Starting phenix.real_space_refine on Thu Jul 2 05:17:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mhz_23837/07_2026/7mhz_23837.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mhz_23837/07_2026/7mhz_23837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mhz_23837/07_2026/7mhz_23837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mhz_23837/07_2026/7mhz_23837.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mhz_23837/07_2026/7mhz_23837.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mhz_23837/07_2026/7mhz_23837.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mhz_23837/07_2026/7mhz_23837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mhz_23837/07_2026/7mhz_23837.cif" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.079 sd= 0.156 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 Fe 1 7.16 5 P 6 5.49 5 S 41 5.16 5 C 4149 2.51 5 N 933 2.21 5 O 1059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 6189 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 51 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "A" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3980 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 16, 'TRANS': 474} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "O" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 793 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 476 Unusual residues: {'AJP': 10, 'HEM': 1, 'PKZ': 3} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 667 Unresolved non-hydrogen angles: 997 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 248 Planarities with less than four sites: {'PKZ:plan-1': 2, 'PKZ:plan-2': 2, 'PKZ:plan-3': 2, 'PKZ:plan-4': 2, 'PKZ:plan-5': 1} Unresolved non-hydrogen planarities: 45 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2698 SG CYS A 324 41.620 48.101 81.893 1.00106.78 S Time building chain proxies: 1.46, per 1000 atoms: 0.24 Number of scatterers: 6189 At special positions: 0 Unit cell: (71.82, 79.8, 118.636, 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) Fe 1 26.01 S 41 16.00 P 6 15.00 O 1059 8.00 N 933 7.00 C 4149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 115 " distance=2.03 Simple disulfide: pdb=" SG CYS P 42 " - pdb=" SG CYS P 112 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 315.6 milliseconds 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 60.6% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 3 through 32 Processing helix chain 'A' and resid 32 through 40 Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.843A pdb=" N SER A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 89 Processing helix chain 'A' and resid 92 through 129 removed outlier: 7.885A pdb=" N THR A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.962A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 163 through 190 removed outlier: 3.967A pdb=" N TYR A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 236 through 265 removed outlier: 3.691A pdb=" N CYS A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 273 Processing helix chain 'A' and resid 273 through 280 removed outlier: 3.630A pdb=" N LEU A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 315 removed outlier: 3.865A pdb=" N VAL A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.730A pdb=" N VAL A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 359 through 380 removed outlier: 4.006A pdb=" N GLY A 363 " --> pdb=" O HIS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 407 Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 420 through 448 removed outlier: 3.933A pdb=" N MET A 438 " --> pdb=" O CYS A 434 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 461 Processing helix chain 'A' and resid 467 through 488 removed outlier: 3.714A pdb=" N GLN A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 51 removed outlier: 3.810A pdb=" N TYR O 51 " --> pdb=" O PHE O 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA2, first strand: chain 'O' and resid 22 through 25 removed outlier: 3.554A pdb=" N VAL O 37 " --> pdb=" O ASN O 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN O 104 " --> pdb=" O VAL O 37 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR O 99 " --> pdb=" O GLU O 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 29 through 30 removed outlier: 6.464A