Starting phenix.real_space_refine on Wed Aug 5 02:26:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfa_49360/08_2026/9nfa_49360.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfa_49360/08_2026/9nfa_49360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nfa_49360/08_2026/9nfa_49360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfa_49360/08_2026/9nfa_49360.map" model { file = "/net/cci-nas-00/data/ceres_data/9nfa_49360/08_2026/9nfa_49360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfa_49360/08_2026/9nfa_49360.cif" } resolution = 2.7 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 4881 2.51 5 N 1371 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8001 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4196 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 17, 'TRANS': 514} Chain: "B" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2712 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 322} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1092 Inner-chain residues flagged as termini: ['pdbres=" C C 26 "'] Classifications: {'RNA': 52} Modifications used: {'5*END': 2, 'rna2p_pur': 2, 'rna2p_pyr': 13, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 14, 'rna3p': 37} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.22 Number of scatterers: 8001 At special positions: 0 Unit cell: (87.318, 113.652, 131.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 50 15.00 Mg 1 11.99 O 1657 8.00 N 1371 7.00 C 4881 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: 0.68 Conformation dependent library (CDL) restraints added in 359.0 milliseconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 59.9% alpha, 7.5% beta 11 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 49 through 67 Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.560A pdb=" N VAL A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 140 removed outlier: 3.643A pdb=" N GLU A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 158 Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 192 through 213 removed outlier: 7.518A pdb=" N TRP A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N LYS A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 235 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 240 through 252 Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 261 through 264 removed outlier: 3.551A pdb=" N LYS A 264 " --> pdb=" O ASN A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.969A pdb=" N GLN A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 320 through 334 removed outlier: 3.744A pdb=" N ILE A 324 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.915A pdb=" N TYR A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.402A pdb=" N GLY A 387 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 407 Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 478 through 490 Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'B' and resid 8 through 26 removed outlier: 3.506A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 23 " --> pdb=" O HIS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.839A pdb=" N LYS B 37 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 55 through 62 removed outlier: 3.683A pdb=" N LEU B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 75 Processing helix chain 'B' and resid 101 through 111 removed outlier: 3.540A pdb=" N LYS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 132 removed outlier: 3.837A pdb=" N LYS B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 187 through 225 removed outlier: 3.567A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 278 through 290 removed outlier: 4.044A pdb=" N ALA B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420 removed outlier: 3.633A pdb=" N ALA A 414 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 372 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE A 467 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA A 374 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 48 removed outlier: 3.648A pdb=" N ARG B 90 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 112 through 115 Processing sheet with id=AA6, first strand: chain 'B' and resid 261 through 263 removed outlier: 4.016A pdb=" N TRP B 261 " --> pdb=" O LEU B 274 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2086 1.33 - 1.45: 1606 1.45 - 1.57: 4385 1.57 - 1.69: 98 1.69 - 1.81: 66 Bond restraints: 8241 Sorted by residual: bond pdb=" CG LEU A 273 " pdb=" CD1 LEU A 273 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.82e+00 bond pdb=" N9 A C 11 " pdb=" C4 A C 11 " ideal model delta sigma weight residual 1.374 1.382 -0.008 6.00e-03 2.78e+04 1.58e+00 bond pdb=" C3' U C 54 " pdb=" O3' U C 54 " ideal model delta sigma weight residual 1.427 1.442 -0.015 1.20e-02 6.94e+03 1.53e+00 bond pdb=" CB ASN B 290 " pdb=" CG ASN B 290 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" N3 C C 26 " pdb=" C4 C C 26 " ideal model delta sigma weight residual 1.335 1.328 0.007 7.00e-03 2.04e+04 1.12e+00 ... (remaining 8236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 10852 1.39 - 2.77: 379 2.77 - 4.16: 69 4.16 - 5.55: 15 5.55 - 6.94: 10 Bond angle restