Starting phenix.real_space_refine on Fri Apr 5 21:49:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/04_2024/8tgl_41240_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/04_2024/8tgl_41240.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/04_2024/8tgl_41240_trim_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/04_2024/8tgl_41240_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/04_2024/8tgl_41240_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/04_2024/8tgl_41240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/04_2024/8tgl_41240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/04_2024/8tgl_41240_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgl_41240/04_2024/8tgl_41240_trim_updated.pdb" } 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= 0.001 sd= 0.019 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 57 5.16 5 C 3817 2.51 5 N 892 2.21 5 O 968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5734 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2838 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 23, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2840 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 21, 'TRANS': 357} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'LNR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.58, per 1000 atoms: 0.62 Number of scatterers: 5734 At special positions: 0 Unit cell: (72.5973, 51.3493, 114.208, 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 57 16.00 O 968 8.00 N 892 7.00 C 3817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 20 through 40 removed outlier: 3.690A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 137 through 186 removed outlier: 3.796A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 159 - end of helix removed outlier: 3.759A pdb=" N ASN A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N TYR A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N HIS A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 190 through 218 Processing helix chain 'A' and resid 222 through 252 removed outlier: 3.632A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 256 through 277 removed outlier: 4.358A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.147A pdb=" N LYS A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 330 Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 338 through 363 removed outlier: 3.949A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 5.254A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 390 through 420 removed outlier: 4.113A pdb=" N GLY A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Proline residue: A 395 - end of helix removed outlier: 4.623A pdb=" N MET A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.620A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 4.802A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 479 Proline residue: A 473 - end of helix removed outlier: 4.177A pdb=" N TYR A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG A 479 " --> pdb=" O CYS A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 42 through 53 Proline residue: B 46 - end of helix removed outlier: 3.676A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.247A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.056A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 190 through 218 Processing helix chain 'B' and resid 224 through 249 removed outlier: 4.000A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 3.550A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 300 through 330 removed outlier: 4.016A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) Proline residue: B 321 - end of helix Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 343 through 363 removed outlier: 5.847A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 Proline residue: B 384 - end of helix Processing helix chain 'B' and resid 390 through 421 removed outlier: 3.936A pdb=" N GLY B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Proline residue: B 395 - end of helix removed outlier: 4.670A pdb=" N MET B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Proline residue: B 412 - end of helix removed outlier: 3.687A pdb=" N LEU B 420 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 421 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 454 Proline residue: B 445 - end of helix removed outlier: 3.567A pdb=" N GLY