Starting phenix.real_space_refine on Wed Feb 12 17:38:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lre_23496/02_2025/7lre_23496.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lre_23496/02_2025/7lre_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/cci-nas-00/data/ceres_data/7lre_23496/02_2025/7lre_23496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lre_23496/02_2025/7lre_23496.map" model { file = "/net/cci-nas-00/data/ceres_data/7lre_23496/02_2025/7lre_23496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lre_23496/02_2025/7lre_23496.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8144 Number of models: 1 Model: "" Number of chains: 2 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: "A" 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 Restraints were copied for chains: B Time building chain proxies: 7.55, per 1000 atoms: 0.93 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.1 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: 0.94 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: 2.31 Time building geometry restraints manager: 2.19 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: 0.00 - 1.25: 10894 1.25 - 2.50: 164 2.50 - 3.76: 39 3.76 - 5.01: 9 5.01 - 6.26: 6 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 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" O GLY A 74 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLU B 13 " pdb=" NZ LYS B 478 " model vdw 2.320 3.120 nonbonded pdb=" OE1 GLU A 13 " pdb=" NZ LYS A 478 " model vdw 2.320 3.120 nonbonded pdb=" OD2 ASP B 6 " pdb=" NZ LYS B 60 " model vdw 2.327 3.120 ... (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 Time spend for trying shortcut: 0.04 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: 3.280 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.920 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:15.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.150 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.896 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 1.4941 time to fit residues: 67.2365 Evaluate side-chains 32 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- 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 = 0.3016 r_free = 0.3016 target = 0.041991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.031744 restraints weight = 33086.710| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 3.72 r_work: 0.2487 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8282 Z= 0.250 Angle : 0.445 6.292 11112 Z= 0.238 Chirality : 0.038 0.134 1232 Planarity : 0.003 0.028 1400 Dihedral : 3.567 14.897 1094 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.10 % Allowed : 2.42 % Favored : 96.48 % 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: 2.27 (0.26), residues: 992 helix: 3.15 (0.28), residues: 366 sheet: 1.83 (0.39), residues: 164 loop : 0.03 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 322 HIS 0.004 0.001 HIS B 274 PHE 0.019 0.001 PHE B 145 TYR 0.006 0.001 TYR B 293 ARG 0.002 0.000 ARG A 155 *********************** 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 to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 1.045 Fit side-chains REVERT: A 414 MET cc_start: 0.9598 (mpp) cc_final: 0.9308 (mpp) REVERT: B 414 MET cc_start: 0.9596 (mpp) cc_final: 0.9312 (mpp) outliers start: 10 outliers final: 0 residues processed: 34 average time/residue: 1.5020 time to fit residues: 55.0149 Evaluate side-chains 32 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.6344 ------------------------------------------------------------------------------- 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 = 0.2992 r_free = 0.2992 target = 0.041156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.030972 restraints weight = 33856.462| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 3.72 r_work: 0.2462 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8282 Z= 0.281 Angle : 0.443 7.204 11112 Z= 0.236 Chirality : 0.039 0.132 1232 Planarity : 0.003 0.034 1400 Dihedral : 3.674 15.094 1094 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.66 % Allowed : 3.08 % 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: 2.29 (0.27), residues: 992 helix: 3.22 (0.28), residues: 366 sheet: 1.73 (0.39), residues: 164 loop : 0.03 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 322 HIS 0.004 0.001 HIS B 274 PHE 0.018 0.001 PHE B 145 TYR 0.006 0.001 TYR A 293 ARG 0.002 0.000 ARG A 526 *********************** 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 38 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.930 Fit side-chains REVERT: A 414 MET cc_start: 0.9654 (mpp) cc_final: 0.9341 (mpp) REVERT: B 414 MET cc_start: 0.9651 (mpp) cc_final: 0.9339 (mpp) outliers start: 6 outliers final: 0 residues processed: 34 average time/residue: 1.4538 time to fit residues: 53.2253 Evaluate side-chains 32 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.0050 chunk 13 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3019 r_free = 0.3019 target = 0.042147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031840 restraints weight = 33016.594| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.78 