Starting phenix.real_space_refine on Wed Feb 12 21:20:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xj9_33222/02_2025/7xj9_33222.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xj9_33222/02_2025/7xj9_33222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xj9_33222/02_2025/7xj9_33222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xj9_33222/02_2025/7xj9_33222.map" model { file = "/net/cci-nas-00/data/ceres_data/7xj9_33222/02_2025/7xj9_33222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xj9_33222/02_2025/7xj9_33222.cif" } resolution = 3.27 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= -0.003 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5306 2.51 5 N 1423 2.21 5 O 1607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8375 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1550 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "C" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Time building chain proxies: 7.68, per 1000 atoms: 0.92 Number of scatterers: 8375 At special positions: 0 Unit cell: (96.76, 124.64, 114.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1607 8.00 N 1423 7.00 C 5306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 101 " - pdb=" SG CYS K 106 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 996.6 milliseconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 9.0% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.539A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.608A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.803A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.612A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.521A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.558A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.526A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.154A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.367A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.529A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.640A pdb=" N PHE J 84 " --> pdb=" O SER J 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 31 removed outlier: 3.963A pdb=" N SER K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 31' Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.154A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.961A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.596A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.526A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.846A pdb=" N SER F 7 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.718A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA F 13 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.582A pdb=" N VAL G 5 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.982A pdb=" N PHE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.684A pdb=" N ASP G 110 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.737A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.768A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 3 through 6 removed outlier: 4.014A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 removed outlier: 8.279A pdb=" N TYR I 32 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE I 57 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.623A pdb=" N ASP I 110 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.907A pdb=" N THR J 75 " --> pdb=" O SER J 64 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER J 64 " --> pdb=" O THR J 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.635A pdb=" N VAL J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AC4, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.532A pdb=" N ALA K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.558A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 264 hydrogen bonds defined for protein. 