Starting phenix.real_space_refine on Tue Apr 9 00:56:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5a_22047/04_2024/6x5a_22047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5a_22047/04_2024/6x5a_22047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5a_22047/04_2024/6x5a_22047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5a_22047/04_2024/6x5a_22047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5a_22047/04_2024/6x5a_22047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5a_22047/04_2024/6x5a_22047.pdb" } resolution = 4.36 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= 0.002 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 288 5.49 5 S 23 5.16 5 C 8541 2.51 5 N 2764 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "K ASP 163": "OD1" <-> "OD2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K GLU 193": "OE1" <-> "OE2" Residue "K TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 213": "OD1" <-> "OD2" Residue "K PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 241": "NH1" <-> "NH2" Residue "K ARG 244": "NH1" <-> "NH2" Residue "K PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 273": "OE1" <-> "OE2" Residue "K GLU 276": "OE1" <-> "OE2" Residue "K GLU 285": "OE1" <-> "OE2" Residue "K ARG 299": "NH1" <-> "NH2" Residue "K GLU 303": "OE1" <-> "OE2" Residue "K ARG 341": "NH1" <-> "NH2" Residue "K ARG 342": "NH1" <-> "NH2" Residue "K GLU 343": "OE1" <-> "OE2" Residue "K GLU 371": "OE1" <-> "OE2" Residue "K GLU 381": "OE1" <-> "OE2" Residue "K GLU 386": "OE1" <-> "OE2" Residue "K GLU 406": "OE1" <-> "OE2" Residue "K ASP 416": "OD1" <-> "OD2" Residue "K PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 434": "OD1" <-> "OD2" Residue "K ASP 437": "OD1" <-> "OD2" Residue "K GLU 458": "OE1" <-> "OE2" Residue "K TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 505": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14963 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 637 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} 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: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2954 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2985 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2994 Unusual residues: {' ZN': 1} Classifications: {'peptide': 362, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 345, None: 1} Not linked: pdbres="LEU K 507 " pdbres=" ZN K 601 " Time building chain proxies: 7.46, per 1000 atoms: 0.50 Number of scatterers: 14963 At special positions: 0 Unit cell: (129.47, 116.63, 133.75, 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 23 16.00 P 288 15.00 O 3346 8.00 N 2764 7.00 C 8541 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 - 3.50 Amino acid : False - 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: 8.27 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 378 " 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 62.9% alpha, 8.2% beta 142 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 6.84 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.687A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.715A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.524A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.254A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.836A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.878A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.592A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.858A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.687A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.715A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.524A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.048A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.599A 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 26 through 36 removed outlier: 3.628A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.845A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.502A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 57 through 84 removed outlier: 3.629A pdb=" N ASN