pdb=" N GLU O 29 " --> pdb=" O THR O 135 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR O 113 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET O 53 " --> pdb=" O TRP O 69 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP O 69 " --> pdb=" O MET O 53 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP O 55 " --> pdb=" O MET O 67 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN O 71 " --> pdb=" O GLU O 76 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU O 76 " --> pdb=" O ASN O 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 29 through 30 removed outlier: 6.464A pdb=" N GLU O 29 " --> pdb=" O THR O 135 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR O 113 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR O 127 " --> pdb=" O ARG O 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 23 through 26 Processing sheet with id=AA6, first strand: chain 'P' and resid 29 through 31 removed outlier: 6.642A pdb=" N TRP P 59 " --> pdb=" O LEU P 71 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 1743 1.35 - 1.53: 3718 1.53 - 1.70: 907 1.70 - 1.87: 63 1.87 - 2.04: 4 Bond restraints: 6435 Sorted by residual: bond pdb=" C1B PKZ A 503 " pdb=" O4B PKZ A 503 " ideal model delta sigma weight residual 1.390 1.651 -0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C1B PKZ A 502 " pdb=" O4B PKZ A 502 " ideal model delta sigma weight residual 1.390 1.648 -0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C1B PKZ A 502 " pdb=" C2B PKZ A 502 " ideal model delta sigma weight residual 1.540 1.327 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C1B PKZ A 503 " pdb=" C2B PKZ A 503 " ideal model delta sigma weight residual 1.540 1.330 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C9P PKZ A 502 " pdb=" N8P PKZ A 502 " ideal model delta sigma weight residual 1.336 1.490 -0.154 2.00e-02 2.50e+03 5.92e+01 ... (remaining 6430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 8740 3.20 - 6.39: 144 6.39 - 9.59: 12 9.59 - 12.78: 4 12.78 - 15.98: 6 Bond angle restraints: 8906 Sorted by residual: angle pdb=" O3A PKZ A 503 " pdb=" P1A PKZ A 503 " pdb=" O5B PKZ A 503 " ideal model delta sigma weight residual 94.17 110.15 -15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" N1A PKZ A 502 " pdb=" C6A PKZ A 502 " pdb=" N6A PKZ A 502 " ideal model delta sigma weight residual 119.11 103.22 15.89 3.00e+00 1.11e-01 2.81e+01 angle pdb=" O3A PKZ A 502 " pdb=" P1A PKZ A 502 " pdb=" O5B PKZ A 502 " ideal model delta sigma weight residual 94.17 108.69 -14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C5A PKZ A 502 " pdb=" C6A PKZ A 502 " pdb=" N6A PKZ A 502 " ideal model delta sigma weight residual 122.65 136.81 -14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O3A PKZ A 502 " pdb=" P2A PKZ A 502 " pdb=" O6A PKZ A 502 " ideal model delta sigma weight residual 97.18 110.35 -13.17 3.00e+00 1.11e-01 1.93e+01 ... (remaining 8901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 3164 24.95 - 49.89: 178 49.89 - 74.84: 18 74.84 - 99.78: 3 99.78 - 124.73: 30 Dihedral angle restraints: 3393 sinusoidal: 1304 harmonic: 2089 Sorted by residual: dihedral pdb=" C02 AJP A 505 " pdb=" C85 AJP A 505 " pdb=" O84 AJP A 505 " pdb=" C05 AJP A 505 " ideal model delta sinusoidal sigma weight residual -57.60 67.13 -124.73 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C02 AJP A 511 " pdb=" C85 AJP A 511 " pdb=" O84 AJP A 511 " pdb=" C05 AJP A 511 " ideal model delta sinusoidal sigma weight residual -57.60 66.69 -124.29 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C02 AJP A 510 " pdb=" C03 AJP A 510 " pdb=" C04 AJP A 510 " pdb=" C05 AJP A 510 " ideal model delta sinusoidal sigma weight residual 52.15 -63.07 115.22 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 3390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.204: 922 1.204 - 2.408: 0 2.408 - 3.612: 0 3.612 - 4.815: 10 4.815 - 6.019: 88 Chirality restraints: 1020 Sorted by residual: chirality pdb=" C12 AJP A 505 " pdb=" C07 AJP A 505 " pdb=" C11 AJP A 505 " pdb=" C13 AJP A 505 " both_signs ideal model delta sigma weight residual False 3.01 -3.01 6.02 2.00e-01 2.50e+01 9.06e+02 chirality pdb=" C12 AJP A 509 " pdb=" C07 AJP A 509 " pdb=" C11 AJP A 509 " pdb=" C13 AJP A 509 " both_signs ideal model delta sigma weight residual