Starting phenix.real_space_refine on Thu Nov 14 08:12:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/11_2024/8j2g_35949.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/11_2024/8j2g_35949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/11_2024/8j2g_35949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/11_2024/8j2g_35949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/11_2024/8j2g_35949.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/11_2024/8j2g_35949.cif" } resolution = 3.4 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= 0.010 sd= 0.143 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3282 2.51 5 N 860 2.21 5 O 874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5058 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2529 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B Time building chain proxies: 4.05, per 1000 atoms: 0.80 Number of scatterers: 5058 At special positions: 0 Unit cell: (73.7, 67.1, 126.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 874 8.00 N 860 7.00 C 3282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 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: 1.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 45.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 removed outlier: 3.658A pdb=" N LEU A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.716A pdb=" N LEU A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 46 " --> pdb=" O HIS A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 46' Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.905A pdb=" N GLU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.591A pdb=" N VAL A 84 " --> pdb=" O MET A 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 85' Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.859A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.540A pdb=" N VAL A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.963A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.521A pdb=" N LEU A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.628A pdb=" N LEU A 314 " --> pdb=" O CYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.680A pdb=" N CYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 322 " --> pdb=" O PRO A 318 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 4.094A pdb=" N TYR A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.864A pdb=" N GLU A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.579A pdb=" N ASN A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.694A pdb=" N ARG A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'B' and resid 11 through 32 removed outlier: 3.659A pdb=" N LEU B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.716A pdb=" N LEU B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 46 " --> pdb=" O HIS B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.904A pdb=" N GLU B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.592A pdb=" N VAL B 84 " --> pdb=" O MET B 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 85' Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.858A pdb=" N ILE B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 removed outlier: 3.539A pdb=" N VAL B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.964A pdb=" N LEU B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.522A pdb=" N LEU B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.627A pdb=" N LEU B 314 " --> pdb=" O CYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.680A pdb=" N CYS B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B 322 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 323 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 removed outlier: 4.093A pdb=" N TYR B 330 " --> pdb=" O CYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.864A pdb=" N GLU B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.580A pdb=" N ASN B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.694A pdb=" N ARG B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 376 removed outlier: 6.697A pdb=" N VAL A 369 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS A 389 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 414 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 376 removed outlier: 6.697A pdb=" N VAL B 369 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS B 389 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS B 387 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 414 " --> pdb=" O ILE B 382 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 372 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: 1.09 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1588 1.34 - 1.46: 950 1.46 - 1.58: 2572 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 5172 Sorted by residual: bond pdb=" CA HIS B 251 " pdb=" C HIS B 251 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CA HIS A 251 " pdb=" C HIS A 251 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CB PRO A 318 " pdb=" CG PRO A 318 " ideal model delta sigma weight residual 1.492 1.388 0.104 5.00e-02 4.00e+02 4.34e+00 bond pdb=" CB PRO B 318 " pdb=" CG PRO B 318 " ideal model delta sigma weight residual 1.492 1.388 0.104 5.00e-02 4.00e+02 4.29e+00 bond pdb=" CB VAL B 248 " pdb=" CG1 VAL B 248 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 5167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 6688 2.37 - 4.73: 298 4.73 - 7.10: 38 7.10 - 9.46: 6 9.46 - 11.83: 4 Bond angle restraints: 7034 Sorted by residual: angle pdb=" N ARG B 246 " pdb=" CA ARG B 246 " pdb=" C ARG B 246 " ideal model delta sigma weight residual 114.64 102.81 11.83 1.52e+00 4.33e-01 6.06e+01 angle pdb=" N ARG A 246 " pdb=" CA ARG A 246 " pdb=" C ARG A 246 " ideal model delta sigma weight residual 114.64 102.86 11.78 1.52e+00 4.33e-01 6.01e+01 angle pdb=" N LEU A 45 " pdb=" CA LEU A 45 " pdb=" C LEU A 45 " ideal model delta sigma weight residual 114.12 108.34 5.78 1.39e+00 5.18e-01 1.73e+01 angle pdb=" N LEU B 45 " pdb=" CA LEU B 45 " pdb=" C LEU B 45 " ideal model delta sigma weight residual 114.12 108.39 5.73 1.39e+00 5.18e-01 1.70e+01 angle pdb=" C PHE A 134 " pdb=" N HIS A 135 " pdb=" CA HIS A 135 " ideal model delta sigma weight residual 120.82 126.73 -5.91 1.47e+00 4.63e-01 1.62e+01 ... (remaining 7029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.98: 2398 7.98 - 15.97: 455 15.97 - 23.95: 117 23.95 - 31.94: 39 31.94 - 39.92: 28 Dihedral angle restraints: 3037 sinusoidal: 1163 harmonic: 1874 Sorted by residual: dihedral pdb=" CA ASN B 299 " pdb=" C ASN B 299 " pdb=" N SER B 300 " pdb=" CA SER B 300 " ideal model delta harmonic sigma weight residual -180.00 -147.40 -32.60 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA ASN A 299 " pdb=" C ASN A 299 " pdb=" N SER A 300 " pdb=" CA SER A 300 " ideal model delta harmonic sigma weight residual -180.00 -147.46 -32.54 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA VAL B 128 " pdb=" C VAL B 128 " pdb=" N LEU B 129 " pdb=" CA LEU B 129 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 3034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 363 0.036 - 0.073: 335 0.073 - 0.109: 98 0.109 - 0.145: 27 0.145 - 0.182: 15 Chirality restraints: 838 Sorted by residual: chirality pdb=" CA PRO A 318 " pdb=" N PRO A 318 " pdb=" C PRO A 318 " pdb=" CB PRO A 318 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA PRO B 318 " pdb=" N PRO B 318 " pdb=" C PRO B 318 " pdb=" CB PRO B 318 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CG LEU B 35 " pdb=" CB LEU B 35 " pdb=" CD1 LEU B 35 " pdb=" CD2 LEU B 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 835 not shown) Planarity restraints: 878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 317 " 0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO B 318 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 317 " -0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 318 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 333 " 0.042 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO A 334 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " 0.035 5.00e-02 4.00e+02 ... (remaining 875 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 33 2.61 - 3.18: 3974 3.18 - 3.75: 6947 3.75 - 4.33: 9631 4.33 - 4.90: 15774 Nonbonded interactions: 36359 Sorted by model distance: nonbonded pdb=" SG CYS B 276 " pdb=" SG CYS B 282 " model vdw 2.033 3.760 nonbonded pdb=" OE2 GLU B 109 " pdb=" NE1 TRP B 273 " model vdw 2.380 3.120 nonbonded pdb=" OE2 GLU A 109 " pdb=" NE1 TRP A 273 " model vdw 2.381 3.120 nonbonded pdb=" NE2 GLN B 376 " pdb=" O GLY B 379 " model vdw 2.382 3.120 nonbonded pdb=" NE2 GLN A 376 " pdb=" O GLY A 379 " model vdw 2.382 3.120 ... (remaining 36354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.380 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.470 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.010 0.104 5172 Z= 0.619 Angle : 1.138 11.829 7034 Z= 0.625 Chirality : 0.057 0.182 838 Planarity : 0.008 0.072 878 Dihedral : 10.183 38.574 1818 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -6.39 (0.24), residues: 642 helix: -5.04 (0.09), residues: 350 sheet: -1.22 (0.89), residues: 46 loop : -3.27 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 375 HIS 0.008 0.002 HIS B 373 PHE 0.022 0.003 PHE A 407 TYR 0.012 0.003 TYR B 270 ARG 0.011 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7886 (ttp-110) REVERT: A 99 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 64 THR cc_start: 0.8794 (p) cc_final: 0.8353 (m) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1698 time to fit residues: 21.9978 Evaluate side-chains 76 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 370 HIS A 409 ASN A 413 HIS B 251 HIS B 284 ASN B 370 HIS B 409 ASN B 413 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5172 Z= 0.233 Angle : 0.727 20.103 7034 Z= 0.351 Chirality : 0.042 0.140 838 Planarity : 0.006 0.055 878 Dihedral : 7.222 29.685 686 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.91 % Allowed : 7.79 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.51 (0.27), residues: 642 helix: -4.23 (0.16), residues: 354 sheet: -1.36 (0.80), residues: 46 loop : -2.86 