Starting phenix.real_space_refine on Wed Jul 30 01:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lgu_23329/07_2025/7lgu_23329.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lgu_23329/07_2025/7lgu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lgu_23329/07_2025/7lgu_23329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lgu_23329/07_2025/7lgu_23329.map" model { file = "/net/cci-nas-00/data/ceres_data/7lgu_23329/07_2025/7lgu_23329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lgu_23329/07_2025/7lgu_23329.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG: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: 7.79, per 1000 atoms: 0.67 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: 3.15 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.49 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: 3.54 Time building geometry restraints manager: 3.60 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: 0.06 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: 1.580 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: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.610 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:15.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (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 TRP 0.008 0.001 TRP A 70 HIS 0.003 0.001 HIS B 640 PHE 0.013 0.001 PHE A 278 TYR 0.013 0.001 TYR A 16 ARG 0.002 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.12186 ( 682) hydrogen bonds : angle 5.79161 ( 1968) covalent geometry : bond 0.00291 (11620) covalent geometry : angle 0.93403 (15392) *********************** 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 : 1.245 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: 1.2061 time to fit residues: 168.9736 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 : 1.286 ------------------------------------------------------------------------------- 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 114 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- 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 638 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.091101 restraints weight = 12119.703| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.83 r_work: 0.2885 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11620 Z= 0.167 Angle : 0.526 6.688 15392 Z= 0.276 Chirality : 0.045 0.146 1744 Planarity : 0.004 0.039 1808 Dihedral : 8.100 91.930 2257 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.73 % Allowed : 12.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.23), residues: 1352 helix: 1.80 (0.17), residues: 886 sheet: 3.32 (0.68), residues: 38 loop : -0.09 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 70 HIS 0.004 0.001 HIS B 640 PHE 0.017 0.002 PHE A 111 TYR 0.016 0.001 TYR B 16 ARG 0.002 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.05075 ( 682) hydrogen bonds : angle 4.73616 ( 1968) covalent geometry : bond 0.00381 (11620) covalent geometry : angle 0.52624 (15392) *********************** 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: 31 poor density : 113 time to evaluate : 1.146 Fit side-chains REVERT: A 207 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: A 257 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7210 (pt) REVERT: B 257 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7180 (pt) outliers start: 31 outliers final: 17 residues processed: 131 average time/residue: 1.2184 time to fit residues: 173.6539 Evaluate side-chains 132 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 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 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 96 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 0.0870 overall best weight: 1.0162 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.136149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096985 restraints weight = 12321.442| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.81 r_work: 0.3010 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11620 Z= 0.104 Angle : 0.449 6.203 15392 Z= 0.234 Chirality : 0.042 0.129 1744 Planarity : 0.004 0.039 1808 Dihedral : 7.288 58.511 2251 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.56 % Allowed : 13.23 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.23), residues: 1352 helix: 2.00 (0.17), residues: 886 sheet: 3.32 (0.68), residues: 38 loop : -0.08 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 70 HIS 0.002 0.001 HIS B 220 PHE 0.011 0.001 PHE B 111 TYR 0.011 0.001 TYR B 16 ARG 0.002 0.000 ARG B 716 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 682) hydrogen bonds : angle 4.49419 ( 1968) covalent geometry : bond 0.00210 (11620) covalent geometry : angle 0.44876 (15392) *********************** 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 142 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 3.507 Fit side-chains outliers start: 29 outliers final: 16 residues processed: 127 average time/residue: 1.7565 time to fit residues: 246.2425 Evaluate side-chains 127 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 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 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 474 THR Chi-restraints excluded: chain B residue 529 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 121 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 58 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3542 r_free = 0.3542 target = 0.132049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.091626 restraints weight = 12230.665| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.83 r_work: 0.2895 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11620 Z= 0.147 Angle : 0.492 5.584 15392 Z= 0.258 Chirality : 0.043 0.144 1744 Planarity : 0.004 0.041 1808 Dihedral : 7.612 55.018 2248 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.82 % Allowed : 12.