B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 478 Proline residue: B 473 - end of helix removed outlier: 4.710A pdb=" N TYR B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1113 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: 1.59 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 849 1.31 - 1.43: 1561 1.43 - 1.56: 3367 1.56 - 1.69: 1 1.69 - 1.81: 100 Bond restraints: 5878 Sorted by residual: bond pdb=" C10 YHR B 601 " pdb=" C11 YHR B 601 " ideal model delta sigma weight residual 1.572 1.431 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" CAI LNR A 601 " pdb=" OAB LNR A 601 " ideal model delta sigma weight residual 1.351 1.452 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C PRO B 481 " pdb=" O PRO B 481 " ideal model delta sigma weight residual 1.246 1.205 0.041 8.50e-03 1.38e+04 2.29e+01 bond pdb=" CAJ LNR A 601 " pdb=" OAC LNR A 601 " ideal model delta sigma weight residual 1.353 1.433 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C13 YHR B 601 " pdb=" C14 YHR B 601 " ideal model delta sigma weight residual 1.567 1.489 0.078 2.00e-02 2.50e+03 1.54e+01 ... (remaining 5873 not shown) Histogram of bond angle deviations from ideal: 98.91 - 106.37: 217 106.37 - 113.84: 3358 113.84 - 121.30: 3305 121.30 - 128.77: 1094 128.77 - 136.23: 34 Bond angle restraints: 8008 Sorted by residual: angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 99.45 132.78 -33.33 3.00e+00 1.11e-01 1.23e+02 angle pdb=" N ARG B 225 " pdb=" CA ARG B 225 " pdb=" C ARG B 225 " ideal model delta sigma weight residual 111.28 103.22 8.06 1.09e+00 8.42e-01 5.46e+01 angle pdb=" N HIS B 223 " pdb=" CA HIS B 223 " pdb=" C HIS B 223 " ideal model delta sigma weight residual 114.12 104.55 9.57 1.39e+00 5.18e-01 4.74e+01 angle pdb=" C25 YHR B 601 " pdb=" C26 YHR B 601 " pdb=" O28 YHR B 601 " ideal model delta sigma weight residual 137.71 119.23 18.48 3.00e+00 1.11e-01 3.80e+01 angle pdb=" C27 YHR B 601 " pdb=" C26 YHR B 601 " pdb=" O28 YHR B 601 " ideal model delta sigma weight residual 101.89 119.45 -17.56 3.00e+00 1.11e-01 3.43e+01 ... (remaining 8003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 3036 22.75 - 45.50: 326 45.50 - 68.26: 38 68.26 - 91.01: 3 91.01 - 113.76: 2 Dihedral angle restraints: 3405 sinusoidal: 1266 harmonic: 2139 Sorted by residual: dihedral pdb=" CA PHE A 294 " pdb=" C PHE A 294 " pdb=" N MET A 295 " pdb=" CA MET A 295 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA VAL B 358 " pdb=" C VAL B 358 " pdb=" N LEU B 359 " pdb=" CA LEU B 359 " ideal model delta harmonic sigma weight residual 180.00 -155.40 -24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA VAL A 358 " pdb=" C VAL A 358 " pdb=" N LEU A 359 " pdb=" CA LEU A 359 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 3402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 781 0.050 - 0.100: 152 0.100 - 0.149: 23 0.149 - 0.199: 5 0.199 - 0.249: 2 Chirality restraints: 963 Sorted by residual: chirality pdb=" CAL LNR A 601 " pdb=" CAH LNR A 601 " pdb=" CAK LNR A 601 " pdb=" OAD LNR A 601 " both_signs ideal model delta sigma weight residual False -2.28 -2.53 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C6 YHR B 601 " pdb=" C15 YHR B 601 " pdb=" C5 YHR B 601 " pdb=" C7 YHR B 601 " both_signs ideal model delta sigma weight residual False 2.70 2.49 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ARG B 225 " pdb=" N ARG B 225 " pdb=" C ARG B 225 " pdb=" CB ARG B 225 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.69e-01 ... (remaining 960 not shown) Planarity restraints: 973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 252 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C GLU A 252 " -0.070 2.00e-02 2.50e+03 pdb=" O GLU A 252 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE A 253 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 225 " -0.013 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C ARG B 225 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG B 225 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 226 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 168 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 169 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " 0.028 5.00e-02 4.00e+02 ... (remaining 970 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 964 2.75 - 3.29: 6162 3.29 - 3.83: 9813 3.83 - 4.36: 10917 4.36 - 4.90: 19435 Nonbonded interactions: 47291 Sorted by model distance: nonbonded pdb=" O VAL B 304 " pdb=" OH TYR B 471 " model vdw 2.218 2.440 nonbonded pdb=" O THR B 291 " pdb=" OG1 THR B 291 " model vdw 2.225 2.440 nonbonded pdb=" O VAL A 375 " pdb=" OG SER A 379 " model vdw 2.236 2.440 nonbonded pdb=" O ARG B 138 " pdb=" OH TYR B 190 " model vdw 2.238 2.440 nonbonded pdb=" O ILE A 277 " pdb=" NE2 GLN A 279 " model vdw 2.246 2.520 ... (remaining 47286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 278 or resid 289 through 483)) selection = (chain 'B' and (resid 19 through 50 or resid 136 through 483)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 6.650 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.070 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 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 : 0.005 0.141 5878 Z= 0.335 Angle : 0.906 33.332 8008 Z= 0.463 Chirality : 0.042 0.249 963 Planarity : 0.006 0.050 973 Dihedral : 17.147 113.759 2045 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 30.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.73 % Favored : 98.13 % Rotamer: Outliers : 0.82 % Allowed : 32.57 % Favored : 66.61 % 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: 1.90 (0.32), residues: 750 helix: 1.78 (0.22), residues: 589 sheet: None (None), residues: 0 loop : -0.59 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 459 HIS 0.018 0.002 HIS B 387 PHE 0.024 0.001 PHE B 28 TYR 0.009 0.001 TYR A 426 ARG 0.002 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 426 TYR cc_start: 0.7150 (m-80) cc_final: 0.6919 (m-80) REVERT: A 447 THR cc_start: 0.7420 (p) cc_final: 0.7003 (m) REVERT: B 410 MET cc_start: 0.6502 (mmp) cc_final: 0.6212 (tpp) outliers start: 5 outliers final: 1 residues processed: 124 average time/residue: 0.1557 time to fit residues: 26.1260 Evaluate side-chains 120 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.0000 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.0040 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 396 ASN B 35 ASN B 154 ASN B 329 GLN B 468 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5878 Z= 0.252 Angle : 0.683 9.998 8008 Z= 0.334 Chirality : 0.044 0.200 963 Planarity : 0.006 0.045 973 Dihedral : 6.206 66.337 823 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.91 % Allowed : 27.33 % Favored : 67.76 % 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: 1.41 (0.31), residues: 750 helix: 1.38 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -0.62 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.006 0.001 HIS B 387 PHE 0.036 0.001 PHE A 206 TYR 0.010 0.001 TYR B 349 ARG 0.002 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 0.569 Fit side-chains REVERT: A 151 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6327 (tt) REVERT: A 233 LEU cc_start: 0.7332 (mt) cc_final: 0.7042 (mp) REVERT: A 279 GLN cc_start: 0.8477 (mp10) cc_final: 0.7950 (mp10) REVERT: B 325 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7574 (mp) REVERT: B 356 PHE cc_start: 0.7699 (m-80) cc_final: 0.7416 (m-80) REVERT: B 410 MET cc_start: 0.6301 (mmp) cc_final: 0.6071 (tpp) outliers start: 30 outliers final: 12 residues processed: 138 average time/residue: 0.1415 time to fit residues: 27.1371 Evaluate side-chains 134 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5878 Z= 0.275 Angle : 0.675 10.268 8008 Z= 0.326 Chirality : 0.042 0.149 963 Planarity : 0.006 0.044 973 Dihedral : 5.928 68.590 820 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.42 % Allowed : 27.82 % Favored : 67.76 % 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: 0.96 (0.31), residues: 750 helix: 1.11 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.18 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.006 0.001 HIS B 387 PHE 0.027 0.001 PHE A 206 TYR 0.009 0.002 TYR B 349 ARG 0.005 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.593 Fit side-chains REVERT: A 279 GLN cc_start: 0.8483 (mp10) cc_final: 0.8203 (mp10) REVERT: A 467 ILE cc_start: 0.7458 (mt) cc_final: 0.7223 (mp) REVERT: B 325 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7589 (mp) outliers start: 27 outliers final: 15 residues processed: 141 average time/residue: 0.1462 time to fit residues: 28.0654 Evaluate side-chains 144 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5878 Z= 0.314 Angle : 0.684 10.616 8008 Z= 0.331 Chirality : 0.043 0.143 963 Planarity : 0.006 0.045 973 Dihedral : 5.970 73.695 820 