Starting phenix.real_space_refine on Fri Sep 11 06:52:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z2h_14466/09_2026/7z2h_14466.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2h_14466/09_2026/7z2h_14466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2h_14466/09_2026/7z2h_14466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2h_14466/09_2026/7z2h_14466.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z2h_14466/09_2026/7z2h_14466.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z2h_14466/09_2026/7z2h_14466.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z2h_14466/09_2026/7z2h_14466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2h_14466/09_2026/7z2h_14466.cif" } resolution = 3.58 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= 0.001 sd= 0.017 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: 7 Type Number sf(0) Gaussians P 36 5.49 5 S 13 5.16 5 Cl 1 4.86 5 C 5333 2.51 5 N 1405 2.21 5 O 1623 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8414 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4254 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 489} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3390 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 741 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2KW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.70, per 1000 atoms: 0.20 Number of scatterers: 8414 At special positions: 0 Unit cell: (97, 110.58, 96.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 13 16.00 P 36 15.00 F 3 9.00 O 1623 8.00 N 1405 7.00 C 5333 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: 0.73 Conformation dependent library (CDL) restraints added in 284.7 milliseconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 39.7% alpha, 10.9% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.558A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 42 " --> pdb=" O CYS A 38 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.790A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.934A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.329A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 384 removed outlier: 3.720A pdb=" N GLN A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 499 through 508 removed outlier: 4.184A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.592A pdb=" N VAL A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.747A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 6.508A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.722A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.929A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.746A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.622A pdb=" N LYS B 138 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.288A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.520A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.729A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.783A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.561A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.770A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 406 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 4.014A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 253 removed outlier: 4.426A pdb=" N TRP A 252 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.718A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA7, first strand: chain 'A' and resid 438 through 441 removed outlier: 4.193A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 532 " --> pdb=" O VAL A 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 444 through 445 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.768A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 132 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 110 Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.691A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 348 through 355 removed outlier: 3.797A pdb=" N TYR B 339 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 325 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LYS B 390 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA B 327 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1304 1.27 - 1.40: 2156 1.40 - 1.54: 5045 1.54 - 1.67: 181 1.67 - 1.81: 24 Bond restraints: 8710 Sorted by residual: bond pdb=" C10 2KW A 601 " pdb=" C9 2KW A 601 " ideal model delta sigma weight residual 1.354 1.522 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" C21 2KW A 601 " pdb=" N20 2KW A 601 " ideal model delta sigma weight residual 1.356 1.500 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3' DC E 1 " pdb=" P OMC E 2 " ideal model delta sigma weight residual 1.607 1.526 0.081 