False 3.01 -3.01 6.01 2.00e-01 2.50e+01 9.04e+02 chirality pdb=" C12 AJP A 511 " pdb=" C07 AJP A 511 " pdb=" C11 AJP A 511 " pdb=" C13 AJP A 511 " both_signs ideal model delta sigma weight residual False 3.01 -3.00 6.01 2.00e-01 2.50e+01 9.03e+02 ... (remaining 1017 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 373 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C ALA A 373 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 373 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A 374 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 69 " -0.012 2.00e-02 2.50e+03 1.10e-02 3.00e+00 pdb=" CG TRP O 69 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP O 69 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP O 69 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP O 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 69 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP O 69 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 69 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 69 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP O 69 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 371 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C THR A 371 " 0.029 2.00e-02 2.50e+03 pdb=" O THR A 371 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 372 " -0.010 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 751 2.75 - 3.29: 5933 3.29 - 3.82: 10550 3.82 - 4.36: 11829 4.36 - 4.90: 21438 Nonbonded interactions: 50501 Sorted by model distance: nonbonded pdb=" NZ LYS P 63 " pdb=" O GLU P 105 " model vdw 2.210 3.120 nonbonded pdb=" NH2 ARG A 176 " pdb=" O VAL A 213 " model vdw 2.252 3.120 nonbonded pdb=" OE2 GLU P 58 " pdb=" OH TYR P 60 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR O 36 " pdb=" O ASN O 104 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR A 207 " pdb=" O LEU A 220 " model vdw 2.271 3.040 ... (remaining 50496 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.850 Find NCS groups from input model: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.012 0.646 6439 Z= 0.505 Angle : 0.991 15.979 8910 Z= 0.405 Chirality : 1.632 6.019 1020 Planarity : 0.004 0.032 992 Dihedral : 19.678 124.730 2059 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.45 (0.32), residues: 713 helix: 1.89 (0.27), residues: 391 sheet: 0.25 (0.49), residues: 119 loop : -0.36 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 117 TYR 0.024 0.002 TYR A 180 PHE 0.015 0.001 PHE A 17 TRP 0.029 0.001 TRP O 69 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00939 / 0.46 ( 6435) covalent geometry : angle 0.99085 / 0.41 ( 8906) SS BOND : bond 0.00354 / 0.17 ( 2) SS BOND : angle 1.00111 / 0.46 ( 4) hydrogen bonds : bond 0.11769 / 7.92 ( 359) hydrogen bonds : angle 5.78917 / 4.17 ( 1038) Misc. bond : bond 0.46256 / 22.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: O 119 TRP cc_start: 0.7507 (t-100) cc_final: 0.7069 (t-100) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0553 time to fit residues: 4.6506 Evaluate side-chains 47 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.0030 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 25 GLN P 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.093950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073897 restraints weight = 12120.638| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.80 r_work: 0.2953 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6439 Z= 0.155 Angle : 2.550 35.827 8910 Z= 0.871 Chirality : 0.258 1.957 1020 Planarity : 0.004 0.031 992 Dihedral : 13.244 106.854 890 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.87 % Allowed : 5.71 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.32), residues: 713 helix: 2.28 (0.26), residues: 395 sheet: 0.35 (0.47), residues: 130 loop : -0.24 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 176 TYR 0.021 0.002 TYR A 180 PHE 0.017 0.001 PHE A 17 TRP 0.014 0.001 TRP O 69 HIS 0.010 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 6435) covalent geometry : angle 2.55091 / 0.87 ( 8906) SS BOND : bond 0.00264 / 0.13 ( 2) SS BOND : angle 1.05621 / 0.50 ( 4) hydrogen bonds : bond 0.03981 / 2.67 ( 359) hydrogen bonds : angle 4.40771 / 3.17 ( 1038) Misc. bond : bond 0.02220 / 1.