Starting phenix.real_space_refine on Thu Jul 2 02:22:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fzr_29638/07_2026/8fzr_29638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fzr_29638/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fzr_29638/07_2026/8fzr_29638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fzr_29638/07_2026/8fzr_29638.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fzr_29638/07_2026/8fzr_29638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fzr_29638/07_2026/8fzr_29638.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fzr_29638/07_2026/8fzr_29638.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fzr_29638/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 0.51 Conformation dependent library (CDL) restraints added in 142.6 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: 0.60 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: 0.61 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: 3293 34.82 - 69.63: 122 69.63 - 104.45: 11 104.45 - 139.26: 0 139.26 - 174.08: 1 Dihedral angle restraints: 3427 sinusoidal: 1953 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 3424 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: 0.850 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.560 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2369 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 : 15.486 174.077 2487 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/Z covalent geometry : bond 0.00198 / 0.12 ( 6006) covalent geometry : angle 0.47673 / 0.27 ( 8497) hydrogen bonds : bond 0.32909 / 21.01 ( 102) hydrogen bonds : angle 11.40266 / 8.15 ( 237) metal coordination : bond 0.08025 / 4.04 ( 4) metal coordination : angle 34.34967 / 16.83 ( 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 : 0.176 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: 0.0889 time to fit residues: 12.1095 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 : 0.151 ------------------------------------------------------------------------------- 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: 10.0000 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... 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 = 0.4898 r_free = 0.4898 target = 0.148449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.130014 restraints weight = 36659.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.131885 restraints weight = 28819.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.133110 restraints weight = 23865.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.133735 restraints weight = 20759.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.134856 restraints weight = 19041.065| |-----------------------------------------------------------------------------| r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6010 Z= 0.171 Angle : 0.709 9.978 8503 Z= 0.351 Chirality : 0.040 0.204 977 Planarity : 0.005 0.032 803 Dihedral : 17.083 175.837 1500 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 7.19 % Allowed : 18.88 % Favored : 73.93 % 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: -1.72 (0.38), residues: 501 helix: -0.80 (0.52), residues: 87 sheet: -2.88 (0.64), residues: 55 loop : -0.96 (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 0.016 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/Z covalent geometry : bond 0.00358 / 0.17 ( 6006) covalent geometry : angle 0.69059 / 0.35 ( 8497) hydrogen bonds : bond 0.06558 / 4.65 ( 102) hydrogen bonds : angle 7.69656 / 5.74 ( 237) metal coordination : bond 0.01293 / 0.64 ( 4) metal coordination : angle 6.01413 / 2.68 ( 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 79 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 47 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8398 (mmp) cc_final: 0.7475 (tpt) REVERT: A 44 TYR cc_start: -0.3091 (OUTLIER) cc_final: -0.3553 (m-80) REVERT: A 48 MET cc_start: 0.8568 (tpp) cc_final: 0.8297 (mmm) REVERT: A 67 VAL cc_start: 0.8890 (m) cc_final: 0.8558 (p) REVERT: A 223 LYS cc_start: 0.8859 (tttp) cc_final: 0.8615 (tmtt) REVERT: A 258 PHE cc_start: -0.0526 (OUTLIER) cc_final: -0.1063 (t80) REVERT: A 293 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6186 (m-80) REVERT: A 310 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.4816 (tp30) REVERT: A 361 PHE cc_start: 0.5566 (OUTLIER) cc_final: 0.4779 (m-80) REVERT: A 394 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9068 (pp) outliers start: 32 outliers final: 17 residues processed: 77 average time/residue: 0.0806 time to fit residues: 7.9806 Evaluate side-chains 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 0.0870 chunk 52 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4747 r_free = 0.4747 target = 0.132869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.114751 restraints weight = 37754.