Starting phenix.real_space_refine on Mon Mar 11 11:35:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/03_2024/7lre_23496.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/03_2024/7lre_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_23496/03_2024/7lre_23496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/03_2024/7lre_23496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/03_2024/7lre_23496.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lre_23496/03_2024/7lre_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.44, per 1000 atoms: 0.55 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: 2.74 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: 1.04 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: 2.24 Time building geometry restraints manager: 2.92 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: 2.080 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: 7.480 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.410 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.050 ------------------------------------------------------------------------------- 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 : 0.975 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 1.3646 time to fit residues: 61.5116 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 : 0.916 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 34 average time/residue: 1.4345 time to fit residues: 52.4022 Evaluate side-chains 34 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 254 MET 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: 0.9980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 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: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8282 Z= 0.151 Angle : 0.392 7.474 11112 Z= 0.209 Chirality : 0.037 0.133 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.506 16.354 1094 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.44 % Allowed : 3.52 % 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: 3.23 (0.28), residues: 366 sheet: 1.81 (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 36 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 1.435 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 34 average time/residue: 1.5333 time to fit residues: 56.0919 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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: 0.8980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 80 optimal weight: 0.0470 chunk 54 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.8180 moved from start: 0.1051 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= 0.130 Angle : 0.388 8.243 11112 Z= 0.204 Chirality : 0.037 0.132 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.423 16.539 1094 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.44 % Allowed : 4.30 % Favored : 95.26 % 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: 2.35 (0.27), residues: 992 helix: 3.28 (0.28), residues: 364 sheet: 1.84 (0.39), residues: 164 loop : 0.04 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 337 HIS 0.003 0.001 HIS A 274 PHE 0.008 0.001 PHE A 145 TYR 0.005 0.001 TYR A 487 ARG 0.001 0.000 ARG A 155 *********************** 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 36 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 1.037 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 34 average time/residue: 1.5173 time to fit residues: 55.4318 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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: 0.8236 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 8282 Z= 0.308 Angle : 0.462 9.883 11112 Z= 0.239 Chirality : 0.038 0.131 1232 Planarity : 0.003 0.024 1400 Dihedral : 3.594 15.952 1094 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.22 % 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: 2.38 (0.27), residues: 992 helix: 3.29 (0.28), residues: 364 sheet: 1.84 (0.39), residues: 164 loop : 0.08 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 322 HIS 0.004 0.001 HIS B 274 PHE 0.018 0.001 PHE A 145 TYR 0.006 0.001 TYR A 293 ARG 0.002 0.000 ARG B 526 *********************** 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 40 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.956 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 34 average time/residue: 1.4171 time to fit residues: 51.9331 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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: 1.9990 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8202 moved from start: 0.1288 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= 0.153 Angle : 0.415 9.819 11112 Z= 0.214 Chirality : 0.037 0.132 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.496 16.614 1094 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.61 % Favored : 98.19 % Rotamer: Outliers : 0.22 % Allowed : 4.63 % 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: 2.37 (0.27), residues: 992 helix: 3.25 (0.28), residues: 364 sheet: 1.84 (0.39), residues: 164 loop : 0.09 (0.27), residues: 464 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 0.016 0.001 PHE B 145 TYR 0.005 0.001 TYR B 487 ARG 0.001 0.000 ARG A 155 *********************** 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 34 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.076 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 1.5032 time to fit residues: 55.0162 Evaluate side-chains 32 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8282 Z= 0.134 Angle : 0.414 11.159 11112 Z= 0.211 Chirality : 0.037 0.132 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.395 16.279 1094 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.81 % Favored : 97.98 % Rotamer: Outliers : 0.66 % Allowed : 4.63 % 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: 2.40 (0.27), residues: 992 helix: 3.24 (0.28), residues: 364 sheet: 1.90 (0.40), residues: 164 loop : 0.13 (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 B 274 PHE 0.015 0.001 PHE A 145 TYR 0.005 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 38 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 1.046 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 1.3287 time to fit residues: 51.7541 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 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 323 HIS B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1416 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= 0.210 Angle : 0.442 11.256 11112 Z= 0.224 Chirality : 0.037 0.131 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.458 15.808 1094 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.51 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: 2.41 (0.27), residues: 992 helix: 3.26 (0.28), residues: 364 sheet: 1.86 (0.40), residues: 164 loop : 0.13 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 322 HIS 0.003 0.001 HIS B 274 PHE 0.016 0.001 PHE A 145 TYR 0.004 0.001 TYR B 293 ARG 0.001 0.000 ARG A 526 *********************** 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 38 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.959 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 1.3980 time to fit residues: 54.4873 Evaluate side-chains 34 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 136 VAL 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: 3.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.8220 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8282 Z= 0.228 Angle : 0.467 11.876 11112 Z= 0.233 Chirality : 0.038 0.131 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.496 15.826 1094 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.81 % Favored : 97.98 % 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: 2.41 (0.27), residues: 992 helix: 3.22 (0.28), residues: 366 sheet: 1.86 (0.40), residues: 164 loop : 0.16 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 322 HIS 0.003 0.001 HIS A 274 PHE 0.016 0.001 PHE A 145 TYR 0.004 0.001 TYR A 529 ARG 0.001 0.000 ARG B 526 *********************** 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 36 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.942 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 1.3484 time to fit residues: 52.4125 Evaluate side-chains 34 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.0570 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 0.0970 chunk 61 optimal weight: 0.0270 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8282 Z= 0.139 Angle : 0.456 12.854 11112 Z= 0.223 Chirality : 0.037 0.133 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.408 16.006 1094 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.45 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: 2.41 (0.27), residues: 992 helix: 3.24 (0.28), residues: 364 sheet: 1.88 (0.40), residues: 164 loop : 0.16 (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 A 274 PHE 0.015 0.001 PHE A 145 TYR 0.004 0.001 TYR A 487 ARG 0.001 0.000 ARG A 37 ********************** 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 : 1.131 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 1.4130 time to fit residues: 54.8709 Evaluate side-chains 34 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.042405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.032447 restraints weight = 33032.901| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.63 r_work: 0.2511 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8282 Z= 0.143 Angle : 0.454 12.998 11112 Z= 0.221 Chirality : 0.037 0.132 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.375 15.802 1094 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.81 % Favored : 97.98 % 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: 2.43 (0.27), residues: 992 helix: 3.23 (0.28), residues: 366 sheet: 1.88 (0.40), residues: 164 loop : 0.18 (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 0.014 0.001 PHE A 145 TYR 0.005 0.001 TYR A 487 ARG 0.001 0.000 ARG A 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.74 seconds wall clock time: 39 minutes 38.46 seconds (2378.46 seconds total)