Starting phenix.real_space_refine on Fri Sep 27 01:23:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/09_2024/7joa_22409.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/09_2024/7joa_22409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/09_2024/7joa_22409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/09_2024/7joa_22409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/09_2024/7joa_22409.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/09_2024/7joa_22409.cif" } resolution = 3.3 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 25 5.16 5 C 8556 2.51 5 N 2771 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14994 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2960 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 342} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13969 SG CYS K 384 23.933 65.763 50.961 1.00 90.89 S ATOM 13975 SG CYS K 385 24.055 69.257 48.730 1.00 83.30 S ATOM 14020 SG CYS K 392 23.001 70.170 51.751 1.00 87.81 S Time building chain proxies: 8.66, per 1000 atoms: 0.58 Number of scatterers: 14994 At special positions: 0 Unit cell: (150.15, 110.11, 116.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 25 16.00 P 290 15.00 O 3351 8.00 N 2771 7.00 C 8556 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: 3.33 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 385 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 392 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 378 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 384 " Number of angles added : 3 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 63.2% alpha, 7.4% beta 138 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 6.05 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.659A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.526A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.609A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.774A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.119A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.529A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.616A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.535A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.643A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.898A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.587A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.105A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.949A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.581A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.702A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.779A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.188A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.587A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.617A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.535A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.642A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.898A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.585A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.104A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 185 removed outlier: 3.797A pdb=" N ARG K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS K 162 " --> pdb=" O ARG K 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA K 167 " --> pdb=" O ASP K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 250 No H-bonds generated for 'chain 'K' and resid 248 through 250' Processing helix chain 'K' and resid 258 through 276 removed outlier: 3.705A pdb=" N GLU K 276 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 325 removed outlier: 4.399A pdb=" N GLU K 324 " --> pdb=" O SER K 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 342 removed outlier: 4.377A pdb=" N VAL K 336 " --> pdb=" O LEU K 332 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG K 337 " --> pdb=" O GLY K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 377 Processing helix chain 'K' and resid 393 through 412 Processing helix chain 'K' and resid 413 through 416 Processing helix chain 'K' and resid 419 through 434 removed outlier: 3.847A pdb=" N VAL K 423 " --> pdb=" O CYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 443 removed outlier: 4.038A pdb=" N ASP K 441 " --> pdb=" O SER K 438 " (cutoff:3.500A) Proline residue: K 442 - end of helix Processing helix chain 'K' and resid 444 through 463 removed outlier: 3.525A pdb=" N PHE K 455 " --> pdb=" O LYS K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 