Starting phenix.real_space_refine on Wed Mar 12 21:14:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2h_14466/03_2025/7z2h_14466.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2h_14466/03_2025/7z2h_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_2025/7z2h_14466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2h_14466/03_2025/7z2h_14466.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2h_14466/03_2025/7z2h_14466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2h_14466/03_2025/7z2h_14466.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.23, per 1000 atoms: 0.62 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: 2.34 Conformation dependent library (CDL) restraints added in 970.4 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: 3.02 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: 2.64 Time building geometry restraints manager: 2.76 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.050 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- 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= 0.354 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 : 9.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.002 TRP B 414 HIS 0.003 0.001 HIS B 208 PHE 0.012 0.001 PHE A 124 TYR 0.027 0.001 TYR A 232 ARG 0.003 0.000 ARG A 277 *********************** 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 : 1.023 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: 0.2098 time to fit residues: 38.6027 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 : 0.936 ------------------------------------------------------------------------------- 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 81 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 overall best weight: 2.1182 ------------------------------------------------------------------------------- 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** B 182 GLN B 269 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.226066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.180863 restraints weight = 9811.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.185732 restraints weight = 5987.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188953 restraints weight = 4399.145| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.0968 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= 0.197 Angle : 0.603 8.593 11997 Z= 0.315 Chirality : 0.043 0.189 1310 Planarity : 0.005 0.056 1382 Dihedral : 16.782 74.780 1384 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 0.36 % Allowed : 7.78 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 921 helix: 1.05 (0.30), residues: 319 sheet: -1.50 (0.41), residues: 155 loop : -0.92 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 402 HIS 0.003 0.001 HIS B 198 PHE 0.012 0.001 PHE A 124 TYR 0.017 0.001 TYR A 501 ARG 0.005 0.001 ARG A 358 *********************** 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 : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.6122 (mmm160) cc_final: 0.5759 (tpt-90) REVERT: B 180 ILE cc_start: 0.7389 (mm) cc_final: 0.6967 (tt) REVERT: B 409 THR cc_start: 0.7219 (m) cc_final: 0.6769 (p) outliers start: 3 outliers final: 2 residues processed: 117 average time/residue: 0.1711 time to fit residues: 29.3503 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 : 0.812 ------------------------------------------------------------------------------- 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 65 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 overall best weight: 4.9986 ------------------------------------------------------------------------------- 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 ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 255 ASN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.217795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.176483 restraints weight = 9942.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.175016 restraints weight = 6834.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.176720 restraints weight = 6222.048| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8710 Z= 0.266 Angle : 0.639 7.971 11997 Z= 0.334 Chirality : 0.044 0.188 1310 Planarity : 0.005 0.049 1382 Dihedral : 16.770 75.038 1382 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.86 % Favored : 94.03 % Rotamer: Outliers : 1.68 % Allowed : 10.30 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.28), residues: 921 helix: 1.08 (0.30), residues: 308 sheet: -1.70 (0.42), residues: 141 loop : -1.07 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 402 HIS 0.005 0.001 HIS A 315 PHE 0.018 0.002 PHE B 130 TYR 0.017 0.002 TYR A 457 ARG 0.004 0.001 ARG A 358 *********************** 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: 14 poor density : 114 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.6220 (mmm160) cc_final: 0.5919 (tpt-90) REVERT: A 357 MET cc_start: 0.5917 (ttt) cc_final: 0.5437 (tpp) REVERT: A 501 TYR cc_start: 0.5986 (t80) cc_final: 0.5601 (t80) REVERT: B 180 ILE cc_start: 0.7441 (mm) cc_final: 0.6993 (tt) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 0.1861 time to fit residues: 32.9520 Evaluate side-chains 112 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 182 GLN 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 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 314 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 0.3980 chunk 32 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 50.0000 chunk 84 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- 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 ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.215212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.173071 restraints weight = 9945.