H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.575A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 183 removed outlier: 3.906A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (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 Processing helix chain 'K' and resid 319 through 323 Processing helix chain 'K' and resid 333 through 342 removed outlier: 3.666A 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 419 through 434 removed outlier: 4.352A pdb=" N VAL K 423 " --> pdb=" O CYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 440 Processing helix chain 'K' and resid 441 through 443 No H-bonds generated for 'chain 'K' and resid 441 through 443' Processing helix chain 'K' and resid 444 through 462 removed outlier: 3.510A pdb=" N THR K 462 " --> pdb=" O GLU K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 499 Processing helix chain 'K' and resid 500 through 506 removed outlier: 6.087A pdb=" N ILE K 503 " --> pdb=" O GLY K 500 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS K 506 " --> pdb=" O ILE K 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.886A 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 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: 7.451A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.255A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.295A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.527A pdb=" N ILE G 78 " --> pdb=" O GLY H 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 192 through 195 removed outlier: 3.978A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU K 310 " --> pdb=" O PRO K 349 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 192 through 195 removed outlier: 3.978A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL K 294 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR K 295 " --> pdb=" O GLU K 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 252 through 253 529 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 8.68 Time building geometry restraints manager: 8.77 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: 3189 1.33 - 1.45: 4638 1.45 - 1.57: 7387 1.57 - 1.69: 577 1.69 - 1.81: 38 Bond restraints: 15829 Sorted by residual: bond pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " ideal model delta sigma weight residual 1.422 1.361 0.061 3.00e-02 1.11e+03 4.20e+00 bond pdb=" CB ILE K 493 " pdb=" CG2 ILE K 493 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.13e+00 bond pdb=" CG ARG K 177 " pdb=" CD ARG K 177 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.22e+00 bond pdb=" C LEU D 101 " pdb=" N LEU D 102 " ideal model delta sigma weight residual 1.340 1.237 0.103 5.87e-02 2.90e+02 3.09e+00 bond pdb=" C LEU K 326 " pdb=" O LEU K 326 " ideal model delta sigma weight residual 1.233 1.225 0.008 4.80e-03 4.34e+04 3.01e+00 ... (remaining 15824 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.28: 1336 105.28 - 112.47: 8717 112.47 - 119.66: 5297 119.66 - 126.85: 6434 126.85 - 134.04: 807 Bond angle restraints: 22591 Sorted by residual: angle pdb=" CA ARG K 299 " pdb=" CB ARG K 299 " pdb=" CG ARG K 299 " ideal model delta sigma weight residual 114.10 123.36 -9.26 2.00e+00 2.50e-01 2.14e+01 angle pdb=" CA LYS K 409 " pdb=" CB LYS K 409 " pdb=" CG LYS K 409 " ideal model delta sigma weight residual 114.10 122.79 -8.69 2.00e+00 2.50e-01 1.89e+01 angle pdb=" CA LYS K 391 " pdb=" CB LYS K 391 " pdb=" CG LYS K 391 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" N LYS K 160 " pdb=" CA LYS K 160 " pdb=" C LYS K 160 " ideal model delta sigma weight residual 111.02 106.37 4.65 1.22e+00 6.72e-01 1.45e+01 angle pdb=" CB ARG K 244 " pdb=" CG ARG K 244 " pdb=" CD ARG K 244 " ideal model delta sigma weight residual 111.30 119.99 -8.69 2.30e+00 1.89e-01 1.43e+01 ... (remaining 22586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 7272 35.36 - 70.72: 1526 70.72 - 106.08: 23 106.08 - 141.43: 1 141.43 - 176.79: 2 Dihedral angle restraints: 8824 sinusoidal: 5557 harmonic: 3267 Sorted by residual: dihedral pdb=" CA LYS K 353 " pdb=" C LYS K 353 " pdb=" N ASP K 354 " pdb=" CA ASP K 354 " ideal model delta harmonic sigma weight residual 180.00 -137.45 -42.55 0 5.00e+00 4.00e-02 7.24e+01 dihedral pdb=" CA LYS A 37 " pdb=" C LYS A 37 " pdb=" N PRO A 38 " pdb=" CA PRO A 38 " ideal model delta harmonic sigma weight residual -180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA LYS E 37 " pdb=" C LYS E 37 " pdb=" N PRO E 38 " pdb=" CA PRO E 38 " ideal model delta harmonic sigma weight residual 180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 8821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1715 0.045 - 0.090: 671 0.090 - 0.135: 127 0.135 - 0.180: 22 0.180 - 0.226: 5 Chirality restraints: 2540 Sorted by residual: chirality pdb=" CG LEU K 415 " pdb=" CB LEU K 415 " pdb=" CD1 LEU K 415 " pdb=" CD2 LEU K 415 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE B 50 " pdb=" CA ILE B 50 " pdb=" CG1 ILE B 50 " pdb=" CG2 ILE B 50 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1' DC I 25 " pdb=" O4' DC I 25 " pdb=" C2' DC I 25 " pdb=" N1 DC I 25 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 2537 not shown) Planarity restraints: 1858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 59 " -0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" CD GLU E 59 " 0.071 2.00e-02 2.50e+03 pdb=" OE1 GLU E 59 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU E 59 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 59 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" CD GLU A 59 " 0.071 2.00e-02 2.50e+03 pdb=" OE1 GLU A 59 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU A 59 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 32 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C PRO F 32 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO F 32 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA F 33 " 0.022 2.00e-02 2.50e+03 ... (remaining 1855 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 535 2.67 - 3.22: 13722 3.22 - 3.78: 27799 3.78 - 4.34: 35201 4.34 - 4.90: 51239 Nonbonded interactions: 128496 Sorted by model distance: nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.107 2.440 nonbonded pdb=" N LYS B 79 " pdb=" OP1 DA J 101 " model vdw 2.125 2.520 nonbonded pdb=" NH2 ARG E 42 " pdb=" OP1 DG J 68 " model vdw 2.154 2.520 nonbonded pdb=" NH2 ARG A 69 " pdb=" OP2 DA J 90 " model vdw 2.171 2.520 nonbonded pdb=" O2 DC I 94 " pdb=" N2 DG J 52 " model vdw 2.174 2.496 ... (remaining 128491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 102) } ncs_group { reference = (chain 'C' and resid 10 through 116) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 124) 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 group one per residue 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: 0.430 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: 3.010 Check model and map are aligned: 0.210 Set scattering table: 0.160 Process input model: 53.020 Find NCS groups from input model: 0.560 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.007 0.103 15829 Z= 0.393 Angle : 0.893 12.088 22591 Z= 0.524 Chirality : 0.048 0.226 2540 Planarity : 0.007 0.057 1858 Dihedral : 26.988 176.793 6712 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.15 % Favored : 93.67 % Rotamer: Outliers : 1.66 % Allowed : 10.27 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.94 (0.22), residues: 1105 helix: -0.44 (0.18), residues: 676 sheet: -1.46 (0.63), residues: 52 loop : -2.76 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP K 440 HIS 0.010 0.002 HIS F 75 PHE 0.029 0.002 PHE K 476 TYR 0.021 0.002 TYR B 72 ARG 0.024 0.001 ARG K 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 260 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8752 (mt-10) REVERT: A 54 TYR cc_start: 0.8712 (m-80) cc_final: 0.8177 (m-80) REVERT: A 55 GLN cc_start: 0.8998 (mt0) cc_final: 0.8104 (tt0) REVERT: A 56 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8550 (mmmt) REVERT: A 67 PHE cc_start: 0.8178 (t80) cc_final: 0.7797 (t80) REVERT: A 73 GLU cc_start: 0.8897 (pt0) cc_final: 0.8488 (pt0) REVERT: A 85 GLN cc_start: 0.9574 (mt0) cc_final: 0.8944 (mm110) REVERT: A 107 THR cc_start: 0.9260 (p) cc_final: 