Starting phenix.real_space_refine on Fri Dec 8 10:41:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/12_2023/7lre_23496.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/12_2023/7lre_23496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/12_2023/7lre_23496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/12_2023/7lre_23496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/12_2023/7lre_23496.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/12_2023/7lre_23496.pdb" } resolution = 2.76 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 58 5.16 5 C 5194 2.51 5 N 1378 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8144 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4071 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 491} Chain breaks: 2 Chain: "B" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4071 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 491} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" 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 2161 SG CYS A 277 78.410 62.514 53.924 1.00 52.28 S ATOM 2434 SG CYS A 311 79.178 61.360 50.357 1.00 41.08 S ATOM 2440 SG CYS A 312 75.929 60.277 52.068 1.00 39.93 S ATOM 6232 SG CYS B 277 40.645 26.778 53.924 1.00 53.47 S ATOM 6505 SG CYS B 311 39.877 27.932 50.357 1.00 41.62 S ATOM 6511 SG CYS B 312 43.126 29.015 52.068 1.00 40.29 S Time building chain proxies: 4.83, per 1000 atoms: 0.59 Number of scatterers: 8144 At special positions: 0 Unit cell: (120.119, 90.355, 89.292, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 58 16.00 O 1512 8.00 N 1378 7.00 C 5194 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: 3.09 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 275 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 277 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 311 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 312 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 275 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 277 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 311 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 312 " Number of angles added : 6 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 41.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 54 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.754A pdb=" N TYR A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 138 through 152 Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.745A pdb=" N MET A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 233 removed outlier: 4.448A pdb=" N LEU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 253 through 271 removed outlier: 3.514A pdb=" N MET A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 403 through 415 removed outlier: 3.979A pdb=" N LYS A 407 " --> pdb=" O HIS A 403 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.631A pdb=" N ASP A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 483 Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.800A pdb=" N PHE A 524 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 33 through 54 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.754A pdb=" N TYR B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 93' Processing helix chain 'B' and resid 138 through 152 Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.745A pdb=" N MET B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 233 removed outlier: 4.448A pdb=" N LEU B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 222 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 253 through 271 removed outlier: 3.514A pdb=" N MET B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 403 through 415 removed outlier: 3.979A pdb=" N LYS B 407 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.631A pdb=" N ASP B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 483 Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.800A pdb=" N PHE B 524 " --> pdb=" O SER B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 541 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.633A pdb=" N VAL A 58 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASP A 17 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A 60 " --> pdb=" O ASP A 17 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY A 19 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 removed outlier: 6.633A pdb=" N VAL B 58 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASP B 17 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS B 60 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY B 19 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 191 removed outlier: 6.663A pdb=" N LEU A 190 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER A 286 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 305 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS A 288 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N CYS A 303 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 290 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR A 301 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 292 " --> pdb=" O CYS A 299 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 391 removed outlier: 5.803A pdb=" N THR A 389 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 424 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A 391 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS A 442 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 510 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A 499 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS A 508 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 127 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 189 through 191 removed outlier: 6.663A pdb=" N LEU B 190 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER B 286 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 305 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS B 288 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N CYS B 303 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B 290 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR B 301 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 292 " --> pdb=" O CYS B 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AB2, first strand: chain 'B' and resid 322 through 325 Processing sheet with id=AB3, first strand: chain 'B' and resid 388 through 391 removed outlier: 5.803A pdb=" N THR B 389 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE B 424 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR B 391 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS B 442 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 510 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR B 499 " --> pdb=" O CYS B 508 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS B 508 " --> pdb=" O TYR B 499 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 3.36 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: 2199 1.33 - 1.45: 1321 1.45 - 1.57: 4674 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8282 Sorted by residual: bond pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.80e+00 bond pdb=" N LYS B 150 " pdb=" CA LYS B 150 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.80e+00 bond pdb=" C ILE A 131 " pdb=" O ILE A 131 " ideal model delta sigma weight residual 1.236 1.215 0.022 1.19e-02 7.06e+03 3.29e+00 bond pdb=" C ILE B 131 " pdb=" O ILE B 131 " ideal model delta sigma weight residual 1.236 1.216 0.021 1.19e-02 7.06e+03 3.02e+00 bond pdb=" CA ASP B 130 " pdb=" C ASP B 130 " ideal model delta sigma weight residual 1.530 1.511 0.018 1.11e-02 8.12e+03 2.77e+00 ... (remaining 8277 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.39: 134 106.39 - 113.28: 4494 113.28 - 120.17: 2888 120.17 - 127.06: 3546 127.06 - 133.96: 50 Bond angle restraints: 11112 Sorted by residual: angle pdb=" N ARG B 129 " pdb=" CA ARG B 129 " pdb=" C ARG B 129 " ideal model delta sigma weight residual 107.99 113.51 -5.52 1.77e+00 3.19e-01 9.74e+00 angle pdb=" N ARG A 129 " pdb=" CA ARG A 129 " pdb=" C ARG A 129 " ideal model delta sigma weight residual 107.99 113.51 -5.52 1.77e+00 3.19e-01 9.74e+00 angle pdb=" N SER A 133 " pdb=" CA SER A 133 " pdb=" C SER A 133 " ideal model delta sigma weight residual 109.95 114.71 -4.76 1.59e+00 3.96e-01 8.95e+00 angle pdb=" N SER B 133 " pdb=" CA SER B 133 " pdb=" C SER B 133 " ideal model delta sigma weight residual 109.95 114.71 -4.76 1.59e+00 3.96e-01 8.95e+00 angle pdb=" C ASP B 130 " pdb=" N ILE B 131 " pdb=" CA ILE B 131 " ideal model delta sigma weight residual 121.97 127.16 -5.19 1.80e+00 3.09e-01 8.31e+00 ... (remaining 11107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 4960 16.67 - 33.34: 96 33.34 - 50.01: 16 50.01 - 66.68: 0 66.68 - 83.36: 2 Dihedral angle restraints: 5074 sinusoidal: 2126 harmonic: 2948 Sorted by residual: dihedral pdb=" CB GLU A 205 " pdb=" CG GLU A 205 " pdb=" CD GLU A 205 " pdb=" OE1 GLU A 205 " ideal model delta sinusoidal sigma weight residual 0.00 -83.36 83.36 1 3.00e+01 1.11e-03 9.43e+00 dihedral pdb=" CB GLU B 205 " pdb=" CG GLU B 205 " pdb=" CD GLU B 205 " pdb=" OE1 GLU B 205 " ideal model delta sinusoidal sigma weight residual 0.00 -83.36 83.36 1 3.00e+01 1.11e-03 9.43e+00 dihedral pdb=" CA ILE A 221 " pdb=" CB ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CD1 ILE A 221 " ideal model delta sinusoidal sigma weight residual 60.00 102.63 -42.63 3 1.50e+01 4.44e-03 7.65e+00 ... (remaining 5071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1038 0.048 - 0.096: 127 0.096 - 0.144: 63 0.144 - 0.192: 2 0.192 - 0.239: 2 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CB ILE B 131 " pdb=" CA ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CG2 ILE B 131 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE A 131 " pdb=" CA ILE A 131 " pdb=" CG1 ILE A 131 " pdb=" CG2 ILE A 131 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE A 59 " pdb=" N ILE A 59 " pdb=" C ILE A 59 " pdb=" CB ILE A 59 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1229 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 130 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C ASP A 130 " -0.026 2.00e-02 2.50e+03 pdb=" O ASP A 130 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 131 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 130 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C