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.172043 restraints weight = 7192.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.173860 restraints weight = 6445.734| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8710 Z= 0.310 Angle : 0.681 9.121 11997 Z= 0.354 Chirality : 0.045 0.194 1310 Planarity : 0.005 0.048 1382 Dihedral : 16.757 75.959 1382 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.30 % Favored : 93.59 % Rotamer: Outliers : 2.63 % Allowed : 13.53 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.27), residues: 921 helix: 0.83 (0.29), residues: 302 sheet: -1.85 (0.40), residues: 139 loop : -1.30 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 229 HIS 0.006 0.001 HIS A 315 PHE 0.019 0.003 PHE B 130 TYR 0.017 0.002 TYR A 457 ARG 0.004 0.001 ARG A 358 *********************** 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: 22 poor density : 111 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 TYR cc_start: 0.7231 (m-80) cc_final: 0.6959 (m-80) REVERT: A 357 MET cc_start: 0.5647 (ttt) cc_final: 0.5314 (tpp) REVERT: B 174 GLN cc_start: 0.6566 (mp10) cc_final: 0.5995 (mp10) outliers start: 22 outliers final: 17 residues processed: 126 average time/residue: 0.1859 time to fit residues: 34.0441 Evaluate side-chains 125 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 326 ILE Chi-restraints excluded: chain A residue 340 GLN 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 31 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 216 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 30 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 51 optimal weight: 40.0000 chunk 91 optimal weight: 0.0040 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- 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 = 0.4615 r_free = 0.4615 target = 0.215861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.175820 restraints weight = 9929.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.174362 restraints weight = 7772.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.176372 restraints weight = 6892.121| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.2086 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= 0.271 Angle : 0.657 9.150 11997 Z= 0.339 Chirality : 0.044 0.195 1310 Planarity : 0.005 0.047 1382 Dihedral : 16.597 76.394 1382 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.65 % Favored : 94.25 % Rotamer: Outliers : 2.87 % Allowed : 15.09 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.27), residues: 921 helix: 0.89 (0.30), residues: 302 sheet: -1.96 (0.40), residues: 141 loop : -1.28 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 229 HIS 0.005 0.001 HIS A 315 PHE 0.017 0.002 PHE B 130 TYR 0.017 0.002 TYR B 354 ARG 0.003 0.001 ARG A 448 *********************** 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 139 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7348 (tt) REVERT: A 232 TYR cc_start: 0.7247 (m-80) cc_final: 0.6920 (m-80) REVERT: A 282 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5877 (mt) REVERT: A 357 MET cc_start: 0.5623 (ttt) cc_final: 0.5295 (tpp) REVERT: A 480 GLN cc_start: 0.5942 (tt0) cc_final: 0.5571 (tt0) REVERT: A 501 TYR cc_start: 0.6642 (t80) cc_final: 0.6395 (t80) REVERT: B 174 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.6094 (mp10) REVERT: B 180 ILE cc_start: 0.7489 (mm) cc_final: 0.6903 (tt) outliers start: 24 outliers final: 18 residues processed: 130 average time/residue: 0.1754 time to fit residues: 33.0502 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 : 0.932 ------------------------------------------------------------------------------- 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 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 123 ASP Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 216 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4610 r_free = 0.4610 target = 0.215434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.175063 restraints weight = 9895.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.173449 restraints weight = 7726.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.175302 restraints weight = 7434.982| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8710 Z= 0.264 Angle : 0.648 9.156 11997 Z= 0.336 Chirality : 0.043 0.196 1310 Planarity : 0.005 0.046 1382 Dihedral : 16.518 77.495 1382 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.08 % Favored : 93.81 % Rotamer: Outliers : 3.35 % Allowed : 15.