0.9050 (p) REVERT: B 72 TYR cc_start: 0.9327 (m-80) cc_final: 0.9048 (m-10) REVERT: B 88 TYR cc_start: 0.9301 (m-10) cc_final: 0.8408 (m-10) REVERT: C 38 ASN cc_start: 0.8638 (m-40) cc_final: 0.8250 (t0) REVERT: D 59 MET cc_start: 0.8549 (tpp) cc_final: 0.8133 (tmm) REVERT: D 83 TYR cc_start: 0.8520 (m-10) cc_final: 0.7344 (m-10) REVERT: E 46 VAL cc_start: 0.8073 (t) cc_final: 0.7365 (t) REVERT: E 50 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8611 (mt-10) REVERT: E 85 GLN cc_start: 0.8770 (mt0) cc_final: 0.8503 (mt0) REVERT: E 106 ASP cc_start: 0.9206 (m-30) cc_final: 0.8904 (m-30) REVERT: F 37 LEU cc_start: 0.9393 (mt) cc_final: 0.9181 (tt) REVERT: F 58 LEU cc_start: 0.9354 (tp) cc_final: 0.9126 (tt) REVERT: F 74 GLU cc_start: 0.8841 (pt0) cc_final: 0.8620 (pt0) REVERT: G 38 ASN cc_start: 0.8907 (m110) cc_final: 0.8349 (m110) REVERT: G 90 ASP cc_start: 0.8807 (t70) cc_final: 0.8581 (t0) REVERT: G 99 LYS cc_start: 0.9002 (mtmm) cc_final: 0.8613 (mmmm) REVERT: H 113 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9099 (mm-30) REVERT: K 215 MET cc_start: 0.7058 (mtt) cc_final: 0.6730 (mpp) REVERT: K 430 MET cc_start: -0.0038 (tpt) cc_final: -0.0257 (ttt) REVERT: K 467 HIS cc_start: 0.7160 (t-90) cc_final: 0.6875 (t-90) outliers start: 16 outliers final: 4 residues processed: 272 average time/residue: 0.3481 time to fit residues: 130.6460 Evaluate side-chains 134 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.0070 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 24 GLN C 31 HIS D 95 GLN E 68 GLN F 75 HIS F 93 GLN G 31 HIS G 89 ASN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN K 183 GLN ** K 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15829 Z= 0.225 Angle : 0.647 8.238 22591 Z= 0.372 Chirality : 0.038 0.155 2540 Planarity : 0.005 0.047 1858 Dihedral : 30.095 175.287 4405 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.12 (0.25), residues: 1105 helix: 1.09 (0.19), residues: 681 sheet: -0.99 (0.71), residues: 50 loop : -2.21 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 331 HIS 0.009 0.001 HIS F 75 PHE 0.014 0.002 PHE K 251 TYR 0.024 0.002 TYR K 373 ARG 0.009 0.001 ARG K 497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8708 (mp0) REVERT: A 54 TYR cc_start: 0.8792 (m-80) cc_final: 0.8090 (m-80) REVERT: A 55 GLN cc_start: 0.9130 (mt0) cc_final: 0.8900 (tt0) REVERT: A 81 ASP cc_start: 0.9330 (t0) cc_final: 0.9058 (t0) REVERT: A 97 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7910 (mt-10) REVERT: B 68 ASP cc_start: 0.9504 (m-30) cc_final: 0.9261 (m-30) REVERT: E 50 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8657 (mm-30) REVERT: E 62 ILE cc_start: 0.7957 (mm) cc_final: 0.7678 (mm) REVERT: F 52 GLU cc_start: 0.8764 (pm20) cc_final: 0.8442 (pm20) REVERT: F 53 GLU cc_start: 0.8810 (mp0) cc_final: 0.8467 (mp0) REVERT: G 38 ASN cc_start: 0.9043 (m110) cc_final: 0.8604 (p0) REVERT: G 51 LEU cc_start: 0.9661 (tp) cc_final: 0.9196 (pp) REVERT: G 90 ASP cc_start: 0.8795 (t70) cc_final: 0.8584 (t0) REVERT: G 99 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8653 (mmmt) REVERT: H 71 GLU cc_start: 0.9441 (tm-30) cc_final: 0.9198 (tm-30) REVERT: H 86 ARG cc_start: 0.9233 (mmt-90) cc_final: 0.9030 (mmm160) REVERT: H 95 GLN cc_start: 0.9467 (tt0) cc_final: 0.9206 (tp40) REVERT: K 201 TYR cc_start: 0.4726 (m-10) cc_final: 0.4313 (m-10) REVERT: K 215 MET cc_start: 0.6960 (mtt) cc_final: 0.6627 (mpp) REVERT: K 326 LEU cc_start: 0.5281 (tp) cc_final: 0.4565 (tp) REVERT: K 369 HIS cc_start: 0.6363 (p-80) cc_final: 0.5883 (p-80) REVERT: K 467 HIS cc_start: 0.7129 (t-90) cc_final: 0.6918 (t-90) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3188 time to fit residues: 80.5776 Evaluate side-chains 109 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 40.0000 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 210 ASN ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 478 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.008 0.120 15829 Z= 0.445 Angle : 0.778 15.511 22591 Z= 0.439 Chirality : 0.043 0.285 2540 Planarity : 0.006 0.045 1858 Dihedral : 30.176 