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.23), residues: 1352 helix: 1.89 (0.17), residues: 888 sheet: 3.23 (0.70), residues: 38 loop : -0.23 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS A 640 PHE 0.016 0.001 PHE B 391 TYR 0.014 0.001 TYR B 16 ARG 0.002 0.000 ARG B 689 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 682) hydrogen bonds : angle 4.53357 ( 1968) covalent geometry : bond 0.00333 (11620) covalent geometry : angle 0.49246 (15392) *********************** 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: 32 poor density : 111 time to evaluate : 1.052 Fit side-chains outliers start: 32 outliers final: 17 residues processed: 129 average time/residue: 1.1515 time to fit residues: 162.4737 Evaluate side-chains 126 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 253 ASN Chi-restraints excluded: chain A residue 285 LYS 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 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 45 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3564 r_free = 0.3564 target = 0.133917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094207 restraints weight = 12187.041| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.82 r_work: 0.2934 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11620 Z= 0.112 Angle : 0.456 5.849 15392 Z= 0.238 Chirality : 0.042 0.134 1744 Planarity : 0.004 0.041 1808 Dihedral : 7.365 59.832 2248 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.38 % Allowed : 12.61 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.23), residues: 1352 helix: 1.94 (0.17), residues: 890 sheet: 3.18 (0.69), residues: 38 loop : -0.19 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 70 HIS 0.002 0.001 HIS A 640 PHE 0.012 0.001 PHE A 391 TYR 0.012 0.001 TYR B 16 ARG 0.002 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 682) hydrogen bonds : angle 4.43340 ( 1968) covalent geometry : bond 0.00235 (11620) covalent geometry : angle 0.45644 (15392) *********************** 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 135 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.188 Fit side-chains REVERT: A 84 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7464 (mt) REVERT: A 207 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: B 84 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7469 (mt) REVERT: B 528 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.6891 (mp0) outliers start: 27 outliers final: 17 residues processed: 123 average time/residue: 1.2193 time to fit residues: 163.8006 Evaluate side-chains 127 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 285 LYS 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 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 285 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 474 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 105 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.132134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091762 restraints weight = 12245.698| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.84 r_work: 0.2899 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11620 Z= 0.148 Angle : 0.490 5.612 15392 Z= 0.257 Chirality : 0.043 0.145 1744 Planarity : 0.004 0.042 1808 Dihedral : 7.718 59.450 2248 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.29 % Allowed : 13.14 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.23), residues: 1352 helix: 1.86 (0.17), residues: 890 sheet: 3.18 (0.71), residues: 38 loop : -0.24 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS B 640 PHE 0.016 0.001 PHE B 391 TYR 0.014 0.001 TYR B 16 ARG 0.002 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 682) hydrogen bonds : angle 4.49312 ( 1968) covalent geometry : bond 0.00336 (11620) covalent geometry : angle 0.49035 (15392) *********************** 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 135 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.278 Fit side-chains REVERT: A 207 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7800 (tt0) outliers start: 26 outliers final: 18 residues processed: 125 average time/residue: 1.1296 time to fit residues: 154.4100 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 : 1.074 ------------------------------------------------------------------------------- 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 285 LYS 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 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 527 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 31 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.091316 restraints weight = 12326.487| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.84 r_work: 0.2894 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11620 Z= 0.152 Angle : 0.498 5.642 15392 Z= 0.260 Chirality : 0.043 0.146 1744 Planarity : 0.004 0.041 1808 Dihedral : 7.916 57.002 2248 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.73 % Allowed : 12.87 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1352 helix: 1.85 (0.17), residues: 890 sheet: 3.07 (0.72), residues: 38 loop : -0.27 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 70 HIS 0.004 0.001 HIS B 640 PHE 0.016 0.001 PHE B 391 TYR 0.014 0.001 TYR B 16 ARG 0.003 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.04731 ( 682) hydrogen bonds : angle 4.52049 ( 1968) covalent geometry : bond 0.00347 (11620) covalent geometry : angle 0.49790 (15392) *********************** 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 143 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 1.237 Fit side-chains REVERT: A 207 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: A 257 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7202 (pt) REVERT: A 285 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6932 (mtpp) REVERT: A 698 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8913 (mp) REVERT: B 207 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: B 257 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7197 (pt) REVERT: B 285 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6946 (mtpp) REVERT: B 698 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8918 (mp) outliers start: 31 outliers final: 16 residues processed: 131 average time/residue: 1.1286 time to fit residues: 162.2997 Evaluate side-chains 134 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 257 LEU Chi-restraints excluded: chain A residue 285 LYS 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 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 257 LEU Chi-restraints excluded: chain B residue 285 LYS 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 70 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.129847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.089226 restraints weight = 12237.800| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.82 r_work: 0.2855 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11620 Z= 0.217 Angle : 0.553 5.495 15392 Z= 0.290 Chirality : 0.046 0.162 1744 Planarity : 0.005 0.046 1808 Dihedral : 8.888 58.137 2248 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.12 % Allowed : 13.