Starting phenix.real_space_refine on Tue Mar 3 19:25:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2h_14466/03_2026/7z2h_14466.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2h_14466/03_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_14466/03_2026/7z2h_14466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2h_14466/03_2026/7z2h_14466.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2h_14466/03_2026/7z2h_14466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2h_14466/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.16, per 1000 atoms: 0.26 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: 0.61 Conformation dependent library (CDL) restraints added in 262.8 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: 0.99 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: 1.51 Time building geometry restraints manager: 0.80 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=" 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 bond pdb=" C18 2KW A 601 " pdb=" N19 2KW A 601 " ideal model delta sigma weight residual 1.287 1.402 -0.115 2.00e-02 2.50e+03 3.28e+01 ... (remaining 8705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 11846 3.04 - 6.08: 132 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=" 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 angle pdb=" N ILE B 382 " pdb=" CA ILE B 382 " pdb=" C ILE B 382 " ideal model delta sigma weight residual 110.74 116.07 -5.33 9.10e-01 1.21e+00 3.44e+01 ... (remaining 11992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4338 17.77 - 35.55: 532 35.55 - 53.32: 171 53.32 - 71.10: 49 71.10 - 88.87: 11 Dihedral angle restraints: 5101 sinusoidal: 2367 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 5098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1279 0.123 - 0.246: 25 0.246 - 0.369: 4 0.369 - 0.492: 0 0.492 - 0.616: 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 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.47e+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=" C4' DC E 3 " pdb=" C5' DC E 3 " pdb=" O4' DC E 3 " pdb=" C3' DC E 3 " both_signs ideal model delta sigma weight residual False -2.53 -2.80 0.27 2.00e-01 2.50e+01 1.84e+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: 0.010 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 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= 0.321 Angle : 0.812 15.210 11997 Z= 0.463 Chirality : 0.055 0.616 1310 Planarity : 0.009 0.253 1382 Dihedral : 17.792 88.870 3335 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 covalent geometry : bond 0.00616 ( 8710) covalent geometry : angle 0.81193 (11997) hydrogen bonds : bond 0.14525 ( 313) hydrogen bonds : angle 7.87090 ( 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 : 0.317 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: 0.0841 time to fit residues: 15.8513 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 : 0.295 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.222851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177990 restraints weight = 9992.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.182552 restraints weight = 6108.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.185667 restraints weight = 4504.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.187185 restraints weight = 3720.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.188376 restraints weight = 3348.334| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8710 Z= 0.170 Angle : 0.638 8.854 11997 Z= 0.334 Chirality : 0.044 0.174 1310 Planarity : 0.005 0.057 1382 Dihedral : 16.900 75.339 1384 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 0.36 % Allowed : 9.46 % Favored : 90.18 % 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: -0.58 (0.28), residues: 921 helix: 1.05 (0.30), residues: 306 sheet: -1.67 (0.42), residues: 145 loop : -0.88 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 206 TYR 0.016 0.002 TYR A 501 PHE 0.014 0.002 PHE A 124 TRP 0.019 0.002 TRP B 402 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8710) covalent geometry : angle 0.63836 (11997) hydrogen bonds : bond 0.04273 ( 313) hydrogen bonds : angle 5.16781 ( 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 119 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.6144 (mmm160) cc_final: 0.5828 (tpt-90) REVERT: B 180 ILE cc_start: 0.7479 (mm) cc_final: 0.7024 (tt) REVERT: B 409 THR cc_start: 0.7317 (m) cc_final: 0.6892 (p) outliers start: 3 outliers final: 2 residues processed: 119 average time/residue: 0.0694 time to fit residues: 12.3722 Evaluate side-chains 105 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 84 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 145 GLN ** 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 = 0.4635 r_free = 0.4635 target = 0.218164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.174827 restraints weight = 9871.