179.003 4405 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.21 % Allowed : 4.98 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1105 helix: 0.86 (0.19), residues: 684 sheet: -1.28 (0.68), residues: 52 loop : -2.14 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 431 HIS 0.012 0.002 HIS K 250 PHE 0.028 0.003 PHE K 251 TYR 0.035 0.003 TYR B 88 ARG 0.006 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8253 (m-10) cc_final: 0.8025 (m-80) REVERT: A 56 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8460 (mmmt) REVERT: A 97 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 31 LYS cc_start: 0.9140 (tmmt) cc_final: 0.8899 (ttpp) REVERT: E 81 ASP cc_start: 0.7373 (t70) cc_final: 0.6993 (t70) REVERT: E 90 MET cc_start: 0.9432 (tpp) cc_final: 0.8996 (tmm) REVERT: E 106 ASP cc_start: 0.9400 (m-30) cc_final: 0.9184 (m-30) REVERT: G 38 ASN cc_start: 0.9050 (m110) cc_final: 0.8788 (m110) REVERT: G 99 LYS cc_start: 0.9317 (mtmm) cc_final: 0.8585 (mmmt) REVERT: H 71 GLU cc_start: 0.9452 (tm-30) cc_final: 0.9031 (tm-30) REVERT: K 215 MET cc_start: 0.6820 (mtt) cc_final: 0.6468 (mpp) REVERT: K 326 LEU cc_start: 0.5542 (tp) cc_final: 0.4738 (tp) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.3110 time to fit residues: 65.1076 Evaluate side-chains 95 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 47 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 15829 Z= 0.354 Angle : 0.699 12.551 22591 Z= 0.395 Chirality : 0.041 0.287 2540 Planarity : 0.005 0.039 1858 Dihedral : 30.624 176.324 4405 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.03 (0.25), residues: 1105 helix: 1.27 (0.19), residues: 679 sheet: -1.35 (0.71), residues: 52 loop : -2.17 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 431 HIS 0.008 0.002 HIS B 75 PHE 0.020 0.002 PHE B 61 TYR 0.042 0.003 TYR B 88 ARG 0.010 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9155 (mt-10) REVERT: A 56 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8515 (mmmt) REVERT: A 120 MET cc_start: 0.7701 (mtp) cc_final: 0.7415 (mtp) REVERT: B 25 ASN cc_start: 0.8683 (m-40) cc_final: 0.8339 (m110) REVERT: B 31 LYS cc_start: 0.9129 (tmmt) cc_final: 0.8882 (ttpp) REVERT: B 68 ASP cc_start: 0.9548 (m-30) cc_final: 0.8676 (m-30) REVERT: B 84 MET cc_start: 0.9004 (mmp) cc_final: 0.8665 (mmt) REVERT: E 90 MET cc_start: 0.9469 (tpp) cc_final: 0.9059 (tmm) REVERT: E 105 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8756 (mm-30) REVERT: E 106 ASP cc_start: 0.9462 (m-30) cc_final: 0.9261 (m-30) REVERT: E 120 MET cc_start: 0.9001 (mmp) cc_final: 0.8607 (mmm) REVERT: G 99 LYS cc_start: 0.9297 (mtmm) cc_final: 0.8593 (mmmt) REVERT: H 45 LEU cc_start: 0.9489 (tt) cc_final: 0.9268 (tp) REVERT: H 46 LYS cc_start: 0.9514 (mmtt) cc_final: 0.8794 (tppt) REVERT: H 71 GLU cc_start: 0.9404 (tm-30) cc_final: 0.8960 (tm-30) REVERT: K 215 MET cc_start: 0.6602 (mtt) cc_final: 0.6328 (mpp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3220 time to fit residues: 63.7687 Evaluate side-chains 97 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15829 Z= 0.287 Angle : 0.652 10.925 22591 Z= 0.374 Chirality : 0.038 0.152 2540 Planarity : 0.004 0.043 1858 Dihedral : 30.545 176.322 4405 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.25), residues: 1105 helix: 1.48 (0.20), residues: 682 sheet: -1.12 (0.74), residues: 52 loop : -2.04 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 431 HIS 0.006 0.001 HIS B 75 PHE 0.018 0.002 PHE K 216 TYR 0.026 0.002 TYR B 88 ARG 0.004 0.000 ARG K 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9155 (mt-10) REVERT: A 55 GLN cc_start: 0.9107 (mt0) cc_final: 0.8552 (mt0) REVERT: A 56 LYS cc_start: 0.8996 (mtmt) cc_final: 0.8464 (mmmt) REVERT: A 97 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8210 (mt-10) REVERT: A 120 MET cc_start: 0.7609 (mtp) cc_final: 0.7230 (mtp) REVERT: B 31 LYS cc_start: 0.9147 (tmmt) cc_final: 0.8922 (ttpp) REVERT: B 84 MET cc_start: 0.8951 (mmp) cc_final: 0.8548 (mmt) REVERT: D 101 LEU cc_start: 0.9414 (tp) cc_final: 0.9131 (tt) REVERT: E 105 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8786 (mm-30) REVERT: E 106 ASP cc_start: 0.9470 (m-30) cc_final: 0.9258 (m-30) REVERT: G 51 LEU cc_start: 0.9764 (tp) cc_final: 0.9457 (pp) REVERT: G 90 ASP cc_start: 0.8723 (t70) cc_final: 0.8241 (t0) REVERT: G 99 LYS cc_start: 0.9256 (mtmm) cc_final: 0.8570 (mmmt) REVERT: H 59 MET cc_start: 0.9483 (mmm) cc_final: 0.8976 (mmm) REVERT: H 71 GLU cc_start: 0.9371 (tm-30) cc_final: 0.8894 (tm-30) REVERT: K 215 MET cc_start: 0.6577 (mtt) cc_final: 0.6286 (mpp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3248 time to fit residues: 63.7190 Evaluate side-chains 94 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.0000 chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15829 Z= 0.202 Angle : 0.621 9.807 22591 Z= 0.358 Chirality : 0.037 0.144 2540 Planarity : 0.004 0.039 1858 Dihedral : 30.377 175.412 4405 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.62 (0.26), residues: 1105 helix: 1.69 (0.20), residues: 682 sheet: -0.90 (0.79), residues: 51 loop : -1.91 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 440 HIS 0.006 0.001 HIS B 75 PHE 0.017 0.001 PHE B 61 TYR 0.024 0.001 TYR B 88 ARG 0.008 0.000 ARG K 483 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9380 (mt-10) cc_final: 0.9127 (mt-10) REVERT: A 55 GLN cc_start: 0.9058 (mt0) cc_final: 0.8441 (mt0) REVERT: A 56 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8453 (mmmt) REVERT: A 120 MET cc_start: 0.7525 (mtp) cc_final: 0.7128 (mtp) REVERT: B 25 ASN cc_start: 0.8435 (t0) cc_final: 0.7994 (t0) REVERT: B 31 LYS cc_start: 0.9138 (tmmt) cc_final: 0.8925 (ttpp) REVERT: B 68 ASP cc_start: 0.9596 (m-30) cc_final: 0.9384 (m-30) REVERT: B 84 MET cc_start: 0.8920 (mmp) cc_final: 0.8536 (mmt) REVERT: D 59 MET cc_start: 0.9047 (ttp) cc_final: 0.8596 (tmm) REVERT: D 101 LEU cc_start: 0.9408 (tp) cc_final: 0.9204 (tt) REVERT: E 59 GLU cc_start: 0.9391 (pt0) cc_final: 0.9075 (mp0) REVERT: E 90 MET cc_start: 0.9065 (tmm) cc_final: 0.8699 (tmm) REVERT: E 94 GLU cc_start: 0.9175 (tp30) cc_final: 0.8952 (tt0) REVERT: E 105 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8837 (mm-30) REVERT: E 106 ASP cc_start: 0.9482 (m-30) cc_final: 0.9274 (m-30) REVERT: E 120 MET cc_start: 0.9135 (mmm) cc_final: 0.8848 (mmm) REVERT: F 84 MET cc_start: 0.9571 (mmm) cc_final: 0.9002 (mmp) REVERT: G 51 LEU cc_start: 0.9747 (tp) cc_final: 0.9416 (pp) REVERT: G 99 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8506 (mmmt) REVERT: H 59 MET cc_start: 0.9411 (mmm) cc_final: 0.8796 (mmm) REVERT: H 71 GLU cc_start: 0.9356 (tm-30) cc_final: 0.8850 (tm-30) REVERT: H 93 GLU cc_start: 0.9129 (mp0) cc_final: 0.8738 (mp0) REVERT: K 215 MET cc_start: 0.6547 (mtt) cc_final: 0.6252 (mpp) REVERT: K 369 HIS cc_start: 0.7466 (p-80) cc_final: 0.7144 (p-80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3148 time to fit residues: 63.3730 Evaluate side-chains 97 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.4980 chunk 74 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 overall best weight: 7.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15829 Z= 0.381 Angle : 0.698 11.144 22591 Z= 0.397 Chirality : 0.040 0.248 2540 Planarity : 0.005 0.042 1858 Dihedral : 30.433 176.432 4405 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.37 (0.26), residues: 1105 helix: 1.45 (0.20), residues: 681 sheet: -0.96 (0.80), residues: 51 loop : -1.91 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 431 HIS 0.006 0.002 HIS K 422 PHE 0.011 0.002 PHE B 100 TYR 0.021 0.002 TYR B 88 ARG 0.007 0.001 ARG K 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9145 (mt-10) REVERT: A 55 GLN cc_start: 0.9151 (mt0) cc_final: 0.8462 (mm-40) REVERT: A 56 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8485 (mmmt) REVERT: A 81 ASP cc_start: 0.9624 (t0) cc_final: 0.9387 (t0) REVERT: A 90 MET cc_start: 0.9088 (mmp) cc_final: 0.8869 (mmp) REVERT: A 120 MET cc_start: 0.7845 (mtp) cc_final: 0.7415 (mtp) REVERT: B 25 ASN cc_start: 0.8601 (t0) cc_final: 0.8266 (t0) REVERT: B 31 LYS cc_start: 0.9155 (tmmt) cc_final: 0.8880 (tptt) REVERT: B 68 ASP cc_start: 0.9619 (m-30) cc_final: 0.9408 (m-30) REVERT: D 