499 Processing helix chain 'K' and resid 500 through 505 removed outlier: 5.995A pdb=" N ILE K 503 " --> pdb=" O GLY K 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.193A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.598A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 8.193A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.953A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.526A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.500A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 8.045A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 193 through 195 removed outlier: 4.626A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP K 281 " --> pdb=" O ARG K 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 193 through 195 removed outlier: 4.626A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU K 310 " --> pdb=" O PRO K 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 223 through 227 Processing sheet with id=AB3, first strand: chain 'K' and resid 252 through 253 507 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 6.89 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2781 1.33 - 1.45: 4959 1.45 - 1.57: 7503 1.57 - 1.69: 578 1.69 - 1.81: 40 Bond restraints: 15861 Sorted by residual: bond pdb=" CA GLN A 55 " pdb=" C GLN A 55 " ideal model delta sigma weight residual 1.524 1.471 0.052 2.25e-02 1.98e+03 5.37e+00 bond pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 1.523 1.496 0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C3' DG I 27 " pdb=" O3' DG I 27 " ideal model delta sigma weight residual 1.422 1.381 0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CG ARG F 39 " pdb=" CD ARG F 39 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.84e+00 bond pdb=" CB VAL F 43 " pdb=" CG2 VAL F 43 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 ... (remaining 15856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 21417 1.61 - 3.21: 1107 3.21 - 4.82: 84 4.82 - 6.43: 21 6.43 - 8.03: 5 Bond angle restraints: 22634 Sorted by residual: angle pdb=" N TRP K 431 " pdb=" CA TRP K 431 " pdb=" CB TRP K 431 " ideal model delta sigma weight residual 110.28 116.47 -6.19 1.55e+00 4.16e-01 1.60e+01 angle pdb=" C TYR A 54 " pdb=" N GLN A 55 " pdb=" CA GLN A 55 " ideal model delta sigma weight residual 122.55 114.52 8.03 2.03e+00 2.43e-01 1.57e+01 angle pdb=" C PHE E 104 " pdb=" N GLU E 105 " pdb=" CA GLU E 105 " ideal model delta sigma weight residual 120.29 115.67 4.62 1.42e+00 4.96e-01 1.06e+01 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 120.60 -7.90 3.00e+00 1.11e-01 6.93e+00 angle pdb=" C ARG K 461 " pdb=" N THR K 462 " pdb=" CA THR K 462 " ideal model delta sigma weight residual 122.38 117.80 4.58 1.81e+00 3.05e-01 6.39e+00 ... (remaining 22629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.59: 7315 33.59 - 67.18: 1493 67.18 - 100.77: 34 100.77 - 134.35: 0 134.35 - 167.94: 1 Dihedral angle restraints: 8843 sinusoidal: 5568 harmonic: 3275 Sorted by residual: dihedral pdb=" CA ASN K 377 " pdb=" C ASN K 377 " pdb=" N HIS K 378 " pdb=" CA HIS K 378 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA HIS D 49 " pdb=" C HIS D 49 " pdb=" N PRO D 50 " pdb=" CA PRO D 50 " ideal model delta harmonic sigma weight residual 180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA HIS H 49 " pdb=" C HIS H 49 " pdb=" N PRO H 50 " pdb=" CA PRO H 50 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 8840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2318 0.073 - 0.146: 223 0.146 - 0.219: 5 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CB ILE K 427 " pdb=" CA ILE K 427 " pdb=" CG1 ILE K 427 " pdb=" CG2 ILE K 427 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB ILE K 269 " pdb=" CA ILE K 269 " pdb=" CG1 ILE K 269 " pdb=" CG2 ILE K 269 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA PHE E 104 " pdb=" N PHE E 104 " pdb=" C PHE E 104 " pdb=" CB PHE E 104 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 2544 not shown) Planarity restraints: 1861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP K 431 " 0.041 2.00e-02 2.50e+03 4.25e-02 4.52e+01 pdb=" CG TRP K 431 " -0.111 2.00e-02 2.50e+03 pdb=" CD1 TRP K 431 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP K 431 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP K 431 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP K 431 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 431 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 431 