1.20e-02 6.94e+03 4.54e+01 bond pdb=" C10 2KW A 601 " pdb=" N11 2KW A 601 " ideal model delta sigma weight residual 1.355 1.489 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C7 2KW A 601 " pdb=" C8 2KW A 601 " ideal model delta sigma weight residual 1.359 1.485 -0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 8705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 11850 3.04 - 6.08: 128 6.08 - 9.13: 14 9.13 - 12.17: 2 12.17 - 15.21: 3 Bond angle restraints: 11997 Sorted by residual: angle pdb=" C LEU A 228 " pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " ideal model delta sigma weight residual 110.24 122.50 -12.26 1.46e+00 4.69e-01 7.05e+01 angle pdb=" N LEU A 228 " pdb=" CA LEU A 228 " pdb=" C LEU A 228 " ideal model delta sigma weight residual 108.13 94.42 13.71 1.72e+00 3.38e-01 6.35e+01 angle pdb=" C ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta sigma weight residual 109.33 94.12 15.21 1.97e+00 2.58e-01 5.96e+01 angle pdb=" O4' DC E 3 " pdb=" C4' DC E 3 " pdb=" C3' DC E 3 " ideal model delta sigma weight residual 106.00 101.95 4.05 6.00e-01 2.78e+00 4.56e+01 angle pdb=" N TRP B 426 " pdb=" CA TRP B 426 " pdb=" C TRP B 426 " ideal model delta sigma weight residual 112.89 105.54 7.35 1.24e+00 6.50e-01 3.51e+01 ... (remaining 11992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4325 17.77 - 35.55: 532 35.55 - 53.32: 171 53.32 - 71.10: 49 71.10 - 88.87: 11 Dihedral angle restraints: 5088 sinusoidal: 2354 harmonic: 2734 Sorted by residual: dihedral pdb=" C ASP A 186 " pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta harmonic sigma weight residual -122.60 -105.98 -16.62 0 2.50e+00 1.60e-01 4.42e+01 dihedral pdb=" C MET A 164 " pdb=" N MET A 164 " pdb=" CA MET A 164 " pdb=" CB MET A 164 " ideal model delta harmonic sigma weight residual -122.60 -135.65 13.05 0 2.50e+00 1.60e-01 2.73e+01 dihedral pdb=" N MET A 164 " pdb=" C MET A 164 " pdb=" CA MET A 164 " pdb=" CB MET A 164 " ideal model delta harmonic sigma weight residual 122.80 134.93 -12.13 0 2.50e+00 1.60e-01 2.35e+01 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1280 0.125 - 0.250: 25 0.250 - 0.376: 3 0.376 - 0.501: 0 0.501 - 0.626: 2 Chirality restraints: 1310 Sorted by residual: chirality pdb=" P DA E -2 " pdb=" OP1 DA E -2 " pdb=" OP2 DA E -2 " pdb=" O5' DA E -2 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.79e+00 chirality pdb=" CA MET A 164 " pdb=" N MET A 164 " pdb=" C MET A 164 " pdb=" CB MET A 164 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.17 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1307 not shown) Planarity restraints: 1382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 125 " -0.565 9.50e-02 1.11e+02 2.53e-01 3.93e+01 pdb=" NE ARG A 125 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 125 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 125 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 125 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 118 " 0.063 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO B 119 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 187 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C LEU A 187 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 187 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR A 188 " 0.017 2.00e-02 2.50e+03 ... (remaining 1379 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2009 2.80 - 3.32: 7739 3.32 - 3.85: 14183 3.85 - 4.37: 16225 4.37 - 4.90: 26618 Nonbonded interactions: 66774 Sorted by model distance: nonbonded pdb=" O GLY B 196 " pdb=" OG1 THR B 200 " model vdw 2.274 3.040 nonbonded pdb=" O 2KW A 601 " pdb=" F15 2KW A 601 " model vdw 2.293 2.990 nonbonded pdb=" O ARG A 277 " pdb=" N SER A 280 " model vdw 2.326 3.120 nonbonded pdb=" OG1 THR A 376 " pdb=" OG1 THR A 386 " model vdw 2.344 3.040 nonbonded pdb=" NZ LYS A 13 " pdb=" O LYS A 82 " model vdw 2.377 3.120 ... (remaining 66769 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: 0.100 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.950 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 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 : 0.006 0.168 8710 Z= 0.338 Angle : 0.798 15.210 11997 Z= 0.475 Chirality : 0.056 0.626 1310 Planarity : 0.009 0.253 1382 Dihedral : 17.826 88.870 3322 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.55 % Rotamer: Outliers : 0.72 % Allowed : 0.84 % Favored : 98.44 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.03 % 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: -0.71 (0.28), residues: 921 helix: 0.86 (0.31), residues: 308 sheet: -1.63 (0.42), residues: 149 loop : -0.94 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.027 0.001 TYR A 232 