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.27), residues: 921 helix: 0.84 (0.30), residues: 302 sheet: -1.93 (0.41), residues: 134 loop : -1.32 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 229 HIS 0.005 0.001 HIS A 315 PHE 0.016 0.002 PHE B 130 TYR 0.017 0.002 TYR B 354 ARG 0.004 0.001 ARG A 358 *********************** 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 141 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7541 (tt) REVERT: A 232 TYR cc_start: 0.7283 (m-80) cc_final: 0.6953 (m-80) REVERT: A 282 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.5968 (mt) REVERT: A 357 MET cc_start: 0.5648 (ttt) cc_final: 0.5317 (tpp) REVERT: A 480 GLN cc_start: 0.5952 (tt0) cc_final: 0.5532 (tt0) REVERT: B 144 TYR cc_start: 0.7893 (m-10) cc_final: 0.7589 (m-10) REVERT: B 174 GLN cc_start: 0.6630 (OUTLIER) cc_final: 0.6109 (mp10) REVERT: B 180 ILE cc_start: 0.7485 (mm) cc_final: 0.6882 (tt) outliers start: 28 outliers final: 18 residues processed: 130 average time/residue: 0.1752 time to fit residues: 33.1930 Evaluate side-chains 126 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 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 123 ASP Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 216 THR 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 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 80 optimal weight: 30.0000 chunk 11 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 65 optimal weight: 0.0040 chunk 69 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- 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 = 0.4638 r_free = 0.4638 target = 0.219355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.178513 restraints weight = 10028.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.176557 restraints weight = 7447.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.177471 restraints weight = 6483.904| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8710 Z= 0.235 Angle : 0.623 9.362 11997 Z= 0.321 Chirality : 0.043 0.185 1310 Planarity : 0.005 0.045 1382 Dihedral : 16.395 80.165 1382 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.79 % Rotamer: Outliers : 3.23 % Allowed : 16.65 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.27), residues: 921 helix: 0.97 (0.30), residues: 303 sheet: -1.86 (0.41), residues: 133 loop : -1.28 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 398 HIS 0.004 0.001 HIS A 198 PHE 0.014 0.002 PHE B 130 TYR 0.016 0.002 TYR B 354 ARG 0.003 0.000 ARG A 448 *********************** 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 140 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7559 (tt) REVERT: A 232 TYR cc_start: 0.7227 (m-80) cc_final: 0.6862 (m-80) REVERT: A 282 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5878 (mt) REVERT: A 357 MET cc_start: 0.5572 (ttt) cc_final: 0.5275 (tpp) REVERT: A 480 GLN cc_start: 0.6088 (tt0) cc_final: 0.5642 (tt0) REVERT: B 24 TRP cc_start: 0.5568 (p90) cc_final: 0.4856 (p90) REVERT: B 174 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.6177 (mp10) REVERT: B 180 ILE cc_start: 0.7519 (mm) cc_final: 0.6924 (tt) outliers start: 27 outliers final: 20 residues processed: 131 average time/residue: 0.1805 time to fit residues: 34.3283 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 : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 VAL 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 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 123 ASP Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 296 THR 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 0 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 0.0010 chunk 25 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- 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 = 0.4652 r_free = 0.4652 target = 0.219690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.175010 restraints weight = 9940.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.179610 restraints weight = 6035.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.182594 restraints weight = 4395.506| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.2326 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= 0.194 Angle : 0.600 9.275 11997 Z= 0.309 Chirality : 0.042 0.172 1310 Planarity : 0.004 0.043 1382 Dihedral : 16.210 80.200 1382 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 2.75 % Allowed : 17.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.28), residues: 921 helix: 1.12 (0.31), residues: 307 sheet: -1.70 (0.41), residues: 139 loop : -1.16 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 398 HIS 0.004 0.001 HIS A 198 PHE 0.011 0.001 PHE B 130 TYR 0.019 0.001 TYR A 501 ARG 0.002 0.000 ARG A 448 *********************** 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 134 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.5074 (m-40) cc_final: 0.4693 (t0) REVERT: A 187 LEU cc_start: 0.8392 (mm) cc_final: 0.8103 (mm) REVERT: A 228 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7503 (tt) REVERT: A 232 TYR cc_start: 0.7200 (m-80) cc_final: 0.6799 (m-80) REVERT: A 357 MET cc_start: 0.5544 (ttt) cc_final: 0.5271 (tpp) REVERT: A 480 GLN cc_start: 0.6125 (tt0) cc_final: 0.5693 (tt0) REVERT: B 24 TRP cc_start: 0.5495 (p90) cc_final: 0.4807 (p90) REVERT: B 174 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6130 (mp10) REVERT: B 180 ILE cc_start: 0.7538 (mm) cc_final: 0.6949 (tt) outliers start: 23 outliers final: 18 residues processed: 125 average time/residue: 0.1878 time to fit residues: 33.5599 Evaluate side-chains 128 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 340 GLN Chi-restraints excluded: chain A residue 362 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 90 optimal weight: 0.0570 chunk 58 optimal weight: 7.9990 chunk 51 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 overall best weight: 3.0104 ------------------------------------------------------------------------------- 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 = 0.4640 r_free = 0.4640 target = 0.218522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.171922 restraints weight = 10089.