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.233 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.0682 time to fit residues: 5.6557 Evaluate side-chains 54 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain P residue 46 GLN Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.075432 restraints weight = 11966.141| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.81 r_work: 0.2997 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6439 Z= 0.136 Angle : 2.491 33.630 8910 Z= 0.849 Chirality : 0.260 1.977 1020 Planarity : 0.004 0.032 992 Dihedral : 12.793 107.090 890 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.87 % Allowed : 7.61 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 2.14 (0.33), residues: 713 helix: 2.57 (0.27), residues: 392 sheet: 0.48 (0.48), residues: 128 loop : -0.33 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 176 TYR 0.021 0.001 TYR A 180 PHE 0.018 0.001 PHE A 17 TRP 0.012 0.001 TRP O 69 HIS 0.007 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 6435) covalent geometry : angle 2.49140 / 0.85 ( 8906) SS BOND : bond 0.00254 / 0.13 ( 2) SS BOND : angle 0.84691 / 0.38 ( 4) hydrogen bonds : bond 0.03477 / 2.34 ( 359) hydrogen bonds : angle 4.08074 / 2.92 ( 1038) Misc. bond : bond 0.01608 / 0.77 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.222 Fit side-chains REVERT: O 57 ARG cc_start: 0.8490 (ptm-80) cc_final: 0.8102 (ptm160) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.0625 time to fit residues: 5.0539 Evaluate side-chains 53 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 71 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.075009 restraints weight = 11946.244| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.79 r_work: 0.2989 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6439 Z= 0.132 Angle : 2.487 33.197 8910 Z= 0.847 Chirality : 0.259 1.926 1020 Planarity : 0.004 0.032 992 Dihedral : 12.796 106.826 890 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.56 % Allowed : 8.82 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 2.19 (0.33), residues: 713 helix: 2.59 (0.26), residues: 392 sheet: 0.55 (0.48), residues: 128 loop : -0.29 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.019 0.002 TYR A 180 PHE 0.018 0.001 PHE A 17 TRP 0.012 0.001 TRP O 69 HIS 0.006 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6435) covalent geometry : angle 2.48742 / 0.85 ( 8906) SS BOND : bond 0.00409 / 0.21 ( 2) SS BOND : angle 0.80395 / 0.36 ( 4) hydrogen bonds : bond 0.03431 / 2.33 ( 359) hydrogen bonds : angle 3.92346 / 2.79 ( 1038) Misc. bond : bond 0.01058 / 0.50 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.191 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 57 average time/residue: 0.0591 time to fit residues: 4.9219 Evaluate side-chains 57 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 0.0270 chunk 8 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.074540 restraints weight = 12159.342| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.82 r_work: 0.2980 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6439 Z= 0.135 Angle : 2.481 33.354 8910 Z= 0.845 Chirality : 0.260 1.935 1020 Planarity : 0.004 0.032 992 Dihedral : 12.454 107.226 890 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.73 % Allowed : 9.52 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 2.23 (0.33), residues: 713 helix: 2.65 (0.26), residues: 390 sheet: 0.59 (0.48), residues: 128 loop : -0.35 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.019 0.001 TYR A 300 PHE 0.017 0.001 PHE A 17 TRP 0.012 0.001 TRP O 69 HIS 0.006 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 6435) covalent geometry : angle 2.48149 / 0.85 ( 8906) SS BOND : bond 0.00322 / 0.16 ( 2) SS BOND : angle 0.76902 / 0.33 ( 4) hydrogen bonds : bond 0.03419 / 2.32 ( 359) hydrogen bonds : angle 3.89478 / 2.76 ( 1038) Misc. bond : bond 0.00909 / 0.43 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.253 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 57 average time/residue: 0.0597 time to fit residues: 5.0168 Evaluate side-chains 56 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 70 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN ** P 46 GLN ** 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 = 0.3458 r_free = 0.3458 target = 