PHE 0.012 0.001 PHE A 124 TRP 0.023 0.002 TRP B 414 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.34 ( 8710) covalent geometry : angle 0.79848 / 0.48 (11997) hydrogen bonds : bond 0.14525 / 9.74 ( 313) hydrogen bonds : angle 7.87090 / 5.62 ( 828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.7794 (m-10) cc_final: 0.7447 (m-10) REVERT: B 180 ILE cc_start: 0.7335 (mm) cc_final: 0.6877 (tt) REVERT: B 198 HIS cc_start: 0.4680 (t70) cc_final: 0.4389 (t70) REVERT: B 409 THR cc_start: 0.7210 (m) cc_final: 0.6812 (p) outliers start: 6 outliers final: 2 residues processed: 133 average time/residue: 0.0791 time to fit residues: 14.9523 Evaluate side-chains 108 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 32 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 255 ASN B 269 GLN B 418 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.223340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.179266 restraints weight = 9987.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.183691 restraints weight = 6244.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.186678 restraints weight = 4648.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.188131 restraints weight = 3872.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.189515 restraints weight = 3500.426| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8710 Z= 0.173 Angle : 0.671 9.177 11997 Z= 0.358 Chirality : 0.046 0.190 1310 Planarity : 0.005 0.055 1382 Dihedral : 17.054 76.957 1371 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 0.36 % Allowed : 8.38 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.65 (0.28), residues: 921 helix: 1.00 (0.30), residues: 308 sheet: -1.65 (0.42), residues: 145 loop : -0.97 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 206 TYR 0.019 0.002 TYR A 501 PHE 0.015 0.002 PHE A 124 TRP 0.018 0.002 TRP B 402 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 8710) covalent geometry : angle 0.67125 / 0.36 (11997) hydrogen bonds : bond 0.04462 / 2.92 ( 313) hydrogen bonds : angle 5.24189 / 3.49 ( 828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.5923 (ttt) cc_final: 0.5249 (tpp) REVERT: B 180 ILE cc_start: 0.7463 (mm) cc_final: 0.6991 (tt) REVERT: B 409 THR cc_start: 0.7270 (m) cc_final: 0.6849 (p) outliers start: 3 outliers final: 3 residues processed: 117 average time/residue: 0.0835 time to fit residues: 14.4040 Evaluate side-chains 103 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 13 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 30 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.1196 > 50:) chunk 34 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.218971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.171439 restraints weight = 9937.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.176218 restraints weight = 6114.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.179263 restraints weight = 4505.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.180871 restraints weight = 3735.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.182343 restraints weight = 3356.802| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8710 Z= 0.189 Angle : 0.673 9.073 11997 Z= 0.359 Chirality : 0.047 0.371 1310 Planarity : 0.005 0.055 1382 Dihedral : 16.929 76.535 1371 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.65 % Favored : 94.25 % Rotamer: Outliers : 2.04 % Allowed : 11.50 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.79 (0.27), residues: 921 helix: 1.02 (0.30), residues: 301 sheet: -1.79 (0.41), residues: 145 loop : -1.10 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 358 TYR 0.017 0.002 TYR A 457 PHE 0.016 0.002 PHE B 130 TRP 0.017 0.002 TRP B 402 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 8710) covalent geometry : angle 0.67281 / 0.36 (11997) hydrogen bonds : bond 0.04463 / 2.90 ( 313) hydrogen bonds : angle 5.22667 / 3.45 ( 828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.5895 (ttt) cc_final: 0.5514 (tpp) outliers start: 17 outliers final: 11 residues processed: 122 average time/residue: 0.0808 time to fit residues: 14.2859 Evaluate side-chains 112 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 7.9990 chunk 69 optimal weight: 0.0870 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 0.2980 chunk 42 optimal weight: 50.0000 chunk 90 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.222799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.178132 restraints weight = 9936.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.182592 restraints weight = 6227.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.185633 restraints weight = 4643.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.187448 restraints weight = 3856.