591 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: 2.44 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2679 1.34 - 1.46: 2195 1.46 - 1.58: 3662 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8584 Sorted by residual: bond pdb=" N SER K 55 " pdb=" CA SER K 55 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.30e-02 5.92e+03 5.18e+00 bond pdb=" N ASP K 108 " pdb=" CA ASP K 108 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.82e+00 bond pdb=" N LYS B 458 " pdb=" CA LYS B 458 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.30e-02 5.92e+03 4.14e+00 bond pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.35e-02 5.49e+03 3.68e+00 bond pdb=" N LYS B 478 " pdb=" CA LYS B 478 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.64e-02 3.72e+03 3.34e+00 ... (remaining 8579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11215 1.28 - 2.55: 338 2.55 - 3.83: 79 3.83 - 5.10: 18 5.10 - 6.38: 4 Bond angle restraints: 11654 Sorted by residual: angle pdb=" N ASN B 487 " pdb=" CA ASN B 487 " pdb=" C ASN B 487 " ideal model delta sigma weight residual 113.23 107.46 5.77 1.22e+00 6.72e-01 2.23e+01 angle pdb=" CA PRO C 521 " pdb=" N PRO C 521 " pdb=" CD PRO C 521 " ideal model delta sigma weight residual 112.00 107.18 4.82 1.40e+00 5.10e-01 1.19e+01 angle pdb=" C PHE B 486 " pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 123.47 118.46 5.01 1.53e+00 4.27e-01 1.07e+01 angle pdb=" N GLY J 16 " pdb=" CA GLY J 16 " pdb=" C GLY J 16 " ideal model delta sigma weight residual 114.92 110.74 4.18 1.30e+00 5.92e-01 1.03e+01 angle pdb=" CB ARG K 87 " pdb=" CG ARG K 87 " pdb=" CD ARG K 87 " ideal model delta sigma weight residual 111.30 116.74 -5.44 2.30e+00 1.89e-01 5.60e+00 ... (remaining 11649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4621 17.73 - 35.45: 394 35.45 - 53.18: 51 53.18 - 70.91: 3 70.91 - 88.63: 10 Dihedral angle restraints: 5079 sinusoidal: 1973 harmonic: 3106 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 165.53 -72.53 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 164.16 -71.16 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 133.17 -40.17 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 5076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 836 0.037 - 0.074: 283 0.074 - 0.111: 109 0.111 - 0.148: 28 0.148 - 0.185: 1 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CG LEU J 34 " pdb=" CB LEU J 34 " pdb=" CD1 LEU J 34 " pdb=" CD2 LEU J 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CB THR J 20 " pdb=" CA THR J 20 " pdb=" OG1 THR J 20 " pdb=" CG2 THR J 20 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE H 106 " pdb=" N ILE H 106 " pdb=" C ILE H 106 " pdb=" CB ILE H 106 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1254 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 8 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO K 9 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO K 9 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO K 9 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.054 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO C 521 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 87 " 0.133 9.50e-02 1.11e+02 6.00e-02 2.84e+00 pdb=" NE ARG K 87 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG K 87 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG K 87 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG K 87 " 0.000 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 166 2.68 - 3.23: 7588 3.23 - 3.79: 11877 3.79 - 4.34: 16550 4.34 - 4.90: 28169 Nonbonded interactions: 64350 Sorted by model distance: nonbonded pdb=" OH TYR F 36 " pdb=" OE1 GLN F 89 " model vdw 2.122 3.040 nonbonded pdb=" O TYR J 50 " pdb=" OG SER J 54 " model vdw 2.159 3.040 nonbonded pdb=" OG SER I 17 " pdb=" OE2 GLU I 82 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASP H 17 " pdb=" N ARG H 18 " model vdw 2.202 3.120 nonbonded pdb=" OG SER F 63 " pdb=" OG1 THR F 74 " model vdw 2.204 3.040 ... (remaining 64345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and resid 335 through 527) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 9.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.800 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 0.070 8584 Z= 0.202 Angle : 0.573 6.375 11654 Z= 0.317 Chirality : 0.044 0.185 1257 Planarity : 0.005 0.088 1498 Dihedral : 12.826 88.633 3060 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.12 (0.26), residues: 1058 helix: -4.33 (0.43), residues: 48 sheet: -0.21 (0.26), residues: 438 loop : -0.78 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 47 HIS 0.004 0.001 HIS K 107 PHE 0.013 0.001 PHE F 83 TYR 0.013 0.001 TYR J 37 ARG 0.014 0.001 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 2 MET cc_start: 0.5927 (ptt) cc_final: 0.5657 (ptt) REVERT: K 81 MET cc_start: 0.7338 (tmm) cc_final: 0.6758 (tmm) REVERT: K 118 VAL cc_start: 0.8334 (t) cc_final: 0.8126 (m) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2246 time to fit residues: 58.5125 Evaluate side-chains 158 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.0570 chunk 26 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.0000 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.115876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093685 restraints weight = 17466.966| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.19 r_work: 0.3293 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8584 Z= 0.141 Angle : 0.543 7.164 11654 Z= 0.287 Chirality : 0.045 0.162 1257 Planarity : 0.004 0.060 1498 Dihedral : 4.039 13.763 1185 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.09 % Allowed : 9.84 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 1058 helix: -4.07 (0.50), residues: 49 sheet: 0.03 (0.27), residues: 417 loop : -0.63 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 36 HIS 0.003 0.000 HIS C 505 PHE 0.012 0.001 PHE F 83 TYR 0.012 0.001 TYR J 50 ARG 0.007 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9177 (m-30) cc_final: 0.8778 (t0) REVERT: F 18 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7899 (ttp-110) REVERT: H 6 GLN cc_start: 0.8610 (mt0) cc_final: 0.8344 (mt0) REVERT: I 87 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7632 (mtm110) REVERT: J 55 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7143 (ttm170) REVERT: K 25 SER cc_start: 0.7863 (t) cc_final: 0.7487 (m) REVERT: K 81 MET cc_start: 0.7317 (tmm) cc_final: 0.6420 (tmm) outliers start: 10 outliers final: 7 residues processed: 195 average time/residue: 0.2226 time to fit residues: 58.0103 Evaluate side-chains 180 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain J residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 92 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 0.0570 chunk 86 optimal weight: 0.0020 chunk 81 optimal weight: 3.9990 overall best weight: 0.3506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN F 6 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.116030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093863 restraints weight = 17527.599| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.20 r_work: 0.3295 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8584 Z= 0.137 Angle : 0.523 6.695 11654 Z= 0.275 Chirality : 0.044 0.152 1257 Planarity : 0.004 0.049 1498 Dihedral : 3.850 14.548 1185 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.64 % Allowed : 11.37 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1058 helix: -3.94 (0.59), residues: 42 sheet: 0.24 (0.28), residues: 401 loop : -0.68 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 113 HIS 0.008 0.001 HIS K 107 PHE 0.016 0.001 PHE K 64 TYR 0.015 0.001 TYR J 50 ARG 0.010 0.000 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9178 (m-30) cc_final: 0.8425 (t0) REVERT: C 460 ASN cc_start: 0.9195 (m-40) cc_final: 0.8499 (m-40) REVERT: I 87 ARG cc_start: 0.7900 (mtm110) cc_final: 0.7595 (mtm110) REVERT: J 37 TYR cc_start: 0.7979 (m-80) cc_final: 0.7555 (m-80) REVERT: J 48 LEU cc_start: 0.7048 (mp) cc_final: 0.6719 (mm) REVERT: J 50 TYR cc_start: 0.5202 (p90) cc_final: 0.4948 (p90) REVERT: J 55 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7328 (mtt180) REVERT: K 25 SER cc_start: 0.7908 (t) cc_final: 0.7502 (m) REVERT: K 81 MET cc_start: 0.7473 (tmm) cc_final: 0.6392 (tmm) REVERT: K 95 TYR cc_start: 0.7200 (m-80) cc_final: 0.6646 (m-80) outliers start: 15 outliers final: 12 residues processed: 192 average time/residue: 0.2136 time to fit residues: 56.0209 Evaluate side-chains 187 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN I 6 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.113802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092058 restraints weight = 17529.768| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.01 r_work: 0.3265 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8584 Z= 0.196 Angle : 0.546 7.038 11654 Z= 