0.093626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.073571 restraints weight = 12001.711| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.75 r_work: 0.2961 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6439 Z= 0.155 Angle : 2.486 33.715 8910 Z= 0.848 Chirality : 0.260 1.936 1020 Planarity : 0.004 0.032 992 Dihedral : 12.383 106.742 890 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.90 % Allowed : 10.55 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 2.11 (0.32), residues: 713 helix: 2.52 (0.26), residues: 391 sheet: 0.44 (0.48), residues: 129 loop : -0.25 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.021 0.002 TYR A 300 PHE 0.019 0.001 PHE A 17 TRP 0.011 0.001 TRP O 69 HIS 0.006 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 6435) covalent geometry : angle 2.48635 / 0.85 ( 8906) SS BOND : bond 0.00315 / 0.16 ( 2) SS BOND : angle 0.81339 / 0.35 ( 4) hydrogen bonds : bond 0.03555 / 2.41 ( 359) hydrogen bonds : angle 3.92451 / 2.77 ( 1038) Misc. bond : bond 0.00528 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.241 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 59 average time/residue: 0.0590 time to fit residues: 5.1541 Evaluate side-chains 58 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.0870 chunk 5 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 0.0030 chunk 60 optimal weight: 3.9990 overall best weight: 0.8572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.075660 restraints weight = 11921.430| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.79 r_work: 0.2997 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6439 Z= 0.121 Angle : 2.471 32.807 8910 Z= 0.840 Chirality : 0.261 1.944 1020 Planarity : 0.004 0.032 992 Dihedral : 12.199 107.001 890 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.21 % Allowed : 11.07 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 2.28 (0.33), residues: 713 helix: 2.69 (0.26), residues: 391 sheet: 0.52 (0.48), residues: 128 loop : -0.26 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 459 TYR 0.020 0.001 TYR A 180 PHE 0.027 0.001 PHE A 17 TRP 0.009 0.001 TRP A 457 HIS 0.006 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6435) covalent geometry : angle 2.47139 / 0.84 ( 8906) SS BOND : bond 0.00294 / 0.15 ( 2) SS BOND : angle 0.76145 / 0.33 ( 4) hydrogen bonds : bond 0.03227 / 2.19 ( 359) hydrogen bonds : angle 3.79270 / 2.68 ( 1038) Misc. bond : bond 0.01088 / 0.52 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.184 Fit side-chains REVERT: O 121 TYR cc_start: 0.7672 (p90) cc_final: 0.7295 (p90) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.0611 time to fit residues: 4.7966 Evaluate side-chains 51 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 9 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN P 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.096257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.076094 restraints weight = 11957.939| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.82 r_work: 0.3026 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6439 Z= 0.114 Angle : 2.461 31.837 8910 Z= 0.836 Chirality : 0.262 1.950 1020 Planarity : 0.003 0.033 992 Dihedral : 12.016 107.628 890 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.73 % Allowed : 11.25 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 2.35 (0.33), residues: 713 helix: 2.71 (0.26), residues: 398 sheet: 0.61 (0.48), residues: 128 loop : -0.33 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 117 TYR 0.020 0.001 TYR A 180 PHE 0.027 0.001 PHE A 17 TRP 0.009 0.001 TRP A 457 HIS 0.005 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 6435) covalent geometry : angle 2.46126 / 0.84 ( 8906) SS BOND : bond 0.00277 / 0.14 ( 2) SS BOND : angle 0.65322 / 0.29 ( 4) hydrogen bonds : bond 0.03026 / 2.06 ( 359) hydrogen bonds : angle 3.63761 / 2.57 ( 1038) Misc. bond : bond 0.00943 / 0.45 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.227 Fit side-chains REVERT: O 53 MET cc_start: 0.8499 (mmm) cc_final: 0.8215 (mmt) REVERT: O 121 TYR cc_start: 0.7708 (p90) cc_final: 0.7224 (p90) outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.0563 time to fit residues: 5.1826 Evaluate side-chains 55 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.096700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076623 