59 MET cc_start: 0.9138 (ttp) cc_final: 0.8695 (tmm) REVERT: E 59 GLU cc_start: 0.9485 (pt0) cc_final: 0.9202 (mp0) REVERT: E 94 GLU cc_start: 0.9425 (tp30) cc_final: 0.8909 (tt0) REVERT: E 105 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8820 (mm-30) REVERT: E 106 ASP cc_start: 0.9516 (m-30) cc_final: 0.9299 (m-30) REVERT: E 120 MET cc_start: 0.9159 (mmm) cc_final: 0.8897 (mmm) REVERT: G 78 ILE cc_start: 0.9431 (pt) cc_final: 0.9021 (mm) REVERT: G 99 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8510 (mmmt) REVERT: H 45 LEU cc_start: 0.9479 (tt) cc_final: 0.9264 (tp) REVERT: H 46 LYS cc_start: 0.9434 (mmtt) cc_final: 0.8747 (tppt) REVERT: H 59 MET cc_start: 0.9505 (mmm) cc_final: 0.9002 (mmm) REVERT: H 71 GLU cc_start: 0.9333 (tm-30) cc_final: 0.8841 (tm-30) REVERT: K 215 MET cc_start: 0.6466 (mtt) cc_final: 0.6163 (mpp) REVERT: K 292 PRO cc_start: -0.0886 (Cg_endo) cc_final: -0.1251 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3055 time to fit residues: 55.8344 Evaluate side-chains 94 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 114 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15829 Z= 0.235 Angle : 0.635 14.233 22591 Z= 0.360 Chirality : 0.037 0.185 2540 Planarity : 0.004 0.061 1858 Dihedral : 30.541 176.213 4405 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.59 (0.26), residues: 1105 helix: 1.63 (0.20), residues: 683 sheet: -0.88 (0.81), residues: 51 loop : -1.85 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 431 HIS 0.007 0.001 HIS B 75 PHE 0.019 0.002 PHE H 65 TYR 0.022 0.001 TYR B 88 ARG 0.008 0.000 ARG K 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9387 (mt-10) cc_final: 0.9132 (mt-10) REVERT: A 55 GLN cc_start: 0.9118 (mt0) cc_final: 0.8734 (mm-40) REVERT: A 97 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 120 MET cc_start: 0.7818 (mtp) cc_final: 0.7386 (mtp) REVERT: B 25 ASN cc_start: 0.8460 (t0) cc_final: 0.8096 (t0) REVERT: B 31 LYS cc_start: 0.9131 (tmmt) cc_final: 0.8921 (ttpp) REVERT: B 68 ASP cc_start: 0.9616 (m-30) cc_final: 0.9371 (m-30) REVERT: D 59 MET cc_start: 0.9143 (ttp) cc_final: 0.8696 (tmm) REVERT: D 102 LEU cc_start: 0.9332 (mm) cc_final: 0.9123 (mm) REVERT: E 59 GLU cc_start: 0.9474 (pt0) cc_final: 0.9116 (mp0) REVERT: E 105 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8764 (mm-30) REVERT: E 106 ASP cc_start: 0.9516 (m-30) cc_final: 0.9306 (m-30) REVERT: E 120 MET cc_start: 0.9180 (mmm) cc_final: 0.8875 (mmm) REVERT: G 51 LEU cc_start: 0.9781 (tp) cc_final: 0.9461 (pp) REVERT: G 78 ILE cc_start: 0.9425 (pt) cc_final: 0.8983 (mm) REVERT: G 99 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8492 (mmmt) REVERT: H 59 MET cc_start: 0.9458 (mmm) cc_final: 0.8834 (mmm) REVERT: H 93 GLU cc_start: 0.9066 (mp0) cc_final: 0.8697 (mp0) REVERT: K 215 MET cc_start: 0.6458 (mtt) cc_final: 0.6162 (mpp) REVERT: K 292 PRO cc_start: -0.0783 (Cg_endo) cc_final: -0.1126 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2907 time to fit residues: 55.6785 Evaluate side-chains 102 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15829 Z= 0.291 Angle : 0.659 12.151 22591 Z= 0.376 Chirality : 0.039 0.166 2540 Planarity : 0.005 0.049 1858 Dihedral : 30.507 177.204 4405 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.48 (0.26), residues: 1105 helix: 1.50 (0.20), residues: 687 sheet: -0.93 (0.81), residues: 51 loop : -1.83 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 431 HIS 0.006 0.001 HIS B 75 PHE 0.025 0.002 PHE B 61 TYR 0.022 0.001 TYR B 88 ARG 0.007 0.000 ARG K 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9407 (mt-10) cc_final: 0.9142 (mt-10) REVERT: A 55 GLN cc_start: 0.9118 (mt0) cc_final: 0.8785 (mm-40) REVERT: A 97 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 120 MET cc_start: 0.7793 (mtp) cc_final: 0.7356 (mtp) REVERT: B 25 ASN cc_start: 0.8432 (t0) cc_final: 0.8130 (t0) REVERT: B 31 LYS cc_start: 0.9158 (tmmt) cc_final: 0.8947 (ttpp) REVERT: C 90 ASP cc_start: 0.8768 (t0) cc_final: 0.8481 (t0) REVERT: D 59 MET cc_start: 0.9191 (ttp) cc_final: 0.8741 (tmm) REVERT: D 102 LEU cc_start: 0.9247 (mm) cc_final: 