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.116551 restraints weight = 29272.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.117758 restraints weight = 24296.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.118857 restraints weight = 21144.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.119511 restraints weight = 18884.315| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6010 Z= 0.285 Angle : 0.868 11.064 8503 Z= 0.435 Chirality : 0.045 0.246 977 Planarity : 0.006 0.056 803 Dihedral : 18.088 178.033 1496 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 30.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 8.76 % Allowed : 18.88 % 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: -1.97 (0.36), residues: 501 helix: -0.95 (0.52), residues: 77 sheet: -2.63 (0.75), residues: 39 loop : -1.33 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 72 TYR 0.022 0.003 TYR A 236 PHE 0.025 0.003 PHE A 78 TRP 0.021 0.003 TRP A 215 HIS 0.007 0.002 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.28 ( 6006) covalent geometry : angle 0.84749 / 0.43 ( 8497) hydrogen bonds : bond 0.07187 / 4.92 ( 102) hydrogen bonds : angle 7.87070 / 6.04 ( 237) metal coordination : bond 0.01356 / 0.67 ( 4) metal coordination : angle 7.08205 / 3.20 ( 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 80 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 41 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.6885 (tpt) cc_final: 0.6142 (tpt) REVERT: A 31 MET cc_start: 0.8553 (mmp) cc_final: 0.7539 (tpt) REVERT: A 44 TYR cc_start: -0.2722 (OUTLIER) cc_final: -0.4064 (m-80) REVERT: A 48 MET cc_start: 0.8758 (tpp) cc_final: 0.8526 (mmm) REVERT: A 168 HIS cc_start: 0.8990 (t70) cc_final: 0.8766 (t70) REVERT: A 223 LYS cc_start: 0.8944 (tttp) cc_final: 0.8619 (tmtt) REVERT: A 260 TRP cc_start: 0.3761 (OUTLIER) cc_final: 0.2673 (m-10) REVERT: A 289 TYR cc_start: 0.7372 (t80) cc_final: 0.6390 (t80) REVERT: A 310 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.5815 (tm-30) REVERT: A 361 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.5148 (m-80) outliers start: 39 outliers final: 25 residues processed: 79 average time/residue: 0.0649 time to fit residues: 6.8927 Evaluate side-chains 67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 38 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 155 THR 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 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 344 VAL 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 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: 0.3980 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.132070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.114239 restraints weight = 37848.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.115966 restraints weight = 29337.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.117144 restraints weight = 24362.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.118129 restraints weight = 21219.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.118751 restraints weight = 19067.975| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6010 Z= 0.235 Angle : 0.772 11.309 8503 Z= 0.389 Chirality : 0.042 0.201 977 Planarity : 0.005 0.062 803 Dihedral : 18.492 173.781 1496 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.19 % Favored : 92.61 % Rotamer: Outliers : 8.09 % Allowed : 20.67 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.91 (0.37), residues: 501 helix: -0.62 (0.54), residues: 83 sheet: -2.96 (0.70), residues: 39 loop : -1.30 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 331 TYR 0.017 0.002 TYR A 257 PHE 0.022 0.002 PHE A 78 TRP 0.015 0.002 TRP A 215 HIS 0.005 0.002 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.24 ( 6006) covalent geometry : angle 0.75995 / 0.39 ( 8497) hydrogen bonds : bond 0.06406 / 4.55 ( 102) hydrogen bonds : angle 7.49247 / 5.80 ( 237) metal coordination : bond 0.01027 / 0.51 ( 4) metal coordination : angle 5.12795 / 2.40 ( 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 74 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 38 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8628 (mmp) cc_final: 0.7919 (tpt) REVERT: A 44 TYR cc_start: -0.2408 (OUTLIER) cc_final: -0.3994 (m-80) REVERT: A 71 ASP cc_start: 0.9083 (t0) cc_final: 0.8714 (p0) REVERT: A 223 LYS cc_start: 0.8935 (tttp) cc_final: 0.8595 (tmmt) REVERT: A 260 TRP cc_start: 0.3765 (OUTLIER) cc_final: 0.2810 (m-10) REVERT: A 289 TYR cc_start: 0.7387 (t80) cc_final: 0.6323 (t80) REVERT: A 310 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.5988 (tm-30) REVERT: A 361 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.5065 (m-80) outliers start: 36 outliers final: 23 residues processed: 71 average time/residue: 0.0597 time to fit residues: 5.7862 Evaluate side-chains 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 36 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 98 TYR Chi-restraints excluded: chain A residue 99 THR 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 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 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 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 455 LEU Chi-restraints excluded: chain A residue 486 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: 5.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 183 ASN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.138841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.121203 restraints weight = 37387.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.123111 restraints weight = 28808.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.124454 restraints weight = 23594.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.125482 restraints weight = 20332.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.126151 restraints weight = 18142.280| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 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 : 0.003 0.026 6010 Z= 0.122 Angle : 0.634 10.417 8503 Z= 0.322 Chirality : 0.039 0.199 977 Planarity : 0.004 0.032 803 Dihedral : 18.194 174.166 1495 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.79 % Favored : 94.01 % Rotamer: Outliers : 6.74 % Allowed : 22.02 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.42 (0.57), residues: 85 sheet: -2.79 (0.72), residues: 39 loop : -1.01 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 43 TYR 0.016 0.002 TYR A 44 PHE 0.013 0.001 PHE A 456 TRP 0.008 0.001 TRP A 40 HIS 0.006 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 6006) covalent geometry : angle 0.62797 / 0.32 ( 8497) hydrogen bonds : bond 0.04915 / 3.52 ( 102) hydrogen bonds : angle 6.76571 / 5.23 ( 237) metal coordination : bond 0.00537 / 0.27 ( 4) metal coordination : angle 3.43514 / 1.51 ( 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: 30 poor density : 41 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8568 (mmp) cc_final: 0.7785 (tpt) REVERT: A 48 MET cc_start: 0.8250 (mmm) cc_final: 0.7491 (mmm) REVERT: A 71 ASP cc_start: 0.9150 (t0) cc_final: 0.8669 (p0) REVERT: A 91 LEU cc_start: 0.7164 (tp) cc_final: 0.6752 (pt) REVERT: A 147 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: A 183 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7809 (m110) REVERT: A 186 LYS cc_start: 0.8933 (pttm) cc_final: 0.8374 (mmtt) REVERT: A 223 LYS cc_start: 0.8886 (tttp) cc_final: 0.8580 (tmmt) REVERT: A 226 HIS cc_start: 0.5951 (p-80) cc_final: 0.5640 (t-90) REVERT: A 248 ILE cc_start: 0.9306 (mt) cc_final: 0.9094 (tt) REVERT: A 289 TYR cc_start: 0.7386 (t80) cc_final: 0.6540 (t80) REVERT: A 310 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5210 (tm-30) REVERT: A 361 PHE cc_start: 0.5761 (OUTLIER) cc_final: 0.5141 (m-10) outliers start: 30 outliers final: 17 residues processed: 68 average time/residue: 0.0645 time to fit residues: 5.9489 Evaluate side-chains 59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 99 THR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 183 ASN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN ** A 412 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 = 0.4699 r_free = 0.4699 target = 0.127568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.110147 restraints weight = 38598.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.111947 restraints weight = 29757.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.113298 restraints weight = 24403.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.113882 restraints weight = 20956.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.114881 restraints weight = 19137.976| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.7185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 6010 Z= 0.278 Angle : 0.837 14.032 8503 Z= 0.421 Chirality : 0.044 0.204 977 Planarity : 0.006 0.054 803 Dihedral : 19.014 174.575 1493 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 32.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.18 % Favored : 90.62 % Rotamer: Outliers : 7.19 % Allowed : 21.57 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.96 (0.37), residues: 501 helix: -0.74 (0.51), residues: 90 sheet: -2.44 (0.81), residues: 39 loop : -1.39 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 72 TYR 0.023 0.003 TYR A 411 PHE 0.027 0.003 PHE A 78 TRP 0.021 0.003 TRP A 40 HIS 0.006 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 ( 6006) covalent geometry : angle 0.82537 / 0.42 ( 8497) hydrogen bonds : bond 0.06295 / 4.38 ( 102) hydrogen bonds : angle 7.35017 / 5.69 ( 237) metal coordination : bond 0.01114 / 0.56 ( 4) metal coordination : angle 5.40938 / 2.49 ( 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 67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 35 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8666 (mmp) cc_final: 0.7862 (tpt) REVERT: A 48 MET cc_start: 0.8241 (mmm) cc_final: 0.7844 (mmm) REVERT: A 71 ASP cc_start: 0.9062 (t0) cc_final: 0.8666 (p0) REVERT: A 145 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8620 (p0) REVERT: A 203 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7312 (tm) REVERT: A 223 LYS cc_start: 0.8873 (tttp) cc_final: 0.8551 (tmmt) REVERT: A 258 PHE cc_start: 0.1119 (OUTLIER) cc_final: 0.0888 (t80) REVERT: A 289 TYR cc_start: 0.7378 (t80) cc_final: 0.6312 (t80) REVERT: A 310 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5851 (tm-30) outliers start: 32 outliers final: 23 residues processed: 64 average time/residue: 0.0620 time to fit residues: 5.5664 Evaluate side-chains 60 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 33 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET 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 99 THR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 145 ASN 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 258 PHE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 298 CYS 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 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: 8.9990 chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.138181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.120878 restraints weight = 37354.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.122664 restraints weight = 28858.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.124078 restraints weight = 23774.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.125144 restraints weight = 20313.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.125811 restraints weight = 18000.668| |-----------------------------------------------------------------------------| r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6010 Z= 0.126 Angle : 0.654 11.337 8503 Z= 0.333 Chirality : 0.040 0.191 977 Planarity : 0.004 0.034 803 Dihedral : 18.611 172.011 1493 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.59 % Favored : 94.21 % Rotamer: Outliers : 5.84 % Allowed : 22.47 % Favored : 71.69 % 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: -1.70 (0.38), residues: 501 helix: -0.64 (0.51), residues: 102 sheet: -2.52 (0.75), residues: 39 loop : -1.15 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 217 TYR 0.017 0.001 TYR A 162 PHE 0.011 0.001 PHE A 78 TRP 0.024 0.002 TRP A 40 HIS 0.006 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 6006) covalent geometry : angle 0.64891 / 0.33 ( 8497) hydrogen bonds : bond 0.04726 / 3.32 ( 102) hydrogen bonds : angle 6.57197 / 5.08 ( 237) metal coordination : bond 0.00482 / 0.25 ( 4) metal coordination : angle 3.21789 / 1.41 ( 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 67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 41 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8274 (mmp) cc_final: 0.7541 (tpt) REVERT: A 48 MET cc_start: 0.8542 (mmm) cc_final: 0.8182 (mmm) REVERT: A 71 ASP cc_start: 0.8961 (t0) cc_final: 0.8481 (m-30) REVERT: A 148 MET cc_start: 0.8556 (mpp) cc_final: 0.8290 (mpp) REVERT: A 186 LYS cc_start: 0.9008 (pttm) cc_final: 0.8423 (mmtt) REVERT: A 203 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7072 (tm) REVERT: A 223 LYS cc_start: 0.8909 (tttp) cc_final: 0.8685 (tmtt) REVERT: A 226 HIS cc_start: 0.5429 (p-80) cc_final: 0.4864 (p90) REVERT: A 258 PHE cc_start: 0.0531 (OUTLIER) cc_final: 0.0193 (t80) REVERT: A 289 TYR cc_start: 0.7314 (t80) cc_final: 0.6336 (t80) REVERT: A 294 TYR cc_start: 0.5014 (t80) cc_final: 0.4606 (t80) REVERT: A 310 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.4919 (tm-30) REVERT: A 361 PHE cc_start: 0.5851 (OUTLIER) cc_final: 0.5136 (m-10) outliers start: 26 outliers final: 17 residues processed: 63 average time/residue: 0.0626 time to fit residues: 5.6341 Evaluate side-chains 60 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 12 MET 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 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 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 56 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.136602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.119440 restraints weight = 37617.