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 431 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP K 431 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 454 " 0.016 2.00e-02 2.50e+03 3.10e-02 9.64e+00 pdb=" C ALA K 454 " -0.054 2.00e-02 2.50e+03 pdb=" O ALA K 454 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE K 455 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER K 446 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C SER K 446 " -0.052 2.00e-02 2.50e+03 pdb=" O SER K 446 " 0.020 2.00e-02 2.50e+03 pdb=" N SER K 447 " 0.018 2.00e-02 2.50e+03 ... (remaining 1858 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1970 2.74 - 3.28: 13642 3.28 - 3.82: 26254 3.82 - 4.36: 30171 4.36 - 4.90: 45898 Nonbonded interactions: 117935 Sorted by model distance: nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 241 " model vdw 2.206 3.120 nonbonded pdb=" O ARG E 129 " pdb=" NH1 ARG E 129 " model vdw 2.232 3.120 nonbonded pdb=" OE2 GLU K 494 " pdb=" ND2 ASN K 498 " model vdw 2.241 3.120 nonbonded pdb=" NH2 ARG K 394 " pdb=" OD1 ASP K 437 " model vdw 2.249 3.120 nonbonded pdb=" O ILE C 78 " pdb=" OG SER D 55 " model vdw 2.252 3.040 ... (remaining 117930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.720 Find NCS groups from input model: 0.290 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.009 0.052 15861 Z= 0.521 Angle : 0.780 8.033 22634 Z= 0.464 Chirality : 0.045 0.365 2547 Planarity : 0.006 0.054 1861 Dihedral : 25.945 167.942 6725 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.33 (0.24), residues: 1107 helix: 0.88 (0.20), residues: 655 sheet: -0.47 (0.64), residues: 57 loop : -2.08 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.111 0.008 TRP K 431 HIS 0.004 0.001 HIS E 39 PHE 0.029 0.003 PHE E 104 TYR 0.017 0.002 TYR K 468 ARG 0.010 0.001 ARG K 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8067 (m-30) cc_final: 0.7862 (m-30) REVERT: G 74 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7246 (mmmt) REVERT: G 110 ASN cc_start: 0.8076 (t0) cc_final: 0.7854 (t0) REVERT: H 88 THR cc_start: 0.8962 (t) cc_final: 0.8630 (m) REVERT: H 90 THR cc_start: 0.8640 (m) cc_final: 0.8432 (p) REVERT: K 273 GLU cc_start: 0.3902 (mm-30) cc_final: 0.3206 (mm-30) REVERT: K 428 PHE cc_start: 0.6931 (m-10) cc_final: 0.6671 (m-10) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.4382 time to fit residues: 134.9045 Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 25 ASN C 38 ASN F 25 ASN F 75 HIS G 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15861 Z= 0.190 Angle : 0.561 7.034 22634 Z= 0.332 Chirality : 0.035 0.123 2547 Planarity : 0.004 0.049 1861 Dihedral : 28.842 170.722 4411 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.34 % Allowed : 6.19 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.36 (0.25), residues: 1107 helix: 2.42 (0.20), residues: 654 sheet: 0.20 (0.72), residues: 52 loop : -1.74 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP K 431 HIS 0.004 0.001 HIS K 429 PHE 0.020 0.002 PHE K 488 TYR 0.015 0.001 TYR K 346 ARG 0.005 0.001 ARG K 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.294 Fit side-chains REVERT: C 95 LYS cc_start: 0.8958 (ttmm) cc_final: 0.8456 (tttm) REVERT: E 42 ARG cc_start: 0.8215 (mtp-110) cc_final: 0.7987 (mtp-110) REVERT: G 74 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7326 (mmmt) REVERT: G 95 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8493 (tttm) REVERT: K 183 GLN cc_start: 0.6682 (mt0) cc_final: 0.6339 (tm-30) REVERT: K 273 GLU cc_start: 0.3640 (mm-30) cc_final: 0.3028 (mm-30) REVERT: K 428 PHE cc_start: 0.6913 (m-10) cc_final: 0.6633 (m-10) outliers start: 13 outliers final: 10 residues processed: 161 average time/residue: 0.3798 time to fit residues: 81.4897 Evaluate side-chains 134 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 230 GLU Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15861 Z= 0.247 Angle : 0.580 10.655 22634 Z= 0.338 Chirality : 0.037 0.131 2547 Planarity : 0.004 0.048 1861 Dihedral : 28.992 174.347 4411 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.65 % Allowed : 8.05 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.48 (0.26), residues: 1107 helix: 2.50 (0.20), residues: 661 sheet: 0.42 (0.72), residues: 52 loop : -1.73 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 431 HIS 0.004 0.001 HIS K 369 PHE 0.021 0.002 PHE G 25 TYR 0.013 0.002 TYR G 57 ARG 0.005 0.001 ARG K 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.359 Fit side-chains REVERT: C 95 