0.288 Chirality : 0.045 0.195 1257 Planarity : 0.004 0.041 1498 Dihedral : 4.062 14.016 1185 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.62 % Allowed : 11.37 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.26), residues: 1058 helix: -3.93 (0.59), residues: 42 sheet: 0.17 (0.27), residues: 401 loop : -0.71 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.005 0.001 HIS K 107 PHE 0.013 0.001 PHE F 83 TYR 0.011 0.001 TYR J 92 ARG 0.010 0.001 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9166 (m-30) cc_final: 0.8745 (t0) REVERT: F 18 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7954 (ttp-110) REVERT: F 100 GLN cc_start: 0.8943 (mp10) cc_final: 0.8643 (mp-120) REVERT: I 46 GLU cc_start: 0.8363 (tt0) cc_final: 0.8134 (tt0) REVERT: I 62 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8738 (tp-100) REVERT: I 87 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7663 (mtm110) REVERT: J 37 TYR cc_start: 0.7963 (m-80) cc_final: 0.7461 (m-80) REVERT: J 48 LEU cc_start: 0.7161 (mp) cc_final: 0.6838 (mm) REVERT: J 55 ARG cc_start: 0.7587 (mtt180) cc_final: 0.7219 (mtt180) REVERT: K 25 SER cc_start: 0.7895 (t) cc_final: 0.7490 (m) REVERT: K 81 MET cc_start: 0.7561 (tmm) cc_final: 0.6429 (tmm) REVERT: K 95 TYR cc_start: 0.7172 (m-80) cc_final: 0.6564 (m-80) outliers start: 24 outliers final: 19 residues processed: 199 average time/residue: 0.2095 time to fit residues: 56.4193 Evaluate side-chains 196 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.0270 chunk 69 optimal weight: 1.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.111296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.090851 restraints weight = 17233.130| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.56 r_work: 0.3254 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 8584 Z= 0.391 Angle : 0.656 7.426 11654 Z= 0.347 Chirality : 0.048 0.199 1257 Planarity : 0.004 0.038 1498 Dihedral : 4.809 17.976 1185 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.50 % Allowed : 13.01 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.07 (0.26), residues: 1058 helix: -3.92 (0.59), residues: 42 sheet: -0.05 (0.27), residues: 406 loop : -0.91 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 36 HIS 0.003 0.001 HIS K 107 PHE 0.014 0.001 PHE F 83 TYR 0.016 0.002 TYR H 91 ARG 0.008 0.001 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8941 (m-30) cc_final: 0.8645 (t0) REVERT: F 18 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.8097 (ttp-110) REVERT: G 48 MET cc_start: 0.8408 (mtt) cc_final: 0.8188 (mtt) REVERT: J 37 TYR cc_start: 0.7856 (m-80) cc_final: 0.7551 (m-80) REVERT: J 48 LEU cc_start: 0.7787 (mp) cc_final: 0.7514 (mm) REVERT: K 25 SER cc_start: 0.7933 (t) cc_final: 0.7461 (m) REVERT: K 27 PHE cc_start: 0.6804 (p90) cc_final: 0.6431 (p90) REVERT: K 81 MET cc_start: 0.7801 (tmm) cc_final: 0.6629 (tmm) outliers start: 32 outliers final: 28 residues processed: 190 average time/residue: 0.2114 time to fit residues: 54.7426 Evaluate side-chains 190 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 17 ASP Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 14 optimal weight: 0.0970 chunk 78 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.112975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091124 restraints weight = 17542.456| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.18 r_work: 0.3246 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8584 Z= 0.169 Angle : 0.552 8.861 11654 Z= 0.289 Chirality : 0.044 0.171 1257 Planarity : 0.004 0.036 1498 Dihedral : 4.238 14.443 1185 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.40 % Allowed : 14.86 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.01 (0.26), residues: 1058 helix: -3.97 (0.59), residues: 42 sheet: -0.01 (0.27), residues: 404 loop : -0.86 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.009 0.001 HIS K 107 PHE 0.019 0.001 PHE F 83 TYR 0.012 0.001 TYR F 94 ARG 0.007 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9160 (m-30) cc_final: 0.8749 (t0) REVERT: F 55 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7504 (tm-30) REVERT: F 100 GLN cc_start: 0.8929 (mp10) cc_final: 0.8621 (mp-120) REVERT: G 48 MET cc_start: 0.8453 (mtt) cc_final: 