Starting phenix.real_space_refine on Tue Mar 3 14:09:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fzr_29638/03_2026/8fzr_29638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fzr_29638/03_2026/8fzr_29638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fzr_29638/03_2026/8fzr_29638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fzr_29638/03_2026/8fzr_29638.map" model { file = "/net/cci-nas-00/data/ceres_data/8fzr_29638/03_2026/8fzr_29638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fzr_29638/03_2026/8fzr_29638.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 76 5.49 5 S 32 5.16 5 C 3342 2.51 5 N 966 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5711 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4071 Classifications: {'peptide': 503} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 477} Chain: "R" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1639 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 158 SG CYS A 20 22.510 31.353 95.799 1.00 0.00 S ATOM 180 SG CYS A 23 23.297 28.877 95.832 1.00 0.00 S ATOM 754 SG CYS A 94 24.926 28.690 98.909 1.00 0.00 S ATOM 760 SG CYS A 95 25.270 30.234 95.400 1.00 0.00 S Time building chain proxies: 1.40, per 1000 atoms: 0.25 Number of scatterers: 5711 At special positions: 0 Unit cell: (66.3176, 78.534, 136.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 76 15.00 O 1294 8.00 N 966 7.00 C 3342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 127.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 23 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 95 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 20 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 94 " Number of angles added : 6 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 3 sheets defined 40.4% alpha, 10.1% beta 4 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.651A pdb=" N LEU A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.988A pdb=" N ARG A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 77 removed outlier: 4.139A pdb=" N ARG A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.807A pdb=" N ILE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 120 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 125' Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.992A pdb=" N ASN A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 178 removed outlier: 3.503A pdb=" N LYS A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.610A pdb=" N LYS A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 214 removed outlier: 3.773A pdb=" N TRP A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.930A pdb=" N LEU A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.590A pdb=" N ARG A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.039A pdb=" N TYR A 303 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.845A pdb=" N GLY A 332 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 382 through 396 removed outlier: 3.836A pdb=" N SER A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.509A pdb=" N THR A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 410 " --> pdb=" O LEU A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.671A pdb=" N ASN A 417 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY A 418 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.709A pdb=" N LEU A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 4.245A pdb=" N ASP A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.838A pdb=" N GLU A 472 " --> pdb=" O PHE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.715A pdb=" N VAL A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.313A pdb=" N PHE A 5 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU A 498 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 7 " --> pdb=" O LEU A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 102 removed outlier: 6.474A pdb=" N TYR A 98 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TYR A 293 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE A 100 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE A 253 " --> pdb=" O TYR A 290 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A 292 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER A 255 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N TYR A 294 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 13.408A pdb=" N TYR A 257 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL A 245 