r_work: 0.2485 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1167 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= 0.127 Angle : 0.400 8.473 11112 Z= 0.213 Chirality : 0.037 0.133 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.569 16.154 1094 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.61 % Favored : 98.19 % 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: 2.30 (0.27), residues: 992 helix: 3.24 (0.28), residues: 366 sheet: 1.59 (0.39), residues: 168 loop : 0.08 (0.27), residues: 458 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 0.016 0.001 PHE A 145 TYR 0.005 0.001 TYR B 487 ARG 0.002 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 34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.962 Fit side-chains REVERT: A 414 MET cc_start: 0.9652 (mpp) cc_final: 0.9392 (mpp) REVERT: B 414 MET cc_start: 0.9651 (mpp) cc_final: 0.9394 (mpp) outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 1.5067 time to fit residues: 55.1188 Evaluate side-chains 32 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 0.0670 overall best weight: 1.1924 ------------------------------------------------------------------------------- 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 = 0.3000 r_free = 0.3000 target = 0.041259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.031273 restraints weight = 33085.180| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 3.70 r_work: 0.2470 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1282 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= 0.213 Angle : 0.418 9.700 11112 Z= 0.222 Chirality : 0.038 0.131 1232 Planarity : 0.003 0.028 1400 Dihedral : 3.576 15.715 1094 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.81 % Favored : 97.98 % Rotamer: Outliers : 0.88 % Allowed : 3.30 % Favored : 95.81 % 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: 3.31 (0.28), residues: 364 sheet: 1.60 (0.39), residues: 168 loop : 0.07 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 337 HIS 0.003 0.001 HIS A 274 PHE 0.011 0.001 PHE A 145 TYR 0.005 0.001 TYR B 529 ARG 0.002 0.000 ARG B 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 40 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.927 Fit side-chains REVERT: A 414 MET cc_start: 0.9672 (mpp) cc_final: 0.9367 (mpp) REVERT: B 414 MET cc_start: 0.9673 (mpp) cc_final: 0.9371 (mpp) outliers start: 8 outliers final: 0 residues processed: 34 average time/residue: 1.5266 time to fit residues: 55.6742 Evaluate side-chains 32 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 0.0770 chunk 96 optimal weight: 0.0060 overall best weight: 0.8296 ------------------------------------------------------------------------------- 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 = 0.3014 r_free = 0.3014 target = 0.041699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.031629 restraints weight = 33062.632| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 3.70 r_work: 0.2489 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8282 Z= 0.161 Angle : 0.416 10.578 11112 Z= 0.218 Chirality : 0.038 0.132 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.519 16.238 1094 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.21 % Favored : 98.59 % Rotamer: Outliers : 0.44 % Allowed : 3.96 % Favored : 95.59 % 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: 2.36 (0.27), residues: 992 helix: 3.32 (0.28), residues: 364 sheet: 1.62 (0.39), residues: 168 loop : 0.10 (0.27), residues: 460 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 487 ARG 0.002 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 36 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 1.086 Fit side-chains REVERT: A 414 MET cc_start: 0.9678 (mpp) cc_final: 0.9359 (mpp) REVERT: B 414 MET cc_start: 0.9678 (mpp) cc_final: 0.9362 (mpp) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 1.4720 time to fit residues: 57.0826 Evaluate side-chains 34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.0670 chunk 94 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3026 r_free = 0.3026 target = 0.042028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.031835 restraints weight = 33161.767| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 3.77 r_work: 0.2492 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 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 : 0.002 0.021 8282 Z= 0.137 Angle : 0.413 11.530 11112 Z= 0.215 Chirality : 0.037 0.131 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.456 16.402 1094 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.61 % Favored : 98.19 % Rotamer: Outliers : 0.66 % Allowed : 3.96 % Favored : 95.37 % 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: 3.33 (0.28), residues: 364 sheet: 1.62 (0.39), residues: 168 loop : 0.11 (0.27), residues: 460 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 A 145 TYR 0.004 0.001 TYR A 487 ARG 0.002 0.000 ARG A 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 to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 1.001 Fit side-chains REVERT: A 414 MET cc_start: 0.9694 (mpp) cc_final: 0.9375 (mpp) REVERT: B 414 MET cc_start: 0.9690 (mpp) cc_final: 0.9374 (mpp) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 1.4558 time to fit residues: 56.5075 Evaluate side-chains 34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 74 optimal weight: 2.