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8511 (tttm) REVERT: D 93 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: G 74 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7434 (mmmt) REVERT: G 95 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8548 (tttm) REVERT: K 183 GLN cc_start: 0.6525 (mt0) cc_final: 0.6244 (tm-30) REVERT: K 273 GLU cc_start: 0.3561 (mm-30) cc_final: 0.3146 (mm-30) REVERT: K 482 ASP cc_start: 0.2781 (t0) cc_final: 0.2109 (m-30) REVERT: K 496 GLU cc_start: 0.2368 (mm-30) cc_final: 0.1191 (mm-30) outliers start: 16 outliers final: 11 residues processed: 141 average time/residue: 0.3764 time to fit residues: 71.1653 Evaluate side-chains 135 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15861 Z= 0.300 Angle : 0.600 7.858 22634 Z= 0.350 Chirality : 0.038 0.132 2547 Planarity : 0.004 0.039 1861 Dihedral : 28.970 177.088 4411 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.65 % Allowed : 10.63 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.37 (0.25), residues: 1107 helix: 2.26 (0.20), residues: 670 sheet: 0.38 (0.69), residues: 52 loop : -1.59 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP K 431 HIS 0.004 0.001 HIS E 39 PHE 0.023 0.002 PHE C 25 TYR 0.013 0.002 TYR G 57 ARG 0.004 0.001 ARG K 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.119 Fit side-chains REVERT: A 56 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8537 (tttp) REVERT: C 42 ARG cc_start: 0.8912 (ptm-80) cc_final: 0.8504 (mtm110) REVERT: C 95 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8541 (tttm) REVERT: D 93 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: E 42 ARG cc_start: 0.8324 (mtp-110) cc_final: 0.8067 (mtp-110) REVERT: E 56 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8541 (tttp) REVERT: G 74 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7572 (mmmt) REVERT: G 95 LYS cc_start: 0.9057 (ttpt) cc_final: 0.8557 (tttm) REVERT: K 183 GLN cc_start: 0.6568 (mt0) cc_final: 0.6278 (tm-30) REVERT: K 273 GLU cc_start: 0.3883 (mm-30) cc_final: 0.3189 (mm-30) REVERT: K 482 ASP cc_start: 0.2924 (t0) cc_final: 0.2350 (m-30) REVERT: K 491 LYS cc_start: 0.4935 (mttt) cc_final: 0.4691 (ptmt) outliers start: 16 outliers final: 10 residues processed: 137 average time/residue: 0.3522 time to fit residues: 65.2497 Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN E 68 GLN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15861 Z= 0.230 Angle : 0.576 10.248 22634 Z= 0.336 Chirality : 0.036 0.146 2547 Planarity : 0.004 0.039 1861 Dihedral : 28.919 176.622 4411 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.34 % Allowed : 11.66 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.53 (0.25), residues: 1107 helix: 2.38 (0.20), residues: 670 sheet: 0.57 (0.71), residues: 52 loop : -1.51 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 431 HIS 0.004 0.001 HIS K 250 PHE 0.013 0.002 PHE K 449 TYR 0.011 0.001 TYR K 346 ARG 0.006 0.000 ARG K 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.263 Fit side-chains REVERT: A 42 ARG cc_start: 0.8417 (mtp-110) cc_final: 0.8208 (mtp-110) REVERT: C 95 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8570 (tttm) REVERT: D 93 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: E 42 ARG cc_start: 0.8264 (mtp-110) cc_final: 0.7990 (mtp-110) REVERT: G 74 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7591 (mmmt) REVERT: G 95 LYS cc_start: 0.9057 (ttpt) cc_final: 0.8571 (tttm) REVERT: K 183 GLN cc_start: 0.6555 (mt0) cc_final: 0.6196 (tm-30) REVERT: K 273 GLU cc_start: 0.3858 (mm-30) cc_final: 0.3434 (mt-10) REVERT: K 322 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7812 (p) REVERT: K 482 ASP cc_start: 0.2899 (t0) cc_final: 0.2336 (m-30) REVERT: K 491 LYS cc_start: 0.4976 (mttt) cc_final: 0.4726 (ptmt) REVERT: K 496 GLU cc_start: 0.2702 (mm-30) cc_final: 0.1717 (mm-30) outliers start: 13 outliers final: 9 residues processed: 130 average time/residue: 0.3664 time to fit residues: 64.1749 Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN K 498 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15861 Z= 0.175 Angle : 0.528 9.584 22634 Z= 0.313 Chirality : 0.034 0.129 2547 Planarity : 0.004 0.035 1861 Dihedral : 28.733 175.981 4411 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.55 % Allowed : 12.28 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1107 helix: 2.60 (0.20), residues: 670 sheet: 0.80 (0.69), residues: 52 loop : -1.42 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 431 HIS 0.004 