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.121300 restraints weight = 28835.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.122676 restraints weight = 23618.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.123599 restraints weight = 20275.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.124426 restraints weight = 18076.790| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6010 Z= 0.125 Angle : 0.650 12.372 8503 Z= 0.328 Chirality : 0.039 0.197 977 Planarity : 0.004 0.032 803 Dihedral : 18.443 171.940 1491 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.19 % Favored : 92.61 % Rotamer: Outliers : 5.17 % Allowed : 23.37 % 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: -1.63 (0.38), residues: 501 helix: -0.75 (0.54), residues: 93 sheet: -2.23 (0.78), residues: 39 loop : -1.09 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.015 0.002 TYR A 162 PHE 0.016 0.001 PHE A 78 TRP 0.015 0.001 TRP A 40 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6006) covalent geometry : angle 0.64519 / 0.33 ( 8497) hydrogen bonds : bond 0.04390 / 3.11 ( 102) hydrogen bonds : angle 6.51436 / 5.06 ( 237) metal coordination : bond 0.00543 / 0.28 ( 4) metal coordination : angle 3.02628 / 1.30 ( 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 61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8392 (mmp) cc_final: 0.7793 (tpp) REVERT: A 48 MET cc_start: 0.8663 (mmm) cc_final: 0.8402 (mmm) REVERT: A 71 ASP cc_start: 0.8877 (t0) cc_final: 0.8414 (m-30) REVERT: A 203 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7147 (tm) REVERT: A 223 LYS cc_start: 0.8910 (tttp) cc_final: 0.8630 (tmmt) REVERT: A 258 PHE cc_start: 0.0407 (OUTLIER) cc_final: 0.0041 (t80) REVERT: A 289 TYR cc_start: 0.7269 (t80) cc_final: 0.6272 (t80) REVERT: A 310 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.4936 (tm-30) outliers start: 23 outliers final: 17 residues processed: 57 average time/residue: 0.0652 time to fit residues: 5.2814 Evaluate side-chains 56 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 53 ILE 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 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: 0.0270 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 0.0040 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 overall best weight: 2.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.132477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.115436 restraints weight = 38228.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.117210 restraints weight = 29051.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.118559 restraints weight = 23844.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.119168 restraints weight = 20441.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.120041 restraints weight = 18647.913| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.7586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6010 Z= 0.160 Angle : 0.693 12.243 8503 Z= 0.348 Chirality : 0.040 0.200 977 Planarity : 0.004 0.033 803 Dihedral : 18.776 171.783 1491 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.78 % Favored : 92.02 % Rotamer: Outliers : 4.72 % Allowed : 23.37 % 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: -1.77 (0.37), residues: 501 helix: -0.80 (0.54), residues: 93 sheet: -2.02 (0.80), residues: 39 loop : -1.24 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.014 0.002 TYR A 162 PHE 0.020 0.002 PHE A 78 TRP 0.015 0.002 TRP A 215 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 6006) covalent geometry : angle 0.68663 / 0.35 ( 8497) hydrogen bonds : bond 0.04533 / 3.18 ( 102) hydrogen bonds : angle 6.70301 / 5.22 ( 237) metal coordination : bond 0.00658 / 0.33 ( 4) metal coordination : angle 3.56274 / 1.61 ( 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 58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8487 (mmp) cc_final: 0.7687 (tpt) REVERT: A 48 MET cc_start: 0.8733 (mmm) cc_final: 0.8371 (mmm) REVERT: A 71 ASP cc_start: 0.9071 (t0) cc_final: 0.8572 (p0) REVERT: A 73 MET cc_start: 0.7329 (ptt) cc_final: 0.6948 (ptp) REVERT: A 186 LYS cc_start: 0.8824 (pttm) cc_final: 0.8149 (mmtt) REVERT: A 203 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7004 (tm) REVERT: A 223 LYS cc_start: 0.8828 (tttp) cc_final: 0.8561 (tmtt) REVERT: A 258 PHE cc_start: 0.0870 (OUTLIER) cc_final: 0.0651 (t80) REVERT: A 289 TYR cc_start: 0.7471 (t80) cc_final: 0.6528 (t80) REVERT: A 310 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5378 (tm-30) outliers start: 21 outliers final: 17 residues processed: 55 average time/residue: 0.0609 time to fit residues: 4.7143 Evaluate side-chains 56 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 53 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.125908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.109034 restraints weight = 39577.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.110883 restraints weight = 29802.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.112226 restraints weight = 24360.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.113122 restraints weight = 20811.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.113907 restraints weight = 18513.382| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.8520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6010 Z= 0.234 Angle : 0.813 12.189 8503 Z= 0.405 Chirality : 0.044 0.205 977 Planarity : 0.005 0.038 803 Dihedral : 19.805 172.792 1491 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 31.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.18 % Favored : 90.62 % Rotamer: Outliers : 5.39 % Allowed : 23.60 % Favored : 71.01 % 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: -0.64 (0.56), residues: 83 sheet: -2.10 (0.80), residues: 39 loop : -1.38 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 217 TYR 0.016 0.002 TYR A 162 PHE 0.026 0.002 PHE A 78 TRP 0.020 0.002 TRP A 215 HIS 0.006 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.23 ( 6006) covalent geometry : angle 0.80283 / 0.40 ( 8497) hydrogen bonds : bond 0.05525 / 3.76 ( 102) hydrogen bonds : angle 7.21744 / 5.58 ( 237) metal coordination : bond 0.00956 / 0.48 ( 4) metal coordination : angle 4.98865 / 2.34 ( 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 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.8507 (mmp) cc_final: 0.7507 (tpt) REVERT: A 48 MET cc_start: 0.8808 (mmm) cc_final: 0.8417 (mmm) REVERT: A 71 ASP cc_start: 0.9024 (t0) cc_final: 0.8604 (p0) REVERT: A 203 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6917 (tm) REVERT: A 223 LYS cc_start: 0.8820 (tttp) cc_final: 0.8470 (tmtt) REVERT: A 289 TYR cc_start: 0.7458 (t80) cc_final: 0.6521 (t80) REVERT: A 310 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.5567 (tm-30) outliers start: 24 outliers final: 17 residues processed: 59 average time/residue: 0.0587 time to fit residues: 4.8102 Evaluate side-chains 57 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 293 TYR Chi-restraints excluded: chain A residue 310 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 39 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.129969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.113226 restraints weight = 38670.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.115065 restraints weight = 29158.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.116357 restraints weight = 23815.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.117352 restraints weight = 20398.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.117803 restraints weight = 18074.231| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.8511 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= 0.158 Angle : 0.723 11.746 8503 Z= 0.361 Chirality : 0.042 0.209 977 Planarity : 0.004 0.032 803 Dihedral : 19.526 171.512 1489 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.99 % Favored : 92.81 % 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: -2.06 (0.37), residues: 501 helix: -1.09 (0.51), residues: 98 sheet: -2.13 (0.79), residues: 39 loop : -1.44 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.016 0.002 TYR A 162 PHE 0.020 0.002 PHE A 78 TRP 0.013 0.002 TRP A 40 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 ( 6006) covalent geometry : angle 0.71688 / 0.36 ( 8497) hydrogen bonds : bond 0.04763 / 3.20 ( 102) hydrogen bonds : angle 6.81596 / 5.26 ( 237) metal coordination : bond 0.00677 / 0.34 ( 4) metal coordination : angle 3.71653 / 1.80 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1464.56 seconds wall clock time: 25 minutes 56.38 seconds (1556.38 seconds total)