391 TRP 0.011 0.002 TRP A 70 HIS 0.005 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00504 (11620) covalent geometry : angle 0.55918 (15392) hydrogen bonds : bond 0.05476 ( 682) hydrogen bonds : angle 4.71626 ( 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 : 0.323 Fit side-chains REVERT: A 257 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7130 (pt) REVERT: A 285 LYS cc_start: 0.7163 (mtpm) cc_final: 0.6864 (mtpp) REVERT: A 528 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: A 698 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8917 (mp) REVERT: B 257 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7147 (pt) REVERT: B 285 LYS cc_start: 0.7162 (mtpm) cc_final: 0.6868 (mtpp) REVERT: B 615 LYS cc_start: 0.6862 (ttpt) cc_final: 0.6633 (ttpt) outliers start: 28 outliers final: 16 residues processed: 126 average time/residue: 0.5937 time to fit residues: 81.0674 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 : 0.344 ------------------------------------------------------------------------------- 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 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 528 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3542 r_free = 0.3542 target = 0.132130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.091891 restraints weight = 12220.595| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.83 r_work: 0.2898 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11620 Z= 0.127 Angle : 0.484 5.966 15392 Z= 0.253 Chirality : 0.042 0.145 1744 Planarity : 0.004 0.041 1808 Dihedral : 8.504 59.172 2246 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.56 % Allowed : 13.76 % 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: 1.78 (0.23), residues: 1352 helix: 1.78 (0.17), residues: 888 sheet: 2.81 (0.74), residues: 36 loop : -0.18 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 689 TYR 0.013 0.001 TYR B 16 PHE 0.012 0.001 PHE B 391 TRP 0.012 0.001 TRP A 70 HIS 0.003 0.001 HIS B 640 Details of bonding type rmsd covalent geometry : bond 0.00275 (11620) covalent geometry : angle 0.48398 (15392) hydrogen bonds : bond 0.04500 ( 682) hydrogen bonds : angle 4.56797 ( 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 : 0.495 Fit side-chains REVERT: A 285 LYS cc_start: 0.7140 (mtpm) cc_final: 0.6874 (mtpp) REVERT: A 528 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: A 615 LYS cc_start: 0.6880 (ttpt) cc_final: 0.6654 (ttpt) REVERT: B 285 LYS cc_start: 0.7143 (mtpm) cc_final: 0.6887 (mtpp) REVERT: B 528 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: B 615 LYS cc_start: 0.6867 (ttpt) cc_final: 0.6625 (ttpt) outliers start: 29 outliers final: 19 residues processed: 128 average time/residue: 0.6050 time to fit residues: 84.1400 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 : 0.426 ------------------------------------------------------------------------------- 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 528 GLU 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 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: 4.9990 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3524 r_free = 0.3524 target = 0.130677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.090121 restraints weight = 12206.310| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.83 r_work: 0.2870 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11620 Z= 0.172 Angle : 0.517 5.656 15392 Z= 0.271 Chirality : 0.045 0.150 1744 Planarity : 0.005 0.042 1808 Dihedral : 8.742 58.422 2246 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.65 % Allowed : 13.76 % 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: 1.69 (0.23), residues: 1352 helix: 1.70 (0.17), residues: 890 sheet: 2.81 (0.76), residues: 36 loop : -0.20 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 689 TYR 0.015 0.001 TYR B 16 PHE 0.016 0.002 PHE A 391 TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS B 640 Details of bonding type rmsd covalent geometry : bond 0.00399 (11620) covalent geometry : angle 0.51673 (15392) hydrogen bonds : bond 0.04972 ( 682) hydrogen bonds : angle 4.61058 ( 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 138 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.434 Fit side-chains REVERT: A 257 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7166 (pt) REVERT: A 285 LYS cc_start: 0.7137 (mtpm) cc_final: 0.6867 (mtpp) REVERT: A 615 LYS cc_start: 0.6870 (ttpt) cc_final: 0.6631 (ttpt) REVERT: B 257 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7170 (pt) REVERT: B 285 LYS cc_start: 0.7139 (mtpm) cc_final: 0.6873 (mtpp) REVERT: B 615 LYS cc_start: 0.6892 (ttpt) cc_final: 0.6631 (ttpt) outliers start: 30 outliers final: 19 residues processed: 125 average time/residue: 0.5911 time to fit residues: 80.4265 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 : 0.434 ------------------------------------------------------------------------------- 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 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 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=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: 6.9990 chunk 115 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3514 r_free = 0.3514 target = 0.129865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.089275 restraints weight = 12194.220| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.82 r_work: 0.2856 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11620 Z= 0.196 Angle : 0.544 5.365 15392 Z= 0.285 Chirality : 0.046 0.157 1744 Planarity : 0.005 0.046 1808 Dihedral : 9.061 55.544 2246 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.47 % Allowed : 13.76 % 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: 1.59 (0.23), residues: 1352 helix: 1.63 (0.17), residues: 888 sheet: 2.73 (0.77), residues: 36 loop : -0.25 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 689 TYR 0.016 0.002 TYR B 16 PHE 0.018 0.002 PHE A 391 TRP 0.011 0.002 TRP B 70 HIS 0.005 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00462 (11620) covalent geometry : angle 0.54448 (15392) hydrogen bonds : bond 0.05257 ( 682) hydrogen bonds : angle 4.67442 ( 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 139 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.425 Fit side-chains REVERT: A 257 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7140 (pt) REVERT: A 285 LYS cc_start: 0.7155 (mtpm) cc_final: 0.6843 (mtpp) REVERT: A 615 LYS cc_start: 0.6856 (ttpt) cc_final: 0.6594 (ttpt) REVERT: A 691 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6402 (mtm-85) REVERT: A 698 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8907 (mp) REVERT: B 257 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7157 (pt) REVERT: B 285 LYS cc_start: 0.7147 (mtpm) cc_final: 0.6878 (mtpp) REVERT: B 615 LYS cc_start: 0.6861 (ttpt) cc_final: 0.6581 (ttpt) REVERT: B 691 ARG cc_start: 0.7066 (mtt180) cc_final: 0.6403 (mtm-85) REVERT: B 698 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8911 (mp) outliers start: 28 outliers final: 21 residues processed: 128 average time/residue: 0.5972 time to fit residues: 83.0095 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 : 0.416 ------------------------------------------------------------------------------- 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 474 THR Chi-restraints excluded: chain A residue 527 GLU 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 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: 6.9990 chunk 108 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.129166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.088638 restraints weight = 12143.242| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.80 r_work: 0.2847 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: 0.8293 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11620 Z= 0.220 Angle : 0.571 5.595 15392 Z= 0.299 Chirality : 0.047 0.163 1744 Planarity : 0.005 0.050 1808 Dihedral : 9.450 57.363 2246 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.38 % Allowed : 13.67 % Favored : 83.95 % 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: 1.54 (0.22), residues: 1352 helix: 1.58 (0.17), residues: 886 sheet: 2.66 (0.76), residues: 36 loop : -0.22 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 689 TYR 0.016 0.002 TYR B 16 PHE 0.018 0.002 PHE B 391 TRP 0.011 0.002 TRP B 70 HIS 0.005 0.001 HIS B 640 Details of bonding type rmsd covalent geometry : bond 0.00523 (11620) covalent geometry : angle 0.57064 (15392) hydrogen bonds : bond 0.05507 ( 682) hydrogen bonds : angle 4.73864 ( 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 138 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.466 Fit side-chains REVERT: A 207 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: A 257 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7183 (pt) REVERT: A 285 LYS cc_start: 0.7181 (mtpm) cc_final: 0.6869 (mtpp) REVERT: A 308 ASN cc_start: 0.7994 (t0) cc_final: 0.7603 (t0) REVERT: A 615 LYS cc_start: 0.6842 (ttpt) cc_final: 0.6572 (ttpt) REVERT: A 691 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6449 (mtm-85) REVERT: A 698 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8920 (mp) REVERT: B 207 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: B 257 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7177 (pt) REVERT: B 285 LYS cc_start: 0.7165 (mtpm) cc_final: 0.6895 (mtpp) REVERT: B 308 ASN cc_start: 0.8015 (t0) cc_final: 0.7641 (t0) REVERT: B 615 LYS cc_start: 0.6880 (ttpt) cc_final: 0.6591 (ttpt) REVERT: B 691 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6464 (mtm-85) REVERT: B 698 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8901 (mp) outliers start: 27 outliers final: 20 residues processed: 128 average time/residue: 0.6416 time to fit residues: 88.9133 Evaluate side-chains 136 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 527 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 121 optimal weight: 0.1980 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3547 r_free = 0.3547 target = 0.132599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.092500 restraints weight = 12258.424| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.83 r_work: 0.2910 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1140 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= 0.119 Angle : 0.483 5.961 15392 Z= 0.252 Chirality : 0.042 0.150 1744 Planarity : 0.004 0.040 1808 Dihedral : 8.460 57.049 2246 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 1.81 (0.23), residues: 1352 helix: 1.80 (0.17), residues: 890 sheet: 2.71 (0.74), residues: 36 loop : -0.16 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 689 TYR 0.012 0.001 TYR A 16 PHE 0.011 0.001 PHE A 391 TRP 0.013 0.002 TRP B 70 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00255 (11620) covalent geometry : angle 0.48347 (15392) hydrogen bonds : bond 0.04327 ( 682) hydrogen bonds : angle 4.56978 ( 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 136 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.428 Fit side-chains REVERT: A 207 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: A 308 ASN cc_start: 0.8033 (t0) cc_final: 0.7642 (t0) REVERT: A 615 LYS cc_start: 0.6925 (ttpt) cc_final: 0.6662 (ttpt) REVERT: B 207 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: B 308 ASN cc_start: 0.8021 (t0) cc_final: 0.7628 (t0) REVERT: B 615 LYS cc_start: 0.6955 (ttpt) cc_final: 0.6662 (ttpt) outliers start: 26 outliers final: 16 residues processed: 126 average time/residue: 0.6219 time to fit residues: 85.0175 Evaluate side-chains 126 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 253 ASN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3508 r_free = 0.3508 target = 0.129429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.089017 restraints weight = 12274.953| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.81 r_work: 0.2847 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11620 Z= 0.228 Angle : 0.574 5.851 15392 Z= 0.301 Chirality : 0.047 0.162 1744 Planarity : 0.005 0.049 1808 Dihedral : 9.280 59.785 2246 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.85 % Allowed : 14.55 % 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: 1.51 (0.22), residues: 1352 helix: 1.57 (0.17), residues: 888 sheet: 2.76 (0.77), 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 0.016 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 covalent geometry : bond 0.00541 (11620) covalent geometry : angle 0.57440 (15392) hydrogen bonds : bond 0.05550 ( 682) hydrogen bonds : angle 4.70395 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4994.41 seconds wall clock time: 85 minutes 36.98 seconds (5136.98 seconds total)