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.07 % Allowed : 27.82 % Favored : 67.10 % 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: 0.76 (0.31), residues: 750 helix: 1.00 (0.22), residues: 603 sheet: None (None), residues: 0 loop : -1.40 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.004 0.001 HIS B 387 PHE 0.025 0.002 PHE A 206 TYR 0.011 0.002 TYR B 476 ARG 0.007 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6314 (tt) REVERT: A 233 LEU cc_start: 0.7495 (mt) cc_final: 0.7242 (mp) REVERT: A 266 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7868 (mp) REVERT: A 359 LEU cc_start: 0.7805 (tt) cc_final: 0.7457 (tp) REVERT: B 254 VAL cc_start: 0.7404 (m) cc_final: 0.7146 (p) REVERT: B 325 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7663 (mp) outliers start: 31 outliers final: 20 residues processed: 150 average time/residue: 0.1472 time to fit residues: 30.2008 Evaluate side-chains 152 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 0.0370 chunk 29 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.0030 chunk 65 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.2468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5878 Z= 0.213 Angle : 0.663 9.235 8008 Z= 0.318 Chirality : 0.042 0.152 963 Planarity : 0.005 0.042 973 Dihedral : 5.809 71.061 820 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.09 % Allowed : 30.11 % Favored : 65.79 % 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: 1.20 (0.31), residues: 750 helix: 1.26 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -0.81 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.004 0.001 HIS B 387 PHE 0.025 0.001 PHE A 206 TYR 0.008 0.001 TYR A 430 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7793 (mp) REVERT: A 447 THR cc_start: 0.7424 (p) cc_final: 0.7162 (m) REVERT: B 261 LEU cc_start: 0.7242 (mm) cc_final: 0.7037 (mm) outliers start: 25 outliers final: 16 residues processed: 141 average time/residue: 0.1362 time to fit residues: 26.6244 Evaluate side-chains 145 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.0010 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 154 ASN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5878 Z= 0.281 Angle : 0.685 10.735 8008 Z= 0.329 Chirality : 0.043 0.161 963 Planarity : 0.006 0.043 973 Dihedral : 5.873 73.528 820 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.26 % Allowed : 30.77 % Favored : 64.98 % 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: 0.86 (0.31), residues: 750 helix: 1.06 (0.22), residues: 599 sheet: None (None), residues: 0 loop : -1.24 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.003 0.001 HIS B 387 PHE 0.026 0.001 PHE A 206 TYR 0.009 0.002 TYR A 430 ARG 0.014 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6298 (tt) REVERT: A 233 LEU cc_start: 0.7493 (mt) cc_final: 0.7256 (mp) REVERT: A 266 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7826 (mp) REVERT: A 359 LEU cc_start: 0.7776 (tt) cc_final: 0.7455 (tp) REVERT: A 376 VAL cc_start: 0.7465 (t) cc_final: 0.7233 (t) outliers start: 26 outliers final: 20 residues processed: 145 average time/residue: 0.1296 time to fit residues: 26.2284 Evaluate side-chains 148 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.0980 chunk 41 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5878 Z= 0.254 Angle : 0.680 9.744 8008 Z= 0.328 Chirality : 0.042 0.154 963 Planarity : 0.006 0.043 973 Dihedral : 5.800 73.132 820 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.76 % Allowed : 31.75 % Favored : 64.48 % 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: 0.87 (0.31), residues: 750 helix: 1.07 (0.22), residues: 599 sheet: None (None), residues: 0 loop : -1.23 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS B 223 PHE 0.020 0.001 PHE B 28 TYR 0.009 0.001 TYR B 476 ARG 0.010 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6297 (tt) REVERT: A 233 LEU cc_start: 0.7492 (mt) cc_final: 0.7271 (mp) REVERT: A 266 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 359 LEU cc_start: 0.7760 (tt) cc_final: 0.7476 (tp) REVERT: A 376 VAL cc_start: 0.7453 (t) cc_final: 0.7229 (t) REVERT: B 179 LEU cc_start: 0.8068 (mp) cc_final: 0.7789 (mp) outliers start: 23 outliers final: 19 residues processed: 143 average time/residue: 0.1387 time to fit residues: 27.4389 Evaluate side-chains 149 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5878 Z= 0.295 Angle : 0.687 9.483 8008 Z= 