ASP B 130 " 0.026 2.00e-02 2.50e+03 pdb=" O ASP B 130 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 131 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 222 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO A 223 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.015 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2311 2.82 - 3.34: 6916 3.34 - 3.86: 13220 3.86 - 4.38: 15692 4.38 - 4.90: 27727 Nonbonded interactions: 65866 Sorted by model distance: nonbonded pdb=" OH TYR B 68 " pdb=" O GLY B 74 " model vdw 2.301 2.440 nonbonded pdb=" OH TYR A 68 " pdb=" O GLY A 74 " model vdw 2.302 2.440 nonbonded pdb=" OE1 GLU B 13 " pdb=" NZ LYS B 478 " model vdw 2.320 2.520 nonbonded pdb=" OE1 GLU A 13 " pdb=" NZ LYS A 478 " model vdw 2.320 2.520 nonbonded pdb=" OD2 ASP B 6 " pdb=" NZ LYS B 60 " model vdw 2.327 2.520 ... (remaining 65861 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 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 7.430 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.180 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8282 Z= 0.155 Angle : 0.437 6.259 11112 Z= 0.275 Chirality : 0.040 0.239 1232 Planarity : 0.003 0.026 1400 Dihedral : 7.410 83.356 3166 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.22 % Allowed : 0.88 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.26), residues: 992 helix: 2.92 (0.28), residues: 376 sheet: 1.81 (0.40), residues: 164 loop : 0.06 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 110 HIS 0.001 0.000 HIS A 274 PHE 0.012 0.001 PHE A 145 TYR 0.006 0.001 TYR A 236 ARG 0.001 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.013 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 1.4186 time to fit residues: 63.9588 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8282 Z= 0.315 Angle : 0.452 6.467 11112 Z= 0.241 Chirality : 0.039 0.134 1232 Planarity : 0.003 0.026 1400 Dihedral : 3.560 15.192 1094 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.10 % Allowed : 2.64 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.26), residues: 992 helix: 3.19 (0.28), residues: 366 sheet: 1.82 (0.39), residues: 164 loop : 0.03 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 337 HIS 0.004 0.001 HIS B 274 PHE 0.019 0.001 PHE A 145 TYR 0.007 0.001 TYR B 293 ARG 0.001 0.000 ARG B 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 1.027 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 34 average time/residue: 1.4041 time to fit residues: 51.5642 Evaluate side-chains 34 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1023 time to fit residues: 3.7170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8282 Z= 0.152 Angle : 0.391 7.268 11112 Z= 0.209 Chirality : 0.037 0.133 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.506 16.338 1094 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.22 % Allowed : 3.74 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.27), residues: 992 helix: 3.24 (0.28), residues: 366 sheet: 1.80 (0.39), residues: 164 loop : 0.05 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 337 HIS 0.003 0.001 HIS B 274 PHE 0.017 0.001 PHE B 145 TYR 0.005 0.001 TYR A 487 ARG 0.001 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.030 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 1.4812 time to fit residues: 54.2509 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 overall best weight: 1.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8282 Z= 0.285 Angle : 0.445 8.356 11112 Z= 0.233 Chirality : 0.038 0.131 1232 Planarity : 0.003 0.026 1400 Dihedral : 3.620 16.189 1094 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.88 % Allowed : 3.96 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.27), residues: 992 helix: 3.29 (0.28), residues: 364 sheet: 1.79 (0.39), residues: 164 loop : 0.05 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 337 HIS 0.004 0.001 HIS A 274 PHE 0.012 0.001 PHE A 145 TYR 0.006 0.001 TYR B 293 ARG 0.002 0.000 ARG B 526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 1.107 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 34 average time/residue: 1.5118 time to fit residues: 55.4808 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8282 Z= 0.205 Angle : 0.420 9.179 11112 Z= 0.219 Chirality : 0.037 0.133 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.572 16.437 1094 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.81 % Favored : 97.98 % Rotamer: Outliers : 0.44 % Allowed : 4.41 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.27), residues: 992 helix: 3.26 (0.28), residues: 364 sheet: 1.78 (0.39), residues: 164 loop : 0.06 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 337 HIS 0.004 0.001 HIS B 274 PHE 0.017 0.001 PHE A 145 TYR 0.005 0.001 TYR A 529 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 1.019 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 34 average time/residue: 1.4841 time to fit residues: 54.2834 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8282 Z= 0.341 Angle : 0.494 10.306 11112 Z= 0.254 Chirality : 0.039 0.132 1232 Planarity : 0.003 0.028 1400 Dihedral : 3.725 16.503 1094 