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N PHE A 258 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 243 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP A 260 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE A 241 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A 236 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 242 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 156 " --> pdb=" O CYS A 233 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.66 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: 1507 1.34 - 1.46: 1549 1.46 - 1.57: 2749 1.57 - 1.69: 152 1.69 - 1.81: 49 Bond restraints: 6006 Sorted by residual: bond pdb=" N GLU A 490 " pdb=" CA GLU A 490 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.73e+00 bond pdb=" N THR A 491 " pdb=" CA THR A 491 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.73e+00 bond pdb=" N PHE A 487 " pdb=" CA PHE A 487 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.61e-02 3.86e+03 4.05e+00 bond pdb=" N GLY A 488 " pdb=" CA GLY A 488 " ideal model delta sigma weight residual 1.449 1.475 -0.026 1.45e-02 4.76e+03 3.24e+00 bond pdb=" N PHE A 489 " pdb=" CA PHE A 489 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.76e+00 ... (remaining 6001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 8372 1.55 - 3.10: 100 3.10 - 4.65: 20 4.65 - 6.20: 4 6.20 - 7.75: 1 Bond angle restraints: 8497 Sorted by residual: angle pdb=" N PHE A 487 " pdb=" CA PHE A 487 " pdb=" C PHE A 487 " ideal model delta sigma weight residual 109.11 115.29 -6.18 1.42e+00 4.96e-01 1.89e+01 angle pdb=" C3' C R 49 " pdb=" O3' C R 49 " pdb=" P G R 50 " ideal model delta sigma weight residual 120.20 125.42 -5.22 1.50e+00 4.44e-01 1.21e+01 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 113.53 110.45 3.08 9.80e-01 1.04e+00 9.86e+00 angle pdb=" O3' C R 49 " pdb=" C3' C R 49 " pdb=" C2' C R 49 " ideal model delta sigma weight residual 109.50 113.86 -4.36 1.50e+00 4.44e-01 8.47e+00 angle pdb=" CA PHE A 487 " pdb=" C PHE A 487 " pdb=" O PHE A 487 " ideal model delta sigma weight residual 121.86 117.92 3.94 1.39e+00 5.18e-01 8.03e+00 ... (remaining 8492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 3447 34.82 - 69.63: 239 69.63 - 104.45: 34 104.45 - 139.26: 0 139.26 - 174.08: 1 Dihedral angle restraints: 3721 sinusoidal: 2247 harmonic: 1474 Sorted by residual: dihedral pdb=" C4' C R 49 " pdb=" C3' C R 49 " pdb=" O3' C R 49 " pdb=" P G R 50 " ideal model delta sinusoidal sigma weight residual 250.00 75.92 174.08 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA TRP A 260 " pdb=" C TRP A 260 " pdb=" N ASP A 261 " pdb=" CA ASP A 261 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" O4' C R 49 " pdb=" C1' C R 49 " pdb=" N1 C R 49 " pdb=" C2 C R 49 " ideal model delta sinusoidal sigma weight residual -128.00 -74.93 -53.07 1 1.70e+01 3.46e-03 1.33e+01 ... (remaining 3718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 787 0.039 - 0.077: 137 0.077 - 0.116: 48 0.116 - 0.154: 4 0.154 - 0.193: 1 Chirality restraints: 977 Sorted by residual: chirality pdb=" C3' C R 49 " pdb=" C4' C R 49 " pdb=" O3' C R 49 " pdb=" C2' C R 49 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ILE A 259 " pdb=" N ILE A 259 " pdb=" C ILE A 259 " pdb=" CB ILE A 259 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE A 253 " pdb=" N ILE A 253 " pdb=" C ILE A 253 " pdb=" CB ILE A 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 974 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 486 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C LEU A 486 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU A 486 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 487 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 487 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C PHE A 487 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE A 487 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 488 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 249 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 250 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " 0.017 5.00e-02 4.00e+02 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1065 2.77 - 3.30: 5148 3.30 - 3.83: 9289 3.83 - 4.37: 10496 4.37 - 4.90: 16735 Nonbonded interactions: 42733 Sorted by model distance: nonbonded pdb=" N ASP A 89 " pdb=" OD1 ASP A 89 " model vdw 2.234 3.120 nonbonded pdb=" O ILE A 253 " pdb=" N TYR A 290 " model vdw 2.252 3.120 nonbonded