restraints weight = 11998.351| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.81 r_work: 0.3014 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6439 Z= 0.122 Angle : 2.463 32.126 8910 Z= 0.838 Chirality : 0.262 1.951 1020 Planarity : 0.003 0.032 992 Dihedral : 12.011 107.239 890 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.38 % Allowed : 11.76 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 2.30 (0.33), residues: 713 helix: 2.67 (0.26), residues: 397 sheet: 0.63 (0.48), residues: 128 loop : -0.37 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 459 TYR 0.019 0.001 TYR A 180 PHE 0.026 0.001 PHE A 17 TRP 0.009 0.001 TRP A 457 HIS 0.005 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6435) covalent geometry : angle 2.46379 / 0.84 ( 8906) SS BOND : bond 0.00308 / 0.16 ( 2) SS BOND : angle 0.65470 / 0.29 ( 4) hydrogen bonds : bond 0.03117 / 2.13 ( 359) hydrogen bonds : angle 3.64291 / 2.57 ( 1038) Misc. bond : bond 0.00819 / 0.39 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.286 Fit side-chains REVERT: A 467 TRP cc_start: 0.8175 (m100) cc_final: 0.7466 (m100) REVERT: O 53 MET cc_start: 0.8552 (mmm) cc_final: 0.8052 (mmt) REVERT: O 121 TYR cc_start: 0.7652 (p90) cc_final: 0.7199 (p90) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.0613 time to fit residues: 5.5685 Evaluate side-chains 59 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.0000 chunk 66 optimal weight: 0.0970 chunk 47 optimal weight: 0.0050 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN ** O 25 GLN ** 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 = 0.3508 r_free = 0.3508 target = 0.096782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076713 restraints weight = 11939.531| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.81 r_work: 0.3015 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6439 Z= 0.118 Angle : 2.461 32.098 8910 Z= 0.837 Chirality : 0.262 1.953 1020 Planarity : 0.003 0.032 992 Dihedral : 11.978 107.381 890 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.56 % Allowed : 11.59 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 2.31 (0.33), residues: 713 helix: 2.68 (0.26), residues: 397 sheet: 0.59 (0.48), residues: 129 loop : -0.32 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 459 TYR 0.019 0.001 TYR A 180 PHE 0.026 0.001 PHE A 17 TRP 0.010 0.001 TRP A 457 HIS 0.005 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6435) covalent geometry : angle 2.46178 / 0.84 ( 8906) SS BOND : bond 0.00303 / 0.15 ( 2) SS BOND : angle 0.65972 / 0.28 ( 4) hydrogen bonds : bond 0.03103 / 2.12 ( 359) hydrogen bonds : angle 3.63334 / 2.56 ( 1038) Misc. bond : bond 0.00902 / 0.43 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.227 Fit side-chains REVERT: A 467 TRP cc_start: 0.8188 (m100) cc_final: 0.7477 (m100) REVERT: O 53 MET cc_start: 0.8572 (mmm) cc_final: 0.8071 (mmt) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.0603 time to fit residues: 5.5226 Evaluate side-chains 61 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 62 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076166 restraints weight = 11954.874| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.81 r_work: 0.3009 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6439 Z= 0.122 Angle : 2.461 32.246 8910 Z= 0.837 Chirality : 0.262 1.953 1020 Planarity : 0.004 0.032 992 Dihedral : 11.961 107.076 890 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.73 % Allowed : 11.59 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 2.36 (0.33), residues: 713 helix: 2.63 (0.26), residues: 403 sheet: 0.54 (0.48), residues: 129 loop : -0.12 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 459 TYR 0.019 0.001 TYR A 180 PHE 0.026 0.001 PHE A 17 TRP 0.011 0.001 TRP A 393 HIS 0.005 0.001 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6435) covalent geometry : angle 2.46169 / 0.84 ( 8906) SS BOND : bond 0.00309 / 0.16 ( 2) SS BOND : angle 0.67441 / 0.29 ( 4) hydrogen bonds : bond 0.03142 / 2.14 ( 359) hydrogen bonds : angle 3.64711 / 2.57 ( 1038) Misc. bond : bond 0.00765 / 0.36 ( 2) =============================================================================== Job complete usr+sys time: 1355.71 seconds wall clock time: 24 minutes 5.24 seconds (1445.24 seconds total)