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.42 % Favored : 97.38 % Rotamer: Outliers : 0.66 % Allowed : 4.19 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.27), residues: 992 helix: 3.24 (0.28), residues: 364 sheet: 1.73 (0.39), residues: 164 loop : 0.04 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 322 HIS 0.004 0.001 HIS B 274 PHE 0.018 0.001 PHE A 145 TYR 0.007 0.001 TYR B 293 ARG 0.002 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 1.040 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 34 average time/residue: 1.3852 time to fit residues: 50.9724 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8282 Z= 0.168 Angle : 0.427 10.404 11112 Z= 0.220 Chirality : 0.037 0.133 1232 Planarity : 0.002 0.023 1400 Dihedral : 3.571 16.460 1094 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.81 % Favored : 97.98 % Rotamer: Outliers : 0.77 % Allowed : 4.07 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.27), residues: 992 helix: 3.20 (0.28), residues: 364 sheet: 1.75 (0.39), residues: 164 loop : 0.04 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 337 HIS 0.003 0.001 HIS B 274 PHE 0.016 0.001 PHE A 145 TYR 0.004 0.001 TYR A 487 ARG 0.001 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 1.009 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 36 average time/residue: 1.3801 time to fit residues: 53.8042 Evaluate side-chains 34 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.4291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.0060 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8282 Z= 0.188 Angle : 0.439 11.143 11112 Z= 0.224 Chirality : 0.037 0.133 1232 Planarity : 0.002 0.023 1400 Dihedral : 3.530 16.223 1094 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.02 % Favored : 97.78 % Rotamer: Outliers : 0.44 % Allowed : 4.85 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.27), residues: 992 helix: 3.20 (0.28), residues: 364 sheet: 1.78 (0.39), residues: 164 loop : 0.10 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 337 HIS 0.003 0.001 HIS A 274 PHE 0.016 0.001 PHE B 145 TYR 0.004 0.001 TYR B 529 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.995 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 1.3731 time to fit residues: 53.4063 Evaluate side-chains 34 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.3679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 0.0170 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8282 Z= 0.178 Angle : 0.455 11.980 11112 Z= 0.227 Chirality : 0.037 0.133 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.511 16.242 1094 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.81 % Favored : 97.98 % Rotamer: Outliers : 0.66 % Allowed : 4.85 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.27), residues: 992 helix: 3.16 (0.28), residues: 366 sheet: 1.79 (0.39), residues: 164 loop : 0.13 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 337 HIS 0.003 0.001 HIS B 274 PHE 0.016 0.001 PHE A 145 TYR 0.004 0.001 TYR A 487 ARG 0.001 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 1.064 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 1.3493 time to fit residues: 52.8230 Evaluate side-chains 34 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.4804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0970 chunk 66 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 0.0570 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 0.0770 chunk 24 optimal weight: 4.9990 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8282 Z= 0.098 Angle : 0.451 12.754 11112 Z= 0.219 Chirality : 0.037 0.134 1232 Planarity : 0.002 0.023 1400 Dihedral : 3.324 16.227 1094 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.61 % Favored : 98.19 % Rotamer: Outliers : 0.44 % Allowed : 5.07 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.27), residues: 992 helix: 3.22 (0.28), residues: 364 sheet: 1.77 (0.39), residues: 168 loop : 0.17 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 322 HIS 0.002 0.001 HIS B 274 PHE 0.014 0.001 PHE A 145 TYR 0.007 0.001 TYR A 487 ARG 0.001 0.000 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 1.027 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 36 average time/residue: 1.4205 time to fit residues: 55.2469 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.031368 restraints weight = 33193.235| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 3.72 r_work: 0.2469 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8282 Z= 0.299 Angle : 0.501 12.432 11112 Z= 0.248 Chirality : 0.038 0.132 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.537 15.825 1094 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.02 % Favored : 97.78 % Rotamer: Outliers : 0.44 % Allowed : 5.07 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.27), residues: 992 helix: 3.26 (0.28), residues: 366 sheet: 1.86 (0.39), residues: 164 loop : 0.15 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 322 HIS 0.005 0.001 HIS A 323 PHE 0.018 0.001 PHE A 145 TYR 0.005 0.001 TYR B 529 ARG 0.001 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2134.20 seconds wall clock time: 39 minutes 47.22 seconds (2387.22 seconds total)