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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 = 0.3020 r_free = 0.3020 target = 0.042037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.031742 restraints weight = 33362.950| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.81 r_work: 0.2476 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1474 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= 0.190 Angle : 0.425 11.194 11112 Z= 0.221 Chirality : 0.038 0.130 1232 Planarity : 0.002 0.025 1400 Dihedral : 3.486 16.167 1094 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.41 % Favored : 98.39 % 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: 2.36 (0.27), residues: 992 helix: 3.32 (0.28), residues: 364 sheet: 1.60 (0.39), residues: 168 loop : 0.11 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 337 HIS 0.003 0.001 HIS A 323 PHE 0.016 0.001 PHE A 145 TYR 0.004 0.001 TYR B 529 ARG 0.002 0.000 ARG B 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 38 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.942 Fit side-chains REVERT: A 414 MET cc_start: 0.9700 (mpp) cc_final: 0.9388 (mpp) REVERT: B 414 MET cc_start: 0.9700 (mpp) cc_final: 0.9390 (mpp) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 1.4262 time to fit residues: 55.4670 Evaluate side-chains 34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 58 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3021 r_free = 0.3021 target = 0.041782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.031619 restraints weight = 33817.193| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.75 r_work: 0.2483 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1512 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= 0.176 Angle : 0.428 12.048 11112 Z= 0.220 Chirality : 0.038 0.131 1232 Planarity : 0.002 0.024 1400 Dihedral : 3.483 16.013 1094 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.17 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: 2.35 (0.27), residues: 992 helix: 3.28 (0.28), residues: 366 sheet: 1.60 (0.39), residues: 168 loop : 0.11 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 337 HIS 0.003 0.001 HIS A 323 PHE 0.016 0.001 PHE A 145 TYR 0.004 0.001 TYR B 456 ARG 0.002 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 36 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 1.047 Fit side-chains REVERT: A 414 MET cc_start: 0.9702 (mpp) cc_final: 0.9396 (mpp) REVERT: B 414 MET cc_start: 0.9704 (mpp) cc_final: 0.9398 (mpp) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 1.4831 time to fit residues: 57.5022 Evaluate side-chains 34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3026 r_free = 0.3026 target = 0.041788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.031781 restraints weight = 33007.011| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.62 r_work: 0.2497 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1542 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= 0.171 Angle : 0.429 12.386 11112 Z= 0.220 Chirality : 0.037 0.131 1232 Planarity : 0.002 0.023 1400 Dihedral : 3.465 16.085 1094 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.23 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: 2.36 (0.27), residues: 992 helix: 3.30 (0.28), residues: 366 sheet: 1.61 (0.39), residues: 168 loop : 0.11 (0.27), residues: 458 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 0.015 0.001 PHE A 145 TYR 0.004 0.001 TYR A 456 ARG 0.002 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 to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 1.036 Fit side-chains REVERT: A 414 MET cc_start: 0.9682 (mpp) cc_final: 0.9397 (mpp) REVERT: B 414 MET cc_start: 0.9680 (mpp) cc_final: 0.9397 (mpp) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 1.4160 time to fit residues: 54.7634 Evaluate side-chains 34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 40 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 0.0050 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3031 r_free = 0.3031 target = 0.042022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.031900 restraints weight = 33482.315| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 3.69 r_work: 0.2501 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 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 : 0.002 0.024 8282 Z= 0.151 Angle : 0.421 12.295 11112 Z= 0.217 Chirality : 0.037 0.131 1232 Planarity : 0.002 0.023 1400 Dihedral : 3.428 16.142 1094 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.61 % Favored : 98.19 % 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: 2.36 (0.27), residues: 992 helix: 3.33 (0.28), residues: 364 sheet: 1.63 (0.39), residues: 168 loop : 0.08 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 337 HIS 0.003 0.001 HIS B 274 PHE 0.015 0.001 PHE A 145 TYR 0.004 0.001 TYR B 487 ARG 0.002 0.000 ARG A 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3891.27 seconds wall clock time: 69 minutes 59.68 seconds (4199.68 seconds total)