pdb=" O2' G R 15 " pdb=" OP1 G R 19 " model vdw 2.254 3.040 nonbonded pdb=" O GLY A 77 " pdb=" OH TYR A 293 " model vdw 2.278 3.040 nonbonded pdb=" O ASP A 71 " pdb=" ND2 ASN A 75 " model vdw 2.290 3.120 ... (remaining 42728 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.030 Find NCS groups from input model: 0.020 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2377 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 6010 Z= 0.136 Angle : 1.029 46.512 8503 Z= 0.317 Chirality : 0.034 0.193 977 Planarity : 0.004 0.031 803 Dihedral : 20.143 174.077 2781 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 1.00 % Allowed : 4.59 % Favored : 94.41 % Rotamer: Outliers : 6.97 % Allowed : 10.56 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.37), residues: 501 helix: -0.88 (0.55), residues: 93 sheet: -2.68 (0.69), residues: 45 loop : -1.19 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 276 TYR 0.007 0.001 TYR A 173 PHE 0.008 0.001 PHE A 139 TRP 0.005 0.001 TRP A 267 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 6006) covalent geometry : angle 0.47673 ( 8497) hydrogen bonds : bond 0.32909 ( 102) hydrogen bonds : angle 11.40266 ( 237) metal coordination : bond 0.08025 ( 4) metal coordination : angle 34.34967 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 PHE cc_start: 0.5898 (OUTLIER) cc_final: 0.5271 (p90) REVERT: A 293 TYR cc_start: 0.4648 (OUTLIER) cc_final: 0.3979 (m-80) REVERT: A 310 GLU cc_start: 0.3033 (OUTLIER) cc_final: 0.2778 (tp30) REVERT: A 361 PHE cc_start: 0.4508 (OUTLIER) cc_final: 0.4082 (m-80) outliers start: 31 outliers final: 8 residues processed: 108 average time/residue: 0.0884 time to fit residues: 12.0031 Evaluate side-chains 55 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 174 GLN A 183 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN A 326 GLN A 416 HIS A 442 GLN A 475 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.142486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.122595 restraints weight = 32653.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.124619 restraints weight = 26140.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.126009 restraints weight = 21849.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.126909 restraints weight = 19089.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.127911 restraints weight = 17338.154| |-----------------------------------------------------------------------------| r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6010 Z= 0.174 Angle : 0.715 9.108 8503 Z= 0.353 Chirality : 0.040 0.203 977 Planarity : 0.005 0.032 803 Dihedral : 23.095 176.319 1794 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 6.97 % Allowed : 19.33 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.38), residues: 501 helix: -0.82 (0.52), residues: 87 sheet: -2.86 (0.64), residues: 55 loop : -0.97 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 79 TYR 0.019 0.002 TYR A 162 PHE 0.015 0.002 PHE A 469 TRP 0.014 0.002 TRP A 215 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6006) covalent geometry : angle 0.69471 ( 8497) hydrogen bonds : bond 0.06713 ( 102) hydrogen bonds : angle 7.70612 ( 237) metal coordination : bond 0.01142 ( 4) metal coordination : angle 6.37448 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 47 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8357 (mmp) cc_final: 0.7445 (tpt) REVERT: A 44 TYR cc_start: -0.3025 (OUTLIER) cc_final: -0.3539 (m-80) REVERT: A 48 MET cc_start: 0.8545 (tpp) cc_final: 0.8288 (mmm) REVERT: A 67 VAL cc_start: 0.8836 (m) cc_final: 0.8516 (p) REVERT: A 73 MET cc_start: 0.7973 (mmm) cc_final: 0.7752 (ptp) REVERT: A 154 TYR cc_start: 0.5871 (OUTLIER) cc_final: 0.5647 (p90) REVERT: A 223 LYS cc_start: 0.8852 (tttp) cc_final: 0.8620 (tmtt) REVERT: A 258 PHE cc_start: -0.0637 (OUTLIER) cc_final: -0.1169 (t80) REVERT: A 293 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.6242 (m-80) REVERT: A 310 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.4798 (tp30) REVERT: A 361 PHE cc_start: 0.5542 (OUTLIER) cc_final: 0.4794 (m-80) REVERT: A 394 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9067 (pp) outliers start: 31 outliers final: 17 residues processed: 76 average time/residue: 0.0867 time to fit residues: 8.3441 Evaluate side-chains 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 316 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.127818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.109872 restraints weight = 38393.