0.332 Chirality : 0.043 0.139 963 Planarity : 0.006 0.044 973 Dihedral : 5.828 76.041 820 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.27 % Allowed : 31.91 % Favored : 64.81 % 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: 0.78 (0.31), residues: 750 helix: 1.03 (0.22), residues: 597 sheet: None (None), residues: 0 loop : -1.31 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.002 0.000 HIS B 223 PHE 0.031 0.002 PHE A 206 TYR 0.009 0.002 TYR B 349 ARG 0.001 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6271 (tt) REVERT: A 233 LEU cc_start: 0.7513 (mt) cc_final: 0.7273 (mp) REVERT: A 266 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7838 (mp) REVERT: A 359 LEU cc_start: 0.7750 (tt) cc_final: 0.7465 (tp) REVERT: A 376 VAL cc_start: 0.7461 (t) cc_final: 0.7228 (t) outliers start: 20 outliers final: 18 residues processed: 138 average time/residue: 0.1369 time to fit residues: 26.1928 Evaluate side-chains 146 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 60 optimal weight: 0.1980 chunk 63 optimal weight: 0.0470 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5878 Z= 0.255 Angle : 0.675 9.905 8008 Z= 0.326 Chirality : 0.042 0.138 963 Planarity : 0.005 0.043 973 Dihedral : 5.743 74.231 820 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.27 % Allowed : 31.91 % Favored : 64.81 % 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: 0.84 (0.31), residues: 750 helix: 1.07 (0.22), residues: 599 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS B 223 PHE 0.021 0.001 PHE B 28 TYR 0.008 0.001 TYR B 301 ARG 0.001 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6268 (tt) REVERT: A 233 LEU cc_start: 0.7494 (mt) cc_final: 0.7236 (mp) REVERT: A 266 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 359 LEU cc_start: 0.7748 (tt) cc_final: 0.7479 (tp) REVERT: A 376 VAL cc_start: 0.7459 (t) cc_final: 0.7231 (t) REVERT: B 179 LEU cc_start: 0.8044 (mp) cc_final: 0.7778 (mp) REVERT: B 356 PHE cc_start: 0.7856 (m-80) cc_final: 0.7649 (m-80) outliers start: 20 outliers final: 18 residues processed: 139 average time/residue: 0.1355 time to fit residues: 26.2864 Evaluate side-chains 148 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.0470 chunk 68 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5878 Z= 0.257 Angle : 0.692 11.825 8008 Z= 0.333 Chirality : 0.043 0.157 963 Planarity : 0.006 0.043 973 Dihedral : 5.736 74.182 820 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.44 % Allowed : 32.24 % Favored : 64.32 % 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: 0.82 (0.31), residues: 750 helix: 1.05 (0.22), residues: 599 sheet: None (None), residues: 0 loop : -1.33 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS B 223 PHE 0.020 0.001 PHE B 28 TYR 0.009 0.001 TYR A 430 ARG 0.001 0.000 ARG B 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6268 (tt) REVERT: A 233 LEU cc_start: 0.7490 (mt) cc_final: 0.7256 (mp) REVERT: A 266 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7845 (mp) REVERT: A 359 LEU cc_start: 0.7762 (tt) cc_final: 0.7506 (tp) REVERT: A 376 VAL cc_start: 0.7456 (t) cc_final: 0.7215 (t) REVERT: B 179 LEU cc_start: 0.8046 (mp) cc_final: 0.7787 (mp) REVERT: B 356 PHE cc_start: 0.7877 (m-80) cc_final: 0.7656 (m-80) outliers start: 21 outliers final: 18 residues processed: 140 average time/residue: 0.1389 time to fit residues: 26.9509 Evaluate side-chains 146 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 61 optimal weight: 0.0870 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.147482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133268 restraints weight = 7939.617| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.13 r_work: 0.3560 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5878 Z= 0.243 Angle : 0.688 11.845 8008 Z= 0.331 Chirality : 0.043 0.158 963 Planarity : 0.005 0.042 973 Dihedral : 5.683 72.931 820 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.44 % Allowed : 32.08 % Favored : 64.48 % 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: 0.80 (0.31), residues: 750 helix: 1.05 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.41 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.001 0.000 HIS B 223 PHE 0.047 0.001 PHE A 206 TYR 0.009 0.001 TYR A 430 ARG 0.001 0.000 ARG B 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.55 seconds wall clock time: 29 minutes 40.04 seconds (1780.04 seconds total)