0.9016 (mm) REVERT: E 105 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8792 (mm-30) REVERT: E 106 ASP cc_start: 0.9516 (m-30) cc_final: 0.9292 (m-30) REVERT: E 120 MET cc_start: 0.9147 (mmm) cc_final: 0.8838 (mmm) REVERT: G 78 ILE cc_start: 0.9424 (pt) cc_final: 0.8984 (mm) REVERT: G 99 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8533 (mmmt) REVERT: H 52 THR cc_start: 0.8780 (m) cc_final: 0.8409 (p) REVERT: H 59 MET cc_start: 0.9493 (mmm) cc_final: 0.8923 (mmm) REVERT: H 93 GLU cc_start: 0.9080 (mp0) cc_final: 0.8715 (mp0) REVERT: K 215 MET cc_start: 0.6414 (mtt) cc_final: 0.6126 (mpp) REVERT: K 292 PRO cc_start: -0.0657 (Cg_endo) cc_final: -0.1032 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2815 time to fit residues: 53.6043 Evaluate side-chains 96 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 135 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 114 optimal weight: 40.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15829 Z= 0.220 Angle : 0.628 12.899 22591 Z= 0.359 Chirality : 0.037 0.176 2540 Planarity : 0.004 0.044 1858 Dihedral : 30.486 178.015 4405 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.63 (0.26), residues: 1105 helix: 1.61 (0.20), residues: 687 sheet: -0.88 (0.82), residues: 51 loop : -1.75 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 431 HIS 0.007 0.001 HIS B 75 PHE 0.018 0.002 PHE H 65 TYR 0.021 0.001 TYR B 88 ARG 0.005 0.000 ARG K 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9396 (mt-10) cc_final: 0.9129 (mt-10) REVERT: A 55 GLN cc_start: 0.9035 (mt0) cc_final: 0.8495 (mt0) REVERT: A 56 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8449 (mmmt) REVERT: A 97 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 120 MET cc_start: 0.7694 (mtp) cc_final: 0.7263 (mtp) REVERT: B 25 ASN cc_start: 0.8400 (t0) cc_final: 0.8127 (t0) REVERT: B 68 ASP cc_start: 0.9619 (m-30) cc_final: 0.9417 (m-30) REVERT: B 84 MET cc_start: 0.8901 (mmp) cc_final: 0.8561 (mmt) REVERT: C 90 ASP cc_start: 0.8730 (t0) cc_final: 0.8444 (t0) REVERT: D 59 MET cc_start: 0.9199 (ttp) cc_final: 0.8839 (tmm) REVERT: D 102 LEU cc_start: 0.9270 (mm) cc_final: 0.9029 (mm) REVERT: E 105 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8753 (mm-30) REVERT: E 106 ASP cc_start: 0.9524 (m-30) cc_final: 0.9316 (m-30) REVERT: E 120 MET cc_start: 0.9171 (mmm) cc_final: 0.8855 (mmm) REVERT: G 51 LEU cc_start: 0.9780 (tp) cc_final: 0.9424 (pp) REVERT: G 78 ILE cc_start: 0.9425 (pt) cc_final: 0.9060 (mm) REVERT: G 99 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8481 (mmmt) REVERT: H 52 THR cc_start: 0.8682 (m) cc_final: 0.8342 (p) REVERT: H 59 MET cc_start: 0.9468 (mmm) cc_final: 0.8876 (mmm) REVERT: H 93 GLU cc_start: 0.9153 (mp0) cc_final: 0.8787 (mp0) REVERT: K 215 MET cc_start: 0.6420 (mtt) cc_final: 0.6120 (mpp) REVERT: K 281 ASP cc_start: 0.8476 (m-30) cc_final: 0.8180 (p0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2853 time to fit residues: 55.0307 Evaluate side-chains 99 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 40.0000 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 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 = 0.3330 r_free = 0.3330 target = 0.052235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.032679 restraints weight = 144517.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.033172 restraints weight = 83495.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.033487 restraints weight = 61107.687| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15829 Z= 0.189 Angle : 0.608 10.169 22591 Z= 0.348 Chirality : 0.037 0.158 2540 Planarity : 0.004 0.047 1858 Dihedral : 30.263 179.418 4405 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.73 (0.26), residues: 1105 helix: 1.68 (0.20), residues: 687 sheet: -0.81 (0.83), residues: 51 loop : -1.69 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 318 HIS 0.008 0.001 HIS B 75 PHE 0.018 0.002 PHE H 65 TYR 0.018 0.001 TYR B 88 ARG 0.005 0.000 ARG B 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.53 seconds wall clock time: 52 minutes 0.40 seconds (3120.40 seconds total)