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.174124 restraints weight = 7051.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.176354 restraints weight = 6419.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.177883 restraints weight = 5239.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.177922 restraints weight = 4861.861| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8710 Z= 0.167 Angle : 0.629 8.210 11997 Z= 0.327 Chirality : 0.043 0.181 1310 Planarity : 0.005 0.049 1382 Dihedral : 16.680 74.131 1382 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 1.68 % Allowed : 11.14 % Favored : 87.19 % 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: -0.70 (0.27), residues: 921 helix: 1.10 (0.30), residues: 307 sheet: -1.73 (0.42), residues: 141 loop : -1.09 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.015 0.002 TYR B 354 PHE 0.015 0.002 PHE B 130 TRP 0.016 0.002 TRP B 402 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8710) covalent geometry : angle 0.62941 (11997) hydrogen bonds : bond 0.03979 ( 313) hydrogen bonds : angle 5.02764 ( 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 129 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.6183 (mmm160) cc_final: 0.5801 (tpt-90) REVERT: A 357 MET cc_start: 0.5908 (ttt) cc_final: 0.5437 (tpp) REVERT: B 180 ILE cc_start: 0.7498 (mm) cc_final: 0.7049 (tt) outliers start: 14 outliers final: 10 residues processed: 125 average time/residue: 0.0717 time to fit residues: 12.9546 Evaluate side-chains 113 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 169 GLU 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: 4.9990 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 0.0000 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 0.0370 chunk 42 optimal weight: 50.0000 chunk 90 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 overall best weight: 2.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 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 = 0.4658 r_free = 0.4658 target = 0.220590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.174632 restraints weight = 10012.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.178239 restraints weight = 6847.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.180511 restraints weight = 5392.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.181718 restraints weight = 4653.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.183006 restraints weight = 4264.340| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.1634 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= 0.126 Angle : 0.573 8.516 11997 Z= 0.298 Chirality : 0.042 0.157 1310 Planarity : 0.004 0.046 1382 Dihedral : 16.466 74.517 1382 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 2.04 % Allowed : 12.46 % Favored : 85.51 % 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: -0.47 (0.28), residues: 921 helix: 1.39 (0.31), residues: 308 sheet: -1.57 (0.42), residues: 141 loop : -1.05 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.022 0.001 TYR A 501 PHE 0.010 0.001 PHE B 130 TRP 0.014 0.001 TRP B 402 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8710) covalent geometry : angle 0.57265 (11997) hydrogen bonds : bond 0.03365 ( 313) hydrogen bonds : angle 4.81422 ( 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 : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 TYR cc_start: 0.6959 (m-80) cc_final: 0.6714 (m-80) REVERT: A 357 MET cc_start: 0.5797 (ttt) cc_final: 0.5432 (tpp) REVERT: B 174 GLN cc_start: 0.6322 (mp10) cc_final: 0.5816 (mp10) REVERT: B 180 ILE cc_start: 0.7431 (mm) cc_final: 0.7003 (tt) outliers start: 17 outliers final: 11 residues processed: 129 average time/residue: 0.0745 time to fit residues: 13.6835 Evaluate side-chains 116 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 169 GLU Chi-restraints excluded: chain A residue 216 THR 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 Chi-restraints excluded: chain B residue 409 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 9.9990 chunk 48 optimal weight: 0.0370 chunk 52 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 79 optimal weight: 0.0270 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.217643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.174424 restraints weight = 9958.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.173591 restraints weight = 7295.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.175903 restraints weight = 6456.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.177415 restraints weight = 5280.