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 375 HIS 0.003 0.001 HIS B 373 PHE 0.012 0.001 PHE B 94 TYR 0.017 0.002 TYR B 270 ARG 0.002 0.001 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7948 (ttm-80) REVERT: A 78 GLU cc_start: 0.7962 (pt0) cc_final: 0.7666 (pt0) REVERT: A 99 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7349 (tm-30) REVERT: B 44 MET cc_start: 0.7778 (mtm) cc_final: 0.7570 (mtp) REVERT: B 78 GLU cc_start: 0.7842 (pt0) cc_final: 0.7558 (pt0) REVERT: B 80 MET cc_start: 0.8787 (ptm) cc_final: 0.8339 (ptm) REVERT: B 99 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7115 (tm-30) REVERT: B 371 GLU cc_start: 0.8092 (tp30) cc_final: 0.7849 (tp30) outliers start: 5 outliers final: 3 residues processed: 86 average time/residue: 0.1675 time to fit residues: 19.8028 Evaluate side-chains 75 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 57 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 255 ASN B 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5172 Z= 0.165 Angle : 0.658 18.786 7034 Z= 0.314 Chirality : 0.041 0.145 838 Planarity : 0.004 0.035 878 Dihedral : 6.390 27.984 686 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.91 % Allowed : 10.87 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.92 (0.28), residues: 642 helix: -3.59 (0.20), residues: 364 sheet: -0.95 (0.80), residues: 46 loop : -2.87 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.002 0.001 HIS A 373 PHE 0.010 0.001 PHE B 281 TYR 0.023 0.002 TYR A 270 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 99 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 80 MET cc_start: 0.8692 (ptm) cc_final: 0.8443 (ptm) REVERT: B 371 GLU cc_start: 0.8016 (tp30) cc_final: 0.7796 (tp30) outliers start: 5 outliers final: 3 residues processed: 85 average time/residue: 0.1456 time to fit residues: 16.5856 Evaluate side-chains 71 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 28 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 61 optimal weight: 7.9990 chunk 55 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5172 Z= 0.152 Angle : 0.629 18.683 7034 Z= 0.296 Chirality : 0.041 0.135 838 Planarity : 0.004 0.032 878 Dihedral : 5.991 26.655 686 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.45 % Allowed : 12.68 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.41 (0.30), residues: 642 helix: -3.17 (0.23), residues: 362 sheet: -0.55 (0.80), residues: 46 loop : -2.70 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.002 0.000 HIS A 373 PHE 0.009 0.001 PHE B 94 TYR 0.016 0.001 TYR B 270 ARG 0.002 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7866 (tt0) cc_final: 0.7495 (tt0) REVERT: A 30 ARG cc_start: 0.7057 (tmt170) cc_final: 0.6540 (tmt170) REVERT: A 58 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7167 (mm-30) REVERT: B 10 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8460 (ttm-80) REVERT: B 30 ARG cc_start: 0.6790 (tmt170) cc_final: 0.6550 (tmt170) REVERT: B 80 MET cc_start: 0.8708 (ptm) cc_final: 0.8348 (ptm) REVERT: B 359 GLU cc_start: 0.7735 (mp0) cc_final: 0.7247 (mt-10) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.1832 time to fit residues: 18.2846 Evaluate side-chains 70 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 339 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN B 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5172 Z= 0.201 Angle : 0.640 18.745 7034 Z= 0.300 Chirality : 0.042 0.134 838 Planarity : 0.004 0.033 878 Dihedral : 5.945 25.780 686 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.36 % Allowed : 13.22 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.94 (0.31), residues: 642 helix: -2.91 (0.24), residues: 352 sheet: -0.27 (0.81), residues: 46 loop : -2.35 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 375 HIS 0.003 0.001 HIS A 373 PHE 0.009 0.001 PHE B 94 TYR 0.015 0.001 TYR B 270 ARG 0.002 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7762 (tt0) cc_final: 0.7513 (tt0) REVERT: B 80 MET cc_start: 0.8766 (ptm) cc_final: 0.8262 (ptm) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.1435 time to fit residues: 16.1274 Evaluate side-chains 69 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 339 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.0010 chunk 51 optimal weight: 0.0870 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 32 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.0270 overall best weight: 0.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN B 255 ASN B 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5172 Z= 0.121 Angle : 0.607 17.551 7034 Z= 0.283 Chirality : 0.040 0.131 838 Planarity : 0.003 0.030 878 Dihedral : 5.310 24.407 686 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.99 % Allowed : 14.