0.8122 (mtt) REVERT: H 17 ASP cc_start: 0.8412 (t0) cc_final: 0.8179 (t0) REVERT: J 37 TYR cc_start: 0.7824 (m-80) cc_final: 0.7425 (m-80) REVERT: J 48 LEU cc_start: 0.7326 (mp) cc_final: 0.7054 (mm) REVERT: K 12 LYS cc_start: 0.7440 (mmmm) cc_final: 0.7047 (mmtp) REVERT: K 25 SER cc_start: 0.7890 (t) cc_final: 0.7525 (m) REVERT: K 29 PHE cc_start: 0.7711 (t80) cc_final: 0.7492 (t80) REVERT: K 81 MET cc_start: 0.7581 (tmm) cc_final: 0.6364 (tmm) outliers start: 22 outliers final: 17 residues processed: 195 average time/residue: 0.2115 time to fit residues: 56.2685 Evaluate side-chains 192 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.111159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.090759 restraints weight = 17371.061| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.55 r_work: 0.3250 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 8584 Z= 0.392 Angle : 0.661 8.149 11654 Z= 0.349 Chirality : 0.048 0.172 1257 Planarity : 0.005 0.039 1498 Dihedral : 4.814 17.901 1185 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.28 % Allowed : 15.74 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.23 (0.25), residues: 1058 helix: -3.94 (0.60), residues: 42 sheet: -0.18 (0.27), residues: 402 loop : -1.01 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 47 HIS 0.008 0.002 HIS K 107 PHE 0.014 0.001 PHE F 83 TYR 0.035 0.002 TYR H 94 ARG 0.006 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.8936 (m-30) cc_final: 0.8623 (t0) REVERT: F 18 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7221 (ttp-110) REVERT: F 55 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7987 (tm-30) REVERT: J 37 TYR cc_start: 0.7766 (m-80) cc_final: 0.7523 (m-80) REVERT: J 48 LEU cc_start: 0.7813 (mp) cc_final: 0.7500 (mm) REVERT: J 55 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7375 (mtm180) REVERT: K 12 LYS cc_start: 0.7535 (mmmm) cc_final: 0.7119 (mmtp) REVERT: K 25 SER cc_start: 0.7982 (t) cc_final: 0.7491 (m) REVERT: K 81 MET cc_start: 0.7797 (tmm) cc_final: 0.6616 (tmm) outliers start: 30 outliers final: 26 residues processed: 183 average time/residue: 0.2189 time to fit residues: 53.9033 Evaluate side-chains 188 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.112257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.090808 restraints weight = 17631.624| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.00 r_work: 0.3245 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8584 Z= 0.202 Angle : 0.577 8.722 11654 Z= 0.303 Chirality : 0.045 0.150 1257 Planarity : 0.004 0.035 1498 Dihedral : 4.367 15.768 1185 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.95 % Allowed : 15.85 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.23 (0.25), residues: 1058 helix: -4.19 (0.53), residues: 48 sheet: -0.13 (0.27), residues: 404 loop : -0.99 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 47 HIS 0.007 0.001 HIS K 107 PHE 0.018 0.001 PHE F 83 TYR 0.027 0.001 TYR H 94 ARG 0.007 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9147 (m-30) cc_final: 0.8738 (t0) REVERT: F 18 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6964 (ttp-110) REVERT: F 55 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7548 (tm-30) REVERT: F 94 TYR cc_start: 0.8550 (m-80) cc_final: 0.8347 (m-80) REVERT: F 100 GLN cc_start: 0.8932 (mp10) cc_final: 0.8674 (mp-120) REVERT: H 17 ASP cc_start: 0.8423 (t0) cc_final: 0.7870 (t0) REVERT: J 37 TYR cc_start: 0.7730 (m-80) cc_final: 0.7371 (m-80) REVERT: J 48 LEU cc_start: 0.7430 (mp) cc_final: 0.7127 (mm) REVERT: J 55 ARG cc_start: 0.7626 (mtt90) cc_final: 0.7314 (mtt90) REVERT: K 12 LYS cc_start: 0.7402 (mmmm) cc_final: 0.7021 (mmtp) REVERT: K 25 SER cc_start: 0.7917 (t) cc_final: 0.7467 (m) REVERT: K 81 MET cc_start: 0.7455 (tmm) cc_final: 0.6323 (tmm) outliers start: 27 outliers final: 25 residues processed: 185 average time/residue: 0.2122 time to fit residues: 53.3135 Evaluate side-chains 189 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 0.0570 chunk 30 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 0.0570 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.114888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.093039 restraints weight = 