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.177378 restraints weight = 4990.824| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8710 Z= 0.167 Angle : 0.625 8.848 11997 Z= 0.325 Chirality : 0.043 0.187 1310 Planarity : 0.005 0.046 1382 Dihedral : 16.464 75.935 1382 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.97 % Favored : 93.92 % Rotamer: Outliers : 2.40 % Allowed : 14.49 % Favored : 83.11 % 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: -0.60 (0.27), residues: 921 helix: 1.26 (0.31), residues: 302 sheet: -1.54 (0.42), residues: 134 loop : -1.12 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.016 0.002 TYR B 354 PHE 0.017 0.002 PHE B 130 TRP 0.012 0.002 TRP A 229 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8710) covalent geometry : angle 0.62515 (11997) hydrogen bonds : bond 0.03883 ( 313) hydrogen bonds : angle 4.98028 ( 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: 20 poor density : 110 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 TYR cc_start: 0.7131 (m-80) cc_final: 0.6834 (m-80) REVERT: A 357 MET cc_start: 0.5686 (ttt) cc_final: 0.5366 (tpp) REVERT: A 480 GLN cc_start: 0.6126 (tt0) cc_final: 0.5718 (tt0) REVERT: B 174 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6158 (mp10) REVERT: B 180 ILE cc_start: 0.7428 (mm) cc_final: 0.7015 (tt) outliers start: 20 outliers final: 16 residues processed: 124 average time/residue: 0.0704 time to fit residues: 12.7765 Evaluate side-chains 122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 169 GLU 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 A residue 497 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: 9.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4625 r_free = 0.4625 target = 0.217061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.174185 restraints weight = 9919.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.173551 restraints weight = 7179.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.175598 restraints weight = 6290.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.176743 restraints weight = 5300.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.176866 restraints weight = 4964.727| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8710 Z= 0.174 Angle : 0.632 8.253 11997 Z= 0.329 Chirality : 0.043 0.189 1310 Planarity : 0.005 0.045 1382 Dihedral : 16.429 76.857 1382 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.43 % Favored : 94.46 % Rotamer: Outliers : 2.75 % Allowed : 16.17 % Favored : 81.08 % 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: 1.14 (0.31), residues: 302 sheet: -1.71 (0.41), residues: 139 loop : -1.24 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.016 0.002 TYR B 354 PHE 0.016 0.002 PHE B 130 TRP 0.014 0.002 TRP B 398 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8710) covalent geometry : angle 0.63229 (11997) hydrogen bonds : bond 0.03901 ( 313) hydrogen bonds : angle 5.06782 ( 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: 23 poor density : 110 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7566 (tt) REVERT: A 232 TYR cc_start: 0.7225 (m-80) cc_final: 0.6911 (m-80) REVERT: A 282 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5893 (mt) REVERT: A 357 MET cc_start: 0.5697 (ttt) cc_final: 0.5376 (tpp) REVERT: A 480 GLN cc_start: 0.6071 (tt0) cc_final: 0.5636 (tt0) REVERT: B 174 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.6150 (mp10) REVERT: B 180 ILE cc_start: 0.7471 (mm) cc_final: 0.7107 (tt) outliers start: 23 outliers final: 17 residues processed: 125 average time/residue: 0.0687 time to fit residues: 12.6972 Evaluate side-chains 122 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 169 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 282 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 53 optimal weight: 0.0030 chunk 62 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4628 r_free = 0.4628 target = 0.217410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.174081 restraints weight = 10132.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.174361 restraints weight = 6706.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.174918 restraints weight = 5718.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.175050 restraints weight = 5130.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.175298 restraints weight = 5104.964| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8710 Z= 0.175 Angle : 0.645 11.014 11997 Z= 0.333 Chirality : 0.043 0.191 1310 Planarity : 0.005 0.044 1382 Dihedral : 16.416 77.318 1382 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.97 % Favored : 93.92 % Rotamer: Outliers : 3.35 % Allowed : 16.89 % Favored : 79.76 % 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: 1.01 (0.30), residues: 302 sheet: -1.71 (0.41), residues: 139 loop : -1.24 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.023 0.002 TYR A 501 PHE 0.016 0.002 PHE B 130 TRP 0.014 0.002 TRP B 398 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8710) covalent geometry : angle 0.64527 (11997) hydrogen bonds : bond 0.04000 ( 313) hydrogen bonds : angle 5.13410 ( 