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.188714 restraints weight = 3458.924| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8710 Z= 0.131 Angle : 0.598 9.532 11997 Z= 0.321 Chirality : 0.044 0.291 1310 Planarity : 0.004 0.045 1382 Dihedral : 16.738 75.965 1371 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 2.04 % Allowed : 12.57 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.52 (0.28), residues: 921 helix: 1.27 (0.31), residues: 306 sheet: -1.58 (0.42), residues: 141 loop : -1.01 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.025 0.001 TYR A 501 PHE 0.011 0.001 PHE B 130 TRP 0.042 0.002 TRP B 402 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 8710) covalent geometry : angle 0.59797 / 0.32 (11997) hydrogen bonds : bond 0.03640 / 2.38 ( 313) hydrogen bonds : angle 4.97486 / 3.26 ( 828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.5822 (ttt) cc_final: 0.5488 (tpp) REVERT: B 174 GLN cc_start: 0.6527 (mp10) cc_final: 0.6025 (mp10) REVERT: B 180 ILE cc_start: 0.7550 (mm) cc_final: 0.7030 (tt) outliers start: 17 outliers final: 9 residues processed: 127 average time/residue: 0.0836 time to fit residues: 15.4868 Evaluate side-chains 113 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 396 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 0.2980 chunk 79 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.219773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.173781 restraints weight = 10107.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.178296 restraints weight = 6354.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.181248 restraints weight = 4720.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.183121 restraints weight = 3934.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.184018 restraints weight = 3520.733| |-----------------------------------------------------------------------------| r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8710 Z= 0.185 Angle : 0.657 9.604 11997 Z= 0.348 Chirality : 0.045 0.281 1310 Planarity : 0.005 0.045 1382 Dihedral : 16.786 76.836 1369 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.86 % Favored : 94.03 % Rotamer: Outliers : 2.16 % Allowed : 15.09 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.79 (0.27), residues: 921 helix: 1.04 (0.30), residues: 302 sheet: -1.69 (0.41), residues: 139 loop : -1.17 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 358 TYR 0.018 0.002 TYR B 354 PHE 0.017 0.002 PHE B 130 TRP 0.014 0.002 TRP A 229 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 8710) covalent geometry : angle 0.65720 / 0.35 (11997) hydrogen bonds : bond 0.04090 / 2.64 ( 313) hydrogen bonds : angle 5.13638 / 3.34 ( 828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: B 174 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.6061 (mp10) REVERT: B 180 ILE cc_start: 0.7490 (mm) cc_final: 0.6913 (tt) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 0.0782 time to fit residues: 13.8190 Evaluate side-chains 121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 overall best weight: 7.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 340 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 = 0.4604 r_free = 0.4604 target = 0.214597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.172189 restraints weight = 10025.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.170860 restraints weight = 8060.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.172506 restraints weight = 6804.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.172645 restraints weight = 5831.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.173434 restraints weight = 5566.679| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8710 Z= 0.235 Angle : 0.742 9.105 11997 Z= 0.391 Chirality : 0.048 0.302 1310 Planarity : 0.006 0.048 1382 Dihedral : 17.046 78.099 1369 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.62 % Favored : 93.27 % Rotamer: Outliers : 2.63 % Allowed : 15.93 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.37 (0.26), residues: 921 helix: 0.47 (0.29), residues: 302 sheet: -2.05 (0.40), residues: 133 loop : -1.47 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 307 TYR 0.019 0.002 TYR B 354 PHE 0.022 0.003 PHE B 130 TRP 0.016 0.002 TRP A 229 HIS 0.008 0.002 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 ( 8710) covalent geometry : angle 0.74197 / 0.39 (11997) hydrogen bonds : bond 0.04771 / 3.10 ( 313) hydrogen bonds : angle 5.46997 / 3.56 ( 828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 480 GLN cc_start: 0.6229 (tt0) cc_final: 0.5854 (tt0) REVERT: B 174 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6034 (mp10) REVERT: B 180 ILE cc_start: 0.7538 (mm) cc_final: 0.7027 (tt) REVERT: B 399 GLU cc_start: 0.6514 (mm-30) cc_final: 0.6258 (mm-30) outliers start: 22 outliers final: 20 residues processed: 127 average time/residue: 0.0810 time to fit residues: 14.9540 Evaluate side-chains 124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.218384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.175049 restraints weight = 10029.