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.111529 restraints weight = 29430.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.112901 restraints weight = 24367.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.113834 restraints weight = 21034.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.114276 restraints weight = 18868.285| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 6010 Z= 0.374 Angle : 1.047 14.384 8503 Z= 0.522 Chirality : 0.051 0.260 977 Planarity : 0.007 0.075 803 Dihedral : 24.341 179.677 1790 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 41.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.18 % Favored : 91.62 % Rotamer: Outliers : 8.99 % Allowed : 19.55 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.36), residues: 501 helix: -1.24 (0.50), residues: 83 sheet: -2.51 (0.75), residues: 38 loop : -1.58 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 80 TYR 0.024 0.003 TYR A 236 PHE 0.027 0.003 PHE A 78 TRP 0.025 0.003 TRP A 215 HIS 0.014 0.003 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00751 ( 6006) covalent geometry : angle 1.01899 ( 8497) hydrogen bonds : bond 0.08803 ( 102) hydrogen bonds : angle 8.51219 ( 237) metal coordination : bond 0.01757 ( 4) metal coordination : angle 9.19006 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 41 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7226 (tpt) cc_final: 0.6434 (tpt) REVERT: A 31 MET cc_start: 0.8630 (mmp) cc_final: 0.7621 (tpt) REVERT: A 44 TYR cc_start: -0.2193 (OUTLIER) cc_final: -0.3792 (m-80) REVERT: A 73 MET cc_start: 0.8534 (mmm) cc_final: 0.8052 (mtp) REVERT: A 106 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: A 147 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: A 153 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6727 (p90) REVERT: A 206 GLN cc_start: 0.9130 (tt0) cc_final: 0.8765 (mm-40) REVERT: A 223 LYS cc_start: 0.8888 (tttp) cc_final: 0.8509 (tmtt) REVERT: A 260 TRP cc_start: 0.3943 (OUTLIER) cc_final: 0.3218 (m-10) REVERT: A 289 TYR cc_start: 0.7421 (t80) cc_final: 0.6401 (t80) outliers start: 40 outliers final: 27 residues processed: 78 average time/residue: 0.0713 time to fit residues: 7.3682 Evaluate side-chains 69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 37 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 2 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 30.0000 chunk 35 optimal weight: 0.0170 chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS A 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.141655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.123912 restraints weight = 36862.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.125769 restraints weight = 28196.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.127059 restraints weight = 23132.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.128081 restraints weight = 19983.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.128548 restraints weight = 17783.911| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6010 Z= 0.127 Angle : 0.668 9.856 8503 Z= 0.336 Chirality : 0.040 0.211 977 Planarity : 0.005 0.034 803 Dihedral : 23.795 174.733 1787 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.79 % Favored : 95.01 % Rotamer: Outliers : 6.97 % Allowed : 23.82 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.38), residues: 501 helix: -0.31 (0.54), residues: 90 sheet: -2.83 (0.69), residues: 40 loop : -1.04 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 276 TYR 0.021 0.002 TYR A 70 PHE 0.017 0.002 PHE A 456 TRP 0.009 0.001 TRP A 209 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6006) covalent geometry : angle 0.66154 ( 8497) hydrogen bonds : bond 0.05427 ( 102) hydrogen bonds : angle 6.86416 ( 237) metal coordination : bond 0.00521 ( 4) metal coordination : angle 3.65217 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 46 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8272 (mmp) cc_final: 0.7128 (tpt) REVERT: A 48 MET cc_start: 0.8312 (mmm) cc_final: 0.7461 (mmt) REVERT: A 73 MET cc_start: 0.8115 (mmm) cc_final: 0.7812 (ptp) REVERT: A 91 LEU cc_start: 0.7211 (tp) cc_final: 0.6701 (pt) REVERT: A 109 MET cc_start: 0.8199 (mtm) cc_final: 0.7704 (mpp) REVERT: A 153 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.5874 (p90) REVERT: A 183 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7365 (m-40) REVERT: A 