17565.779| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.04 r_work: 0.3281 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8584 Z= 0.156 Angle : 0.560 8.802 11654 Z= 0.290 Chirality : 0.044 0.163 1257 Planarity : 0.004 0.037 1498 Dihedral : 4.047 14.494 1185 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.30 % Allowed : 17.05 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.11 (0.26), residues: 1058 helix: -4.16 (0.54), residues: 48 sheet: -0.05 (0.27), residues: 403 loop : -0.90 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP K 47 HIS 0.006 0.001 HIS K 107 PHE 0.018 0.001 PHE F 83 TYR 0.021 0.001 TYR H 94 ARG 0.011 0.000 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9131 (m-30) cc_final: 0.8688 (t0) REVERT: F 55 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7542 (tm-30) REVERT: F 100 GLN cc_start: 0.8942 (mp10) cc_final: 0.8658 (mp-120) REVERT: G 91 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7799 (t) REVERT: H 17 ASP cc_start: 0.8364 (t0) cc_final: 0.7853 (t0) REVERT: I 87 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7634 (mtm110) REVERT: J 37 TYR cc_start: 0.7735 (m-80) cc_final: 0.7372 (m-80) REVERT: J 48 LEU cc_start: 0.7315 (mp) cc_final: 0.6995 (mm) REVERT: J 55 ARG cc_start: 0.7629 (mtt90) cc_final: 0.7228 (mtt90) REVERT: K 12 LYS cc_start: 0.7378 (mmmm) cc_final: 0.6985 (mmtp) REVERT: K 25 SER cc_start: 0.7922 (t) cc_final: 0.7445 (m) REVERT: K 47 TRP cc_start: 0.6611 (t60) cc_final: 0.6375 (t60) REVERT: K 81 MET cc_start: 0.7463 (tmm) cc_final: 0.6253 (tmm) outliers start: 21 outliers final: 20 residues processed: 193 average time/residue: 0.2117 time to fit residues: 55.4380 Evaluate side-chains 193 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.111747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090186 restraints weight = 17651.074| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.99 r_work: 0.3233 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8584 Z= 0.271 Angle : 0.616 9.296 11654 Z= 0.323 Chirality : 0.046 0.157 1257 Planarity : 0.004 0.046 1498 Dihedral : 4.420 17.491 1185 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.62 % Allowed : 17.16 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.21 (0.26), residues: 1058 helix: -4.17 (0.53), residues: 48 sheet: -0.14 (0.27), residues: 404 loop : -0.95 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP K 47 HIS 0.006 0.001 HIS K 107 PHE 0.017 0.001 PHE F 83 TYR 0.026 0.002 TYR H 94 ARG 0.009 0.001 ARG I 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9121 (m-30) cc_final: 0.8698 (t0) REVERT: F 55 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7545 (tm-30) REVERT: F 94 TYR cc_start: 0.8627 (m-80) cc_final: 0.8360 (m-80) REVERT: F 100 GLN cc_start: 0.8926 (mp10) cc_final: 0.8634 (mp-120) REVERT: H 17 ASP cc_start: 0.8368 (t0) cc_final: 0.7852 (t0) REVERT: J 48 LEU cc_start: 0.7300 (mp) cc_final: 0.7015 (mm) REVERT: J 55 ARG cc_start: 0.7539 (mtt90) cc_final: 0.7187 (mtt90) REVERT: K 12 LYS cc_start: 0.7425 (mmmm) cc_final: 0.7046 (mmtp) REVERT: K 25 SER cc_start: 0.8012 (t) cc_final: 0.7734 (m) REVERT: K 81 MET cc_start: 0.7380 (tmm) cc_final: 0.6228 (tmm) outliers start: 24 outliers final: 24 residues processed: 179 average time/residue: 0.2138 time to fit residues: 52.1179 Evaluate side-chains 182 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.113283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091188 restraints weight = 17599.917| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.19 r_work: 0.3254 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8584 Z= 0.175 Angle : 0.577 9.754 11654 Z= 0.300 Chirality : 0.045 0.167 1257 Planarity : 0.004 0.037 1498 Dihedral : 4.207 15.884 1185 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.40 % Allowed : 17.70 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.16 (0.26), residues: 1058 helix: -4.16 (0.54), residues: 48 sheet: -0.12 (0.27), residues: 404 loop : -0.90 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP K 47 HIS 0.006 0.001 HIS K 107 PHE 0.019 0.001 PHE F 83 TYR 0.023 0.001 TYR H 94 ARG 0.009 0.000 ARG I 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4463.80 seconds wall clock time: 80 minutes 10.08 seconds (4810.08 seconds total)