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.174587 restraints weight = 7102.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.176852 restraints weight = 6580.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178776 restraints weight = 5178.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178674 restraints weight = 4812.960| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8710 Z= 0.138 Angle : 0.631 12.485 11997 Z= 0.331 Chirality : 0.043 0.156 1310 Planarity : 0.005 0.046 1382 Dihedral : 16.685 76.352 1369 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 2.87 % Allowed : 16.89 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.92 (0.27), residues: 921 helix: 0.99 (0.30), residues: 301 sheet: -1.86 (0.41), residues: 135 loop : -1.27 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 307 TYR 0.015 0.002 TYR B 354 PHE 0.012 0.002 PHE B 130 TRP 0.050 0.002 TRP B 402 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 8710) covalent geometry : angle 0.63071 / 0.33 (11997) hydrogen bonds : bond 0.03852 / 2.52 ( 313) hydrogen bonds : angle 5.13171 / 3.34 ( 828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 281 LYS cc_start: 0.5427 (mmtt) cc_final: 0.5126 (mmtt) REVERT: A 357 MET cc_start: 0.5705 (ttt) cc_final: 0.5395 (tpp) REVERT: A 480 GLN cc_start: 0.6119 (tt0) cc_final: 0.5727 (tt0) REVERT: B 174 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6177 (mp10) REVERT: B 180 ILE cc_start: 0.7497 (mm) cc_final: 0.6962 (tt) outliers start: 24 outliers final: 16 residues processed: 127 average time/residue: 0.0885 time to fit residues: 16.1775 Evaluate side-chains 121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 20 optimal weight: 0.0170 chunk 70 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 91 optimal weight: 0.0270 overall best weight: 3.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.217845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.174801 restraints weight = 9951.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.174290 restraints weight = 7251.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.176627 restraints weight = 6425.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.178228 restraints weight = 5183.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.178203 restraints weight = 4848.871| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8710 Z= 0.148 Angle : 0.628 10.218 11997 Z= 0.329 Chirality : 0.043 0.172 1310 Planarity : 0.005 0.043 1382 Dihedral : 16.614 78.162 1369 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.43 % Favored : 94.46 % Rotamer: Outliers : 2.63 % Allowed : 16.89 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.85 (0.27), residues: 921 helix: 1.05 (0.30), residues: 301 sheet: -1.80 (0.41), residues: 142 loop : -1.21 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.018 0.002 TYR B 354 PHE 0.013 0.002 PHE B 130 TRP 0.029 0.002 TRP A 229 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 8710) covalent geometry : angle 0.62847 / 0.33 (11997) hydrogen bonds : bond 0.03801 / 2.47 ( 313) hydrogen bonds : angle 5.07393 / 3.30 ( 828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 281 LYS cc_start: 0.5441 (mmtt) cc_final: 0.5146 (mmtt) REVERT: A 357 MET cc_start: 0.5713 (ttt) cc_final: 0.5366 (tpp) REVERT: A 480 GLN cc_start: 0.6104 (tt0) cc_final: 0.5698 (tt0) REVERT: B 174 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6170 (mp10) REVERT: B 180 ILE cc_start: 0.7519 (mm) cc_final: 0.7004 (tt) outliers start: 22 outliers final: 18 residues processed: 123 average time/residue: 0.0892 time to fit residues: 15.7717 Evaluate side-chains 123 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.219501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.176211 restraints weight = 9910.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.175970 restraints weight = 6973.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.178261 restraints weight = 6375.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.181472 restraints weight = 4923.