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.175428 restraints weight = 6893.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.177902 restraints weight = 5408.249| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.2415 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= 0.207 Angle : 0.613 8.977 11997 Z= 0.312 Chirality : 0.042 0.174 1310 Planarity : 0.005 0.043 1382 Dihedral : 16.171 80.779 1382 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.01 % Rotamer: Outliers : 2.99 % Allowed : 17.96 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.28), residues: 921 helix: 1.10 (0.31), residues: 309 sheet: -1.76 (0.41), residues: 142 loop : -1.13 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 398 HIS 0.004 0.001 HIS A 198 PHE 0.013 0.001 PHE B 130 TYR 0.023 0.002 TYR A 501 ARG 0.003 0.000 ARG A 448 *********************** 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 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7544 (tt) REVERT: A 232 TYR cc_start: 0.7220 (m-80) cc_final: 0.6822 (m-80) REVERT: A 357 MET cc_start: 0.5537 (ttt) cc_final: 0.5273 (tpp) REVERT: A 480 GLN cc_start: 0.6073 (tt0) cc_final: 0.5641 (tt0) REVERT: B 24 TRP cc_start: 0.5488 (p90) cc_final: 0.4808 (p90) REVERT: B 174 GLN cc_start: 0.6536 (OUTLIER) cc_final: 0.6019 (mp10) REVERT: B 180 ILE cc_start: 0.7522 (mm) cc_final: 0.6914 (tt) REVERT: B 235 HIS cc_start: 0.6169 (m90) cc_final: 0.5944 (m90) outliers start: 25 outliers final: 21 residues processed: 124 average time/residue: 0.1775 time to fit residues: 31.7843 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 : 0.772 ------------------------------------------------------------------------------- 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 90 VAL 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 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 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 95 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 = 0.4625 r_free = 0.4625 target = 0.217025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.171797 restraints weight = 9967.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.175200 restraints weight = 6945.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.177244 restraints weight = 5503.176| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.2503 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= 0.239 Angle : 0.634 9.121 11997 Z= 0.325 Chirality : 0.043 0.184 1310 Planarity : 0.005 0.043 1382 Dihedral : 16.210 81.592 1382 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.75 % Favored : 94.14 % Rotamer: Outliers : 2.75 % Allowed : 18.68 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.28), residues: 921 helix: 1.01 (0.30), residues: 309 sheet: -1.73 (0.41), residues: 140 loop : -1.19 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 398 HIS 0.004 0.001 HIS A 198 PHE 0.016 0.002 PHE B 130 TYR 0.019 0.002 TYR A 501 ARG 0.004 0.000 ARG A 448 ********************** 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 133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7618 (tt) REVERT: A 357 MET cc_start: 0.5611 (ttt) cc_final: 0.5382 (tpp) REVERT: A 480 GLN cc_start: 0.6063 (tt0) cc_final: 0.5613 (tt0) REVERT: B 24 TRP cc_start: 0.5580 (p90) cc_final: 0.4859 (p90) REVERT: B 144 TYR cc_start: 0.7944 (m-10) cc_final: 0.7622 (m-80) REVERT: B 174 GLN cc_start: 0.6497 (OUTLIER) cc_final: 0.5951 (mp10) REVERT: B 180 ILE cc_start: 0.7514 (mm) cc_final: 0.6962 (tt) REVERT: B 258 GLN cc_start: 0.6254 (mt0) cc_final: 0.6025 (tp40) outliers start: 23 outliers final: 21 residues processed: 125 average time/residue: 0.1831 time to fit residues: 32.8480 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 : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 VAL 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 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 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 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 25 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 = 0.4644 r_free = 0.4644 target = 0.219113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.173708 restraints weight = 10042.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.177269 restraints weight = 6867.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.179637 restraints weight = 5350.124| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.2527 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= 0.190 Angle : 0.599 8.595 11997 Z= 0.305 Chirality : 0.042 0.164 1310 Planarity : 0.004 0.043 1382 Dihedral : 16.036 80.240 1382 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 2.75 % Allowed : 18.68 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.28), residues: 921 helix: 1.17 (0.31), residues: 307 sheet: -1.56 (0.42), residues: 135 loop : -1.04 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 398 HIS 0.004 0.001 HIS A 198 PHE 0.010 0.001 PHE B 130 TYR 0.016 0.001 TYR B 354 ARG 0.003 0.000 ARG A 448 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.84 seconds wall clock time: 44 minutes 54.74 seconds (2694.74 seconds total)