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.76 (0.32), residues: 642 helix: -2.62 (0.25), residues: 362 sheet: 0.25 (0.84), residues: 46 loop : -2.59 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.002 0.000 HIS B 108 PHE 0.007 0.001 PHE B 21 TYR 0.011 0.001 TYR B 270 ARG 0.003 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7291 (mm-30) REVERT: B 80 MET cc_start: 0.8555 (ptm) cc_final: 0.8354 (ptm) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.1303 time to fit residues: 12.2355 Evaluate side-chains 63 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 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 409 ASN B 68 GLN B 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5172 Z= 0.165 Angle : 0.609 18.109 7034 Z= 0.283 Chirality : 0.041 0.133 838 Planarity : 0.003 0.033 878 Dihedral : 5.395 23.678 686 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.27 % Allowed : 14.13 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.34 (0.33), residues: 642 helix: -2.39 (0.26), residues: 352 sheet: 0.50 (0.86), residues: 46 loop : -2.26 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.002 0.001 HIS A 373 PHE 0.008 0.001 PHE A 94 TYR 0.013 0.001 TYR B 270 ARG 0.001 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: B 80 MET cc_start: 0.8590 (ptm) cc_final: 0.8017 (ptm) outliers start: 7 outliers final: 6 residues processed: 68 average time/residue: 0.1470 time to fit residues: 13.8516 Evaluate side-chains 61 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5172 Z= 0.158 Angle : 0.599 18.039 7034 Z= 0.278 Chirality : 0.041 0.136 838 Planarity : 0.003 0.031 878 Dihedral : 5.292 23.037 686 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.17 % Allowed : 13.41 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.16 (0.33), residues: 642 helix: -2.20 (0.26), residues: 352 sheet: 0.52 (0.86), residues: 46 loop : -2.25 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 375 HIS 0.002 0.001 HIS A 373 PHE 0.008 0.001 PHE A 94 TYR 0.015 0.001 TYR B 270 ARG 0.001 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 381 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6600 (ttt90) REVERT: B 80 MET cc_start: 0.8574 (ptm) cc_final: 0.8146 (tmm) REVERT: B 388 ILE cc_start: 0.7959 (mt) cc_final: 0.7505 (pt) outliers start: 12 outliers final: 10 residues processed: 68 average time/residue: 0.1518 time to fit residues: 14.1482 Evaluate side-chains 65 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 332 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN B 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5172 Z= 0.141 Angle : 0.604 17.922 7034 Z= 0.276 Chirality : 0.041 0.131 838 Planarity : 0.003 0.031 878 Dihedral : 5.105 22.285 686 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.99 % Allowed : 13.77 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.94 (0.33), residues: 642 helix: -1.98 (0.27), residues: 352 sheet: 0.62 (0.85), residues: 46 loop : -2.22 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.002 0.000 HIS A 373 PHE 0.008 0.001 PHE A 94 TYR 0.012 0.001 TYR B 270 ARG 0.001 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 381 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6595 (ttt90) REVERT: B 80 MET cc_start: 0.8513 (ptm) cc_final: 0.7957 (ptm) REVERT: B 388 ILE cc_start: 0.7954 (mt) cc_final: 0.7586 (pt) outliers start: 11 outliers final: 10 residues processed: 64 average time/residue: 0.1488 time to fit residues: 13.1108 Evaluate side-chains 62 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN B 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5172 Z= 0.176 Angle : 0.605 17.855 7034 Z= 0.280 Chirality : 0.042 0.132 838 Planarity : 0.003 0.031 878 Dihedral : 5.173 22.163 686 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.17 % Allowed : 13.95 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.82 (0.33), residues: 642 helix: -1.87 (0.27), residues: 352 sheet: 0.63 (0.85), residues: 46 loop : -2.17 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.002 0.001 HIS B 373 PHE 0.009 0.001 PHE A 94 TYR 0.013 0.001 TYR B 270 ARG 0.001 0.000 ARG A 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 381 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6587 (ttt90) outliers start: 12 outliers final: 11 residues processed: 62 average time/residue: 0.1464 time to fit residues: 12.5760 Evaluate side-chains 63 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 332 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN B 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.192460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132981 restraints weight = 5339.627| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.83 r_work: 0.3451 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5172 Z= 0.149 Angle : 0.614 17.764 7034 Z= 0.279 Chirality : 0.041 0.131 838 Planarity : 0.003 0.030 878 Dihedral : 5.053 21.786 686 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.17 % Allowed : 14.49 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.63 (0.34), residues: 642 helix: -1.66 (0.28), residues: 354 sheet: 0.68 (0.85), residues: 46 loop : -2.18 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.002 0.000 HIS A 373 PHE 0.009 0.001 PHE A 94 TYR 0.013 0.001 TYR B 270 ARG 0.001 0.000 ARG A 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1480.51 seconds wall clock time: 28 minutes 25.16 seconds (1705.16 seconds total)