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 134 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7551 (tt) REVERT: A 232 TYR cc_start: 0.7188 (m-80) cc_final: 0.6848 (m-80) REVERT: A 282 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5919 (mt) REVERT: A 357 MET cc_start: 0.5613 (ttt) cc_final: 0.5320 (tpp) REVERT: A 480 GLN cc_start: 0.6134 (tt0) cc_final: 0.5705 (tt0) REVERT: B 174 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6238 (mp10) REVERT: B 180 ILE cc_start: 0.7451 (mm) cc_final: 0.7085 (tt) outliers start: 28 outliers final: 21 residues processed: 126 average time/residue: 0.0706 time to fit residues: 13.1480 Evaluate side-chains 124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 169 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 282 LEU 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 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 497 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4624 r_free = 0.4624 target = 0.217202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.175185 restraints weight = 9963.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.175042 restraints weight = 6835.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.175734 restraints weight = 5927.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.176318 restraints weight = 5269.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.176572 restraints weight = 5205.180| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8710 Z= 0.162 Angle : 0.633 10.139 11997 Z= 0.325 Chirality : 0.043 0.187 1310 Planarity : 0.005 0.044 1382 Dihedral : 16.319 77.448 1382 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 2.99 % Allowed : 17.25 % Favored : 79.76 % 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: -0.78 (0.28), residues: 921 helix: 1.09 (0.31), residues: 300 sheet: -1.68 (0.41), residues: 139 loop : -1.19 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 448 TYR 0.018 0.002 TYR A 501 PHE 0.015 0.002 PHE B 130 TRP 0.017 0.002 TRP B 398 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8710) covalent geometry : angle 0.63333 (11997) hydrogen bonds : bond 0.03824 ( 313) hydrogen bonds : angle 5.04315 ( 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 135 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7557 (tt) REVERT: A 232 TYR cc_start: 0.7227 (m-80) cc_final: 0.6882 (m-80) REVERT: A 357 MET cc_start: 0.5651 (ttt) cc_final: 0.5349 (tpp) REVERT: A 480 GLN cc_start: 0.6071 (tt0) cc_final: 0.5643 (tt0) REVERT: B 24 TRP cc_start: 0.5564 (p90) cc_final: 0.4777 (p90) REVERT: B 144 TYR cc_start: 0.7859 (m-10) cc_final: 0.7579 (m-10) REVERT: B 174 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6208 (mp10) REVERT: B 180 ILE cc_start: 0.7488 (mm) cc_final: 0.7116 (tt) REVERT: B 328 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6498 (mt-10) outliers start: 25 outliers final: 20 residues processed: 127 average time/residue: 0.0676 time to fit residues: 12.8220 Evaluate side-chains 126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 169 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 282 LEU 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 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 497 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 328 GLU 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: 10.0000 chunk 87 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 63 optimal weight: 0.3980 chunk 78 optimal weight: 0.3980 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4653 r_free = 0.4653 target = 0.220387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.175396 restraints weight = 9897.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.178808 restraints weight = 6817.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.181129 restraints weight = 5393.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.182270 restraints weight = 4646.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.183499 restraints weight = 4261.488| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.2374 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= 0.124 Angle : 0.601 10.665 11997 Z= 0.303 Chirality : 0.042 0.162 1310 Planarity : 0.004 0.044 1382 Dihedral : 16.063 76.126 1382 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 2.75 % Allowed : 18.32 % Favored : 78.92 % 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: -0.46 (0.28), residues: 921 helix: 1.34 (0.31), residues: 304 sheet: -1.49 (0.43), residues: 136 loop : -1.01 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.018 0.001 TYR A 501 PHE 0.009 0.001 PHE B 130 TRP 0.015 0.001 TRP B 398 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8710) covalent geometry : angle 0.60051 (11997) hydrogen bonds : bond 0.03315 ( 313) hydrogen bonds : angle 4.81040 ( 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 130 