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.23), residues: 1352 helix: 1.69 (0.17), residues: 888 sheet: 2.77 (0.74), residues: 38 loop : -0.37 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 70 HIS 0.005 0.001 HIS B 640 PHE 0.018 0.002 PHE A 391 TYR 0.016 0.002 TYR B 16 ARG 0.003 0.001 ARG B 689 Details of bonding type rmsd hydrogen bonds : bond 0.05450 ( 682) hydrogen bonds : angle 4.66288 ( 1968) covalent geometry : bond 0.00514 (11620) covalent geometry : angle 0.55322 (15392) *********************** 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 135 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 1.186 Fit side-chains REVERT: A 207 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: A 257 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7158 (pt) REVERT: A 285 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6892 (mtpp) REVERT: B 207 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: B 257 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7165 (pt) REVERT: B 285 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6881 (mtpp) REVERT: B 615 LYS cc_start: 0.6884 (ttpt) cc_final: 0.6652 (ttpt) outliers start: 24 outliers final: 12 residues processed: 126 average time/residue: 1.1785 time to fit residues: 162.2526 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 : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 257 LEU Chi-restraints excluded: chain A residue 285 LYS 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 84 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.130588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.090051 restraints weight = 12203.759| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.82 r_work: 0.2871 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11620 Z= 0.177 Angle : 0.528 5.699 15392 Z= 0.276 Chirality : 0.045 0.153 1744 Planarity : 0.005 0.044 1808 Dihedral : 8.807 59.518 2246 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.12 % Allowed : 13.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.23), residues: 1352 helix: 1.71 (0.17), residues: 888 sheet: 2.78 (0.76), residues: 36 loop : -0.28 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS B 640 PHE 0.017 0.002 PHE B 391 TYR 0.015 0.001 TYR B 16 ARG 0.003 0.000 ARG B 689 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 682) hydrogen bonds : angle 4.64765 ( 1968) covalent geometry : bond 0.00412 (11620) covalent geometry : angle 0.52768 (15392) *********************** 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 132 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.134 Fit side-chains REVERT: A 207 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: A 257 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7152 (pt) REVERT: A 285 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6892 (mtpp) REVERT: A 615 LYS cc_start: 0.6866 (ttpt) cc_final: 0.6650 (ttpt) REVERT: A 698 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8910 (mp) REVERT: B 207 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: B 257 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7180 (pt) REVERT: B 285 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6878 (mtpp) REVERT: B 615 LYS cc_start: 0.6880 (ttpt) cc_final: 0.6648 (ttpt) REVERT: B 698 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8916 (mp) outliers start: 24 outliers final: 14 residues processed: 122 average time/residue: 1.1590 time to fit residues: 154.5388 Evaluate side-chains 129 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 257 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 698 LEU 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 257 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 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 94 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.131222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.090732 restraints weight = 12170.296| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.82 r_work: 0.2885 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1122 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= 0.158 Angle : 0.513 5.978 15392 Z= 0.268 Chirality : 0.044 0.148 1744 Planarity : 0.004 0.041 1808 Dihedral : 8.622 59.654 2244 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.94 % Allowed : 13.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.23), residues: 1352 helix: 1.76 (0.17), residues: 888 sheet: 2.85 (0.76), residues: 36 loop : -0.27 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS B 640 PHE 0.016 0.001 PHE A 391 TYR 0.014 0.001 TYR A 16 ARG 0.004 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 682) hydrogen bonds : angle 4.61704 ( 1968) covalent geometry : bond 0.00363 (11620) covalent geometry : angle 0.51336 (15392) ********************** 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 129 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.125 Fit side-chains REVERT: A 207 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: A 257 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7186 (pt) REVERT: A 285 LYS cc_start: 0.7198 (mtpm) cc_final: 0.6890 (mtpp) REVERT: A 308 ASN cc_start: 0.8034 (t0) cc_final: 0.7605 (t0) REVERT: A 615 LYS cc_start: 0.6867 (ttpt) cc_final: 0.6654 (ttpt) REVERT: A 698 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8905 (mp) REVERT: B 207 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: B 257 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7176 (pt) REVERT: B 285 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6946 (mtpp) REVERT: B 308 ASN cc_start: 0.8035 (t0) cc_final: 0.7593 (t0) REVERT: B 615 LYS cc_start: 0.6889 (ttpt) cc_final: 0.6653 (ttpt) REVERT: B 698 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8910 (mp) outliers start: 22 outliers final: 14 residues processed: 120 average time/residue: 1.1523 time to fit residues: 151.0279 Evaluate side-chains 127 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 257 LEU Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 698 LEU 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 257 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 446 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 69 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.130206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.089629 restraints weight = 12208.504| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.82 r_work: 0.2865 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11620 Z= 0.194 Angle : 0.544 5.859 15392 Z= 0.285 Chirality : 0.045 0.156 1744 Planarity : 0.005 0.044 1808 Dihedral : 8.901 55.858 2244 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.94 % Allowed : 13.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.23), residues: 1352 helix: 1.66 (0.17), residues: 888 sheet: 2.77 (0.77), residues: 36 loop : -0.29 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 70 HIS 0.005 0.001 HIS B 640 PHE 0.017 0.002 PHE B 391 TYR 0.015 0.002 TYR A 16 ARG 0.004 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.05224 ( 682) hydrogen bonds : angle 4.66629 ( 1968) covalent geometry : bond 0.00456 (11620) covalent geometry : angle 0.54412 (15392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10666.25 seconds wall clock time: 186 minutes 3.99 seconds (11163.99 seconds total)