0.001 HIS K 369 PHE 0.009 0.001 PHE K 449 TYR 0.009 0.001 TYR K 346 ARG 0.009 0.000 ARG K 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.483 Fit side-chains REVERT: A 42 ARG cc_start: 0.8370 (mtp-110) cc_final: 0.8154 (mtp-110) REVERT: C 95 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8549 (tttm) REVERT: D 33 ARG cc_start: 0.7209 (ptt180) cc_final: 0.6999 (ptt180) REVERT: D 93 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: G 42 ARG cc_start: 0.8891 (ptm-80) cc_final: 0.8537 (mtm110) REVERT: G 74 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7452 (mmmt) REVERT: G 95 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8548 (tttm) REVERT: K 183 GLN cc_start: 0.6476 (mt0) cc_final: 0.6196 (tm-30) REVERT: K 273 GLU cc_start: 0.3702 (mm-30) cc_final: 0.3464 (mt-10) REVERT: K 322 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7712 (p) REVERT: K 482 ASP cc_start: 0.2779 (t0) cc_final: 0.2282 (m-30) REVERT: K 496 GLU cc_start: 0.2619 (mm-30) cc_final: 0.1644 (mm-30) outliers start: 15 outliers final: 10 residues processed: 129 average time/residue: 0.4267 time to fit residues: 75.1202 Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15861 Z= 0.250 Angle : 0.561 8.102 22634 Z= 0.329 Chirality : 0.036 0.135 2547 Planarity : 0.004 0.036 1861 Dihedral : 28.796 177.298 4411 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.55 % Allowed : 13.31 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.76 (0.25), residues: 1107 helix: 2.54 (0.20), residues: 672 sheet: 0.77 (0.68), residues: 52 loop : -1.39 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP K 431 HIS 0.005 0.001 HIS K 369 PHE 0.014 0.002 PHE C 25 TYR 0.010 0.001 TYR K 346 ARG 0.009 0.000 ARG K 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.208 Fit side-chains REVERT: A 42 ARG cc_start: 0.8372 (mtp-110) cc_final: 0.8146 (mtp-110) REVERT: A 56 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8514 (tttp) REVERT: C 42 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8464 (mtm110) REVERT: C 95 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8552 (tttm) REVERT: D 33 ARG cc_start: 0.7313 (ptt180) cc_final: 0.7108 (ptt180) REVERT: D 93 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: E 42 ARG cc_start: 0.8260 (mtp-110) cc_final: 0.7983 (mtp-110) REVERT: G 74 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7516 (mmmt) REVERT: G 95 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8544 (tttm) REVERT: H 68 ASP cc_start: 0.8422 (t0) cc_final: 0.8169 (t0) REVERT: K 183 GLN cc_start: 0.6424 (mt0) cc_final: 0.6151 (tm-30) REVERT: K 242 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8113 (mm) REVERT: K 273 GLU cc_start: 0.3844 (mm-30) cc_final: 0.3635 (mt-10) REVERT: K 322 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7739 (p) REVERT: K 482 ASP cc_start: 0.2868 (t0) cc_final: 0.2374 (m-30) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 0.3519 time to fit residues: 61.3517 Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15861 Z= 0.274 Angle : 0.587 6.927 22634 Z= 0.343 Chirality : 0.037 0.129 2547 Planarity : 0.004 0.036 1861 Dihedral : 28.844 178.259 4411 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.34 % Allowed : 13.73 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1107 helix: 2.47 (0.20), residues: 670 sheet: 0.73 (0.66), residues: 52 loop : -1.41 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP K 431 HIS 0.005 0.001 HIS K 369 PHE 0.013 0.002 PHE C 25 TYR 0.013 0.002 TYR K 346 ARG 0.006 0.000 ARG K 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.541 Fit side-chains REVERT: A 42 ARG cc_start: 0.8369 (mtp-110) cc_final: 0.8163 (mtp-110) REVERT: C 42 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8447 (mtm110) REVERT: C 95 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8556 (tttm) REVERT: D 33 ARG cc_start: 0.7371 (ptt180) cc_final: 0.7122 (ptt180) REVERT: D 93 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: E 42 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7974 (mtp-110) REVERT: G 74 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7577 (mmmt) REVERT: G 95 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8548 (tttm) REVERT: H 68 ASP cc_start: 0.8451 (t0) cc_final: 0.8192 (t0) REVERT: H 86 ARG cc_start: 0.8238 (mmt90) cc_final: 0.7973 (mpt-90) REVERT: K 183 GLN cc_start: 0.6418 (mt0) cc_final: 0.6118 (tm-30) REVERT: K 482 ASP cc_start: 0.2875 (t0) cc_final: 0.2370 (m-30) REVERT: K 496 GLU cc_start: 0.2296 (mm-30) cc_final: 0.1881 (mm-30) outliers start: 13 outliers final: 10 residues processed: 126 average time/residue: 0.3670 time to fit residues: 62.5462 Evaluate side-chains 125 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15861 Z= 0.354 Angle : 0.641 11.763 22634 Z= 0.369 Chirality : 0.040 0.140 2547 Planarity : 0.005 0.038 1861 Dihedral : 28.990 179.444 4411 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.24 % Allowed : 13.52 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.38 (0.25), residues: 1107 helix: 2.21 (0.20), residues: 672 sheet: 0.76 (0.65), residues: 52 loop : -1.52 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP K 431 HIS 0.006 0.001 HIS E 39 PHE 0.019 0.002 PHE C 25 TYR 0.014 0.002 TYR K 346 ARG 0.007 0.001 ARG K 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.139 Fit side-chains REVERT: A 42 ARG cc_start: 0.8375 (mtp-110) cc_final: 0.8166 (mtp-110) REVERT: A 56 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8573 (tttp) REVERT: C 42 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8056 (ptm-80) REVERT: C 95 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8570 (tttm) REVERT: D 33 ARG cc_start: 0.7411 (ptt180) cc_final: 0.7129 (ptt180) REVERT: D 93 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: E 42 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.8002 (mtp-110) REVERT: G 74 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7569 (mmmt) REVERT: G 95 LYS cc_start: 0.9069 (ttpt) cc_final: 0.8530 (tttm) REVERT: H 86 ARG cc_start: 0.8275 (mmt90) cc_final: 0.8010 (mpt-90) REVERT: K 183 GLN cc_start: 0.6488 (mt0) cc_final: 0.6083 (tm-30) outliers start: 12 outliers final: 10 residues processed: 124 average time/residue: 0.4007 time to fit residues: 67.6310 Evaluate side-chains 125 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 85 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15861 Z= 0.190 Angle : 0.546 11.695 22634 Z= 0.321 Chirality : 0.035 0.125 2547 Planarity : 0.004 0.037 1861 Dihedral : 28.658 177.102 4411 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.03 % Allowed : 13.93 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.76 (0.25), residues: 1107 helix: 2.52 (0.20), residues: 671 sheet: 0.93 (0.67), residues: 52 loop : -1.39 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP K 431 HIS 0.005 0.001 HIS K 369 PHE 0.009 0.001 PHE G 25 TYR 0.009 0.001 TYR K 346 ARG 0.007 0.000 ARG K 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.342 Fit side-chains REVERT: A 42 ARG cc_start: 0.8343 (mtp-110) cc_final: 0.8113 (mtp-110) REVERT: A 56 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8547 (tttp) REVERT: C 42 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8413 (mtm110) REVERT: C 95 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8534 (tttm) REVERT: D 33 ARG cc_start: 0.7318 (ptt180) cc_final: 0.6999 (ptt180) REVERT: E 42 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7995 (mtp-110) REVERT: G 74 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7549 (mmmt) REVERT: G 95 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8532 (tttm) REVERT: H 68 ASP cc_start: 0.8563 (t0) cc_final: 0.8357 (t0) REVERT: K 183 GLN cc_start: 0.6380 (mt0) cc_final: 0.6096 (tm-30) REVERT: K 322 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7588 (p) REVERT: K 496 GLU cc_start: 0.2364 (mm-30) cc_final: 0.1341 (mm-30) outliers start: 10 outliers final: 8 residues processed: 120 average time/residue: 0.3830 time to fit residues: 61.9730 Evaluate side-chains 116 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 322 THR Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.145478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105027 restraints weight = 23625.228| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.34 r_work: 0.2958 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15861 Z= 0.209 Angle : 0.556 11.712 22634 Z= 0.326 Chirality : 0.035 0.169 2547 Planarity : 0.004 0.035 1861 Dihedral : 28.718 178.007 4411 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.14 % Allowed : 13.93 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.83 (0.25), residues: 1107 helix: 2.63 (0.20), residues: 665 sheet: 1.03 (0.67), residues: 52 loop : -1.41 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP K 431 HIS 0.006 0.001 HIS K 369 PHE 0.011 0.001 PHE C 25 TYR 0.010 0.001 TYR K 346 ARG 0.007 0.000 ARG K 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2663.76 seconds wall clock time: 48 minutes 18.20 seconds (2898.20 seconds total)