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.5622 (tmtt) cc_final: 0.5413 (tmtt) REVERT: A 228 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7286 (tt) REVERT: A 232 TYR cc_start: 0.7111 (m-80) cc_final: 0.6764 (m-80) REVERT: A 357 MET cc_start: 0.5520 (ttt) cc_final: 0.5282 (tpp) REVERT: A 480 GLN cc_start: 0.6173 (tt0) cc_final: 0.5774 (tt0) REVERT: B 24 TRP cc_start: 0.5444 (p90) cc_final: 0.4728 (p90) REVERT: B 174 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.5952 (mp10) REVERT: B 180 ILE cc_start: 0.7581 (mm) cc_final: 0.7205 (tt) outliers start: 23 outliers final: 19 residues processed: 123 average time/residue: 0.0765 time to fit residues: 13.7105 Evaluate side-chains 128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 169 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 497 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 50.0000 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 77 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 51 optimal weight: 40.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4626 r_free = 0.4626 target = 0.217299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.172091 restraints weight = 9974.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.175326 restraints weight = 6958.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.177631 restraints weight = 5535.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.178722 restraints weight = 4774.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179885 restraints weight = 4388.691| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8710 Z= 0.162 Angle : 0.648 10.376 11997 Z= 0.327 Chirality : 0.043 0.188 1310 Planarity : 0.005 0.043 1382 Dihedral : 16.184 77.838 1382 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.75 % Favored : 94.14 % Rotamer: Outliers : 2.51 % Allowed : 18.68 % Favored : 78.80 % 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: -0.66 (0.28), residues: 921 helix: 1.13 (0.31), residues: 305 sheet: -1.53 (0.43), residues: 140 loop : -1.13 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 448 TYR 0.018 0.002 TYR A 501 PHE 0.016 0.002 PHE B 130 TRP 0.016 0.002 TRP B 398 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8710) covalent geometry : angle 0.64813 (11997) hydrogen bonds : bond 0.03729 ( 313) hydrogen bonds : angle 4.94751 ( 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 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.4322 (mpp) cc_final: 0.3674 (mpp) REVERT: A 228 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7401 (tt) REVERT: A 232 TYR cc_start: 0.7193 (m-80) cc_final: 0.6807 (m-80) REVERT: A 357 MET cc_start: 0.5613 (ttt) cc_final: 0.5337 (tpp) REVERT: A 480 GLN cc_start: 0.6152 (tt0) cc_final: 0.5753 (tt0) REVERT: B 24 TRP cc_start: 0.5481 (p90) cc_final: 0.4784 (p90) REVERT: B 144 TYR cc_start: 0.7940 (m-10) cc_final: 0.7667 (m-80) REVERT: B 174 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.5977 (mp10) REVERT: B 180 ILE cc_start: 0.7449 (mm) cc_final: 0.7091 (tt) outliers start: 21 outliers final: 18 residues processed: 120 average time/residue: 0.0715 time to fit residues: 12.6549 Evaluate side-chains 124 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 169 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 365 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 75 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN ** 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 = 0.4645 r_free = 0.4645 target = 0.219893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.173638 restraints weight = 10012.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.177065 restraints weight = 7036.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.179346 restraints weight = 5603.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.180744 restraints weight = 4856.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.181386 restraints weight = 4455.004| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8710 Z= 0.161 Angle : 0.650 10.214 11997 Z= 0.329 Chirality : 0.043 0.185 1310 Planarity : 0.005 0.044 1382 Dihedral : 16.179 77.569 1382 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.54 % Favored : 94.35 % Rotamer: Outliers : 2.63 % Allowed : 18.56 % Favored : 78.80 % 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: -0.72 (0.28), residues: 921 helix: 1.08 (0.30), residues: 304 sheet: -1.57 (0.43), residues: 139 loop : -1.15 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 448 TYR 0.017 0.002 TYR B 354 PHE 0.015 0.002 PHE B 130 TRP 0.019 0.002 TRP B 398 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8710) covalent geometry : angle 0.64998 (11997) hydrogen bonds : bond 0.03774 ( 313) hydrogen bonds : angle 5.01762 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1268.17 seconds wall clock time: 22 minutes 37.80 seconds (1357.80 seconds total)