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.180968 restraints weight = 4545.755| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8710 Z= 0.128 Angle : 0.601 10.989 11997 Z= 0.314 Chirality : 0.042 0.173 1310 Planarity : 0.004 0.043 1382 Dihedral : 16.430 78.348 1369 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.42 % Rotamer: Outliers : 2.04 % Allowed : 17.96 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.64 (0.28), residues: 921 helix: 1.16 (0.30), residues: 306 sheet: -1.58 (0.42), residues: 141 loop : -1.10 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.017 0.001 TYR A 501 PHE 0.010 0.001 PHE B 130 TRP 0.024 0.001 TRP B 402 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 8710) covalent geometry : angle 0.60127 / 0.31 (11997) hydrogen bonds : bond 0.03444 / 2.24 ( 313) hydrogen bonds : angle 4.91025 / 3.20 ( 828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.5284 (mmtt) cc_final: 0.5013 (mmtt) REVERT: A 282 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5896 (mt) REVERT: A 357 MET cc_start: 0.5723 (ttt) cc_final: 0.5386 (tpp) REVERT: A 480 GLN cc_start: 0.6078 (tt0) cc_final: 0.5685 (tt0) REVERT: B 174 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.6126 (mp10) outliers start: 17 outliers final: 14 residues processed: 122 average time/residue: 0.0909 time to fit residues: 15.7429 Evaluate side-chains 122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 40.0000 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 77 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.222400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.175750 restraints weight = 9935.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.179497 restraints weight = 6768.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.182027 restraints weight = 5290.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.183326 restraints weight = 4536.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.184525 restraints weight = 4153.194| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8710 Z= 0.118 Angle : 0.595 11.264 11997 Z= 0.307 Chirality : 0.042 0.160 1310 Planarity : 0.004 0.042 1382 Dihedral : 16.255 78.156 1369 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 1.92 % Allowed : 18.80 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.36 (0.28), residues: 921 helix: 1.31 (0.31), residues: 307 sheet: -1.38 (0.44), residues: 136 loop : -0.91 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 448 TYR 0.017 0.001 TYR A 501 PHE 0.008 0.001 PHE B 130 TRP 0.019 0.001 TRP B 402 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 8710) covalent geometry : angle 0.59464 / 0.31 (11997) hydrogen bonds : bond 0.03245 / 2.13 ( 313) hydrogen bonds : angle 4.76792 / 3.12 ( 828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.5147 (mmtt) cc_final: 0.4937 (mmtt) REVERT: A 357 MET cc_start: 0.5725 (ttt) cc_final: 0.5445 (tpp) REVERT: B 174 GLN cc_start: 0.6439 (OUTLIER) cc_final: 0.6007 (mp10) REVERT: B 184 MET cc_start: 0.7162 (mmt) cc_final: 0.6902 (mmp) outliers start: 16 outliers final: 14 residues processed: 119 average time/residue: 0.0924 time to fit residues: 15.4823 Evaluate side-chains 121 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 92 optimal weight: 0.0060 chunk 7 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 78 optimal weight: 0.0980 chunk 38 optimal weight: 9.9990 chunk 94 optimal weight: 50.0000 chunk 76 optimal weight: 5.9990 overall best weight: 4.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 519 ASN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.218530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.172918 restraints weight = 9921.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.176434 restraints weight = 6922.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.178345 restraints weight = 5470.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.180133 restraints weight = 4747.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.180926 restraints weight = 4319.161| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8710 Z= 0.152 Angle : 0.625 10.325 11997 Z= 0.324 Chirality : 0.043 0.185 1310 Planarity : 0.005 0.041 1382 Dihedral : 16.409 79.541 1369 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 2.40 % Allowed : 18.92 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.52 (0.28), residues: 921 helix: 1.22 (0.30), residues: 307 sheet: -1.47 (0.43), residues: 139 loop : -1.02 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.018 0.002 TYR B 354 PHE 0.014 0.002 PHE B 130 TRP 0.021 0.002 TRP A 229 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 8710) covalent geometry : angle 0.62522 / 0.32 (11997) hydrogen bonds : bond 0.03605 / 2.32 ( 313) hydrogen bonds : angle 4.88374 / 3.18 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1444.69 seconds wall clock time: 25 minutes 44.52 seconds (1544.52 seconds total)