186 LYS cc_start: 0.9017 (pttm) cc_final: 0.8457 (mmtt) REVERT: A 223 LYS cc_start: 0.8942 (tttp) cc_final: 0.8657 (tmtt) REVERT: A 258 PHE cc_start: 0.0380 (OUTLIER) cc_final: 0.0076 (t80) REVERT: A 289 TYR cc_start: 0.7416 (t80) cc_final: 0.6436 (t80) REVERT: A 293 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.6583 (m-80) REVERT: A 310 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.4947 (tm-30) REVERT: A 361 PHE cc_start: 0.5831 (OUTLIER) cc_final: 0.5118 (m-10) outliers start: 31 outliers final: 15 residues processed: 73 average time/residue: 0.0591 time to fit residues: 5.9704 Evaluate side-chains 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 21 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.141882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.124220 restraints weight = 37211.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.126193 restraints weight = 28285.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.127507 restraints weight = 23009.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.128139 restraints weight = 19795.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.129148 restraints weight = 18072.419| |-----------------------------------------------------------------------------| r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6010 Z= 0.120 Angle : 0.630 14.491 8503 Z= 0.317 Chirality : 0.039 0.232 977 Planarity : 0.004 0.032 803 Dihedral : 23.537 175.140 1784 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.19 % Favored : 93.61 % Rotamer: Outliers : 5.84 % Allowed : 21.35 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.38), residues: 501 helix: -0.28 (0.53), residues: 98 sheet: -2.54 (0.72), residues: 40 loop : -1.04 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.018 0.002 TYR A 70 PHE 0.012 0.001 PHE A 456 TRP 0.030 0.002 TRP A 40 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6006) covalent geometry : angle 0.62450 ( 8497) hydrogen bonds : bond 0.04659 ( 102) hydrogen bonds : angle 6.72137 ( 237) metal coordination : bond 0.00474 ( 4) metal coordination : angle 3.10561 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8430 (mmp) cc_final: 0.7604 (tpt) REVERT: A 48 MET cc_start: 0.8149 (mmm) cc_final: 0.7703 (mmm) REVERT: A 73 MET cc_start: 0.7886 (mmm) cc_final: 0.7380 (ptp) REVERT: A 76 MET cc_start: 0.5669 (ttt) cc_final: 0.4509 (ptm) REVERT: A 91 LEU cc_start: 0.7194 (tp) cc_final: 0.6636 (pt) REVERT: A 109 MET cc_start: 0.8274 (mtm) cc_final: 0.7830 (mpp) REVERT: A 153 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.5756 (p90) REVERT: A 223 LYS cc_start: 0.8886 (tttp) cc_final: 0.8613 (tmmt) REVERT: A 226 HIS cc_start: 0.5745 (p90) cc_final: 0.5366 (t70) REVERT: A 247 ASP cc_start: 0.7536 (t0) cc_final: 0.7313 (t0) REVERT: A 258 PHE cc_start: 0.0065 (OUTLIER) cc_final: -0.0293 (t80) REVERT: A 289 TYR cc_start: 0.7442 (t80) cc_final: 0.6682 (t80) REVERT: A 293 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: A 310 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.4777 (tm-30) REVERT: A 361 PHE cc_start: 0.5740 (OUTLIER) cc_final: 0.5054 (m-10) outliers start: 26 outliers final: 13 residues processed: 69 average time/residue: 0.0660 time to fit residues: 6.2642 Evaluate side-chains 59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 13 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.137693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.120248 restraints weight = 37335.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.122061 restraints weight = 28628.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.123311 restraints weight = 23587.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.124131 restraints weight = 20396.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.125072 restraints weight = 18352.934| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6010 Z= 0.147 Angle : 0.656 11.423 8503 Z= 0.332 Chirality : 0.039 0.240 977 Planarity : 0.005 0.094 803 Dihedral : 23.672 175.157 1784 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.99 % Favored : 93.81 % Rotamer: Outliers : 6.52 % Allowed : 22.02 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.38), residues: 501 helix: -0.12 (0.57), residues: 89 sheet: -2.68 (0.73), residues: 39 loop : -1.11 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 276 TYR 0.016 0.002 TYR A 70 PHE 0.022 0.002 PHE A 456 TRP 0.012 0.001 TRP A 215 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6006) covalent geometry : angle 0.65049 ( 8497) hydrogen bonds : bond 0.04555 ( 102) hydrogen bonds : angle 6.86326 ( 237) metal coordination : bond 0.00601 ( 4) metal coordination : angle 3.21597 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8522 (mmp) cc_final: 0.7639 (tpt) REVERT: A 48 MET cc_start: 0.8571 (mmm) cc_final: 0.8177 (mmm) REVERT: A 71 ASP cc_start: 0.9167 (t0) cc_final: 0.8563 (m-30) REVERT: A 73 MET cc_start: 0.8035 (mmm) cc_final: 0.7537 (mmm) REVERT: A 76 MET cc_start: 0.5673 (ttt) cc_final: 0.4511 (ptm) REVERT: A 91 LEU cc_start: 0.7022 (tp) cc_final: 0.6491 (pt) REVERT: A 109 MET cc_start: 0.8404 (mtm) cc_final: 0.8002 (mpp) REVERT: A 186 LYS cc_start: 0.8964 (pttm) cc_final: 0.8397 (mmtt) REVERT: A 203 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7415 (tm) REVERT: A 223 LYS cc_start: 0.8874 (tttp) cc_final: 0.8584 (tmmt) REVERT: A 258 PHE cc_start: 0.0738 (OUTLIER) cc_final: 0.0402 (t80) REVERT: A 289 TYR cc_start: 0.7541 (t80) cc_final: 0.6747 (t80) REVERT: A 310 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5353 (tm-30) REVERT: A 361 PHE cc_start: 0.5728 (OUTLIER) cc_final: 0.5038 (m-80) outliers start: 29 outliers final: 20 residues processed: 67 average time/residue: 0.0607 time to fit residues: 5.5686 Evaluate side-chains 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.141482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.123888 restraints weight = 37093.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.125841 restraints weight = 28301.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.127138 restraints weight = 23067.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.128124 restraints weight = 19884.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.128956 restraints weight = 17750.088| |-----------------------------------------------------------------------------| r_work (final): 0.4552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.6459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6010 Z= 0.111 Angle : 0.612 11.972 8503 Z= 0.308 Chirality : 0.039 0.205 977 Planarity : 0.004 0.057 803 Dihedral : 23.591 174.425 1784 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.59 % Favored : 94.21 % Rotamer: Outliers : 6.29 % Allowed : 21.35 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.39), residues: 501 helix: -0.05 (0.58), residues: 91 sheet: -2.41 (0.76), residues: 39 loop : -0.95 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.015 0.001 TYR A 70 PHE 0.014 0.001 PHE A 456 TRP 0.009 0.001 TRP A 40 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6006) covalent geometry : angle 0.60720 ( 8497) hydrogen bonds : bond 0.04346 ( 102) hydrogen bonds : angle 6.35475 ( 237) metal coordination : bond 0.00482 ( 4) metal coordination : angle 2.83758 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4492 (tpt) cc_final: 0.3839 (tpt) REVERT: A 31 MET cc_start: 0.8321 (mmp) cc_final: 0.7493 (tpt) REVERT: A 48 MET cc_start: 0.8599 (mmm) cc_final: 0.8303 (mmm) REVERT: A 71 ASP cc_start: 0.8949 (t0) cc_final: 0.8518 (m-30) REVERT: A 73 MET cc_start: 0.7922 (mmm) cc_final: 0.7456 (ptp) REVERT: A 76 MET cc_start: 0.5478 (ttt) cc_final: 0.4316 (ptm) REVERT: A 91 LEU cc_start: 0.7074 (tp) cc_final: 0.6583 (pt) REVERT: A 109 MET cc_start: 0.8324 (mtm) cc_final: 0.8025 (mpp) REVERT: A 153 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.6518 (p90) REVERT: A 186 LYS cc_start: 0.9003 (pttm) cc_final: 0.8253 (tptt) REVERT: A 203 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7451 (tm) REVERT: A 223 LYS cc_start: 0.8870 (tttp) cc_final: 0.8624 (tmmt) REVERT: A 258 PHE cc_start: 0.0343 (OUTLIER) cc_final: 0.0040 (t80) REVERT: A 289 TYR cc_start: 0.7432 (t80) cc_final: 0.6698 (t80) REVERT: A 293 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: A 294 TYR cc_start: 0.4552 (t80) cc_final: 0.4156 (t80) REVERT: A 310 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.4792 (tm-30) REVERT: A 361 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.5100 (m-10) outliers start: 28 outliers final: 17 residues processed: 66 average time/residue: 0.0604 time to fit residues: 5.5479 Evaluate side-chains 66 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 56 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.137907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.120518 restraints weight = 37107.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.122411 restraints weight = 28292.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.123753 restraints weight = 23077.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.124725 restraints weight = 19806.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.125315 restraints weight = 17675.404| |-----------------------------------------------------------------------------| r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.6786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6010 Z= 0.135 Angle : 0.633 11.936 8503 Z= 0.318 Chirality : 0.039 0.242 977 Planarity : 0.005 0.056 803 Dihedral : 23.748 174.380 1784 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.99 % Favored : 92.81 % Rotamer: Outliers : 6.07 % Allowed : 22.02 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.39), residues: 501 helix: -0.17 (0.57), residues: 92 sheet: -2.33 (0.77), residues: 39 loop : -0.99 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.014 0.001 TYR A 70 PHE 0.013 0.001 PHE A 78 TRP 0.014 0.001 TRP A 215 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6006) covalent geometry : angle 0.62801 ( 8497) hydrogen bonds : bond 0.04210 ( 102) hydrogen bonds : angle 6.62463 ( 237) metal coordination : bond 0.00567 ( 4) metal coordination : angle 3.11388 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 40 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4833 (tpt) cc_final: 0.4104 (tpt) REVERT: A 31 MET cc_start: 0.8433 (mmp) cc_final: 0.7559 (tpt) REVERT: A 48 MET cc_start: 0.8676 (mmm) cc_final: 0.8389 (mmm) REVERT: A 71 ASP cc_start: 0.8901 (t0) cc_final: 0.8492 (m-30) REVERT: A 73 MET cc_start: 0.8022 (mmm) cc_final: 0.7486 (ptp) REVERT: A 76 MET cc_start: 0.5467 (ttt) cc_final: 0.4353 (ptm) REVERT: A 91 LEU cc_start: 0.6999 (tp) cc_final: 0.6521 (pt) REVERT: A 109 MET cc_start: 0.8425 (mtm) cc_final: 0.8071 (mpp) REVERT: A 153 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.5626 (p90) REVERT: A 203 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7173 (tm) REVERT: A 223 LYS cc_start: 0.8931 (tttp) cc_final: 0.8671 (tmmt) REVERT: A 258 PHE cc_start: 0.0597 (OUTLIER) cc_final: 0.0344 (t80) REVERT: A 289 TYR cc_start: 0.7425 (t80) cc_final: 0.6563 (t80) REVERT: A 310 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.5188 (tm-30) REVERT: A 361 PHE cc_start: 0.5747 (OUTLIER) cc_final: 0.5061 (m-10) outliers start: 27 outliers final: 18 residues processed: 64 average time/residue: 0.0603 time to fit residues: 5.3850 Evaluate side-chains 59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 36 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 14 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 0.2980 chunk 6 optimal weight: 9.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** 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 = 0.4720 r_free = 0.4720 target = 0.128312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.111244 restraints weight = 38553.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.113090 restraints weight = 28799.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.114343 restraints weight = 23480.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.115350 restraints weight = 20204.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.115813 restraints weight = 17890.891| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.7892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6010 Z= 0.235 Angle : 0.806 11.620 8503 Z= 0.404 Chirality : 0.044 0.205 977 Planarity : 0.006 0.064 803 Dihedral : 24.608 174.707 1784 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 29.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.18 % Favored : 90.62 % Rotamer: Outliers : 4.94 % Allowed : 23.60 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.37), residues: 501 helix: -0.42 (0.54), residues: 88 sheet: -2.40 (0.75), residues: 39 loop : -1.39 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 276 TYR 0.019 0.002 TYR A 70 PHE 0.025 0.002 PHE A 78 TRP 0.028 0.003 TRP A 215 HIS 0.005 0.002 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 6006) covalent geometry : angle 0.79463 ( 8497) hydrogen bonds : bond 0.05441 ( 102) hydrogen bonds : angle 7.25259 ( 237) metal coordination : bond 0.01030 ( 4) metal coordination : angle 5.07373 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 37 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8474 (mmp) cc_final: 0.7507 (tpt) REVERT: A 71 ASP cc_start: 0.9065 (t0) cc_final: 0.8437 (m-30) REVERT: A 109 MET cc_start: 0.8765 (mtm) cc_final: 0.7976 (mpp) REVERT: A 186 LYS cc_start: 0.8801 (pttm) cc_final: 0.8077 (mmtt) REVERT: A 203 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7012 (tm) REVERT: A 223 LYS cc_start: 0.8911 (tttp) cc_final: 0.8547 (tmtt) REVERT: A 227 MET cc_start: 0.7363 (tmm) cc_final: 0.7035 (tpt) outliers start: 22 outliers final: 20 residues processed: 56 average time/residue: 0.0597 time to fit residues: 4.7363 Evaluate side-chains 56 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.0570 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.133425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.116280 restraints weight = 38849.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.118170 restraints weight = 29079.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.119651 restraints weight = 23662.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.120668 restraints weight = 20023.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.121503 restraints weight = 17607.265| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.7831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6010 Z= 0.141 Angle : 0.675 11.118 8503 Z= 0.340 Chirality : 0.041 0.274 977 Planarity : 0.004 0.049 803 Dihedral : 24.377 172.707 1784 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.39 % Favored : 92.42 % Rotamer: Outliers : 4.72 % Allowed : 24.49 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.38), residues: 501 helix: -0.48 (0.52), residues: 97 sheet: -2.50 (0.75), residues: 39 loop : -1.38 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 276 TYR 0.013 0.002 TYR A 162 PHE 0.016 0.002 PHE A 78 TRP 0.012 0.002 TRP A 40 HIS 0.004 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6006) covalent geometry : angle 0.66950 ( 8497) hydrogen bonds : bond 0.04353 ( 102) hydrogen bonds : angle 6.90198 ( 237) metal coordination : bond 0.00593 ( 4) metal coordination : angle 3.25004 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4703 (tpt) cc_final: 0.4137 (tpt) REVERT: A 31 MET cc_start: 0.8396 (mmp) cc_final: 0.7596 (tpp) REVERT: A 71 ASP cc_start: 0.9220 (t0) cc_final: 0.8756 (m-30) REVERT: A 76 MET cc_start: 0.5760 (ttt) cc_final: 0.4767 (ptm) REVERT: A 109 MET cc_start: 0.8748 (mtm) cc_final: 0.8412 (mpp) REVERT: A 186 LYS cc_start: 0.8778 (pttm) cc_final: 0.8043 (mmtt) REVERT: A 203 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6984 (tm) REVERT: A 223 LYS cc_start: 0.8944 (tttp) cc_final: 0.8612 (tmtt) REVERT: A 361 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.5084 (m-10) outliers start: 21 outliers final: 17 residues processed: 54 average time/residue: 0.0674 time to fit residues: 5.0983 Evaluate side-chains 53 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 34 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 486 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.0370 chunk 44 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.128884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.112141 restraints weight = 38416.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.113875 restraints weight = 28767.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.115305 restraints weight = 23420.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.116197 restraints weight = 19972.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.116675 restraints weight = 17750.340| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.8252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6010 Z= 0.195 Angle : 0.741 11.730 8503 Z= 0.370 Chirality : 0.042 0.204 977 Planarity : 0.005 0.047 803 Dihedral : 24.590 173.345 1782 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.98 % Favored : 89.82 % Rotamer: Outliers : 4.94 % Allowed : 24.27 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.37), residues: 501 helix: -0.54 (0.54), residues: 90 sheet: -2.59 (0.75), residues: 39 loop : -1.38 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 276 TYR 0.015 0.002 TYR A 70 PHE 0.023 0.002 PHE A 78 TRP 0.018 0.002 TRP A 215 HIS 0.007 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6006) covalent geometry : angle 0.73343 ( 8497) hydrogen bonds : bond 0.04949 ( 102) hydrogen bonds : angle 6.98474 ( 237) metal coordination : bond 0.00823 ( 4) metal coordination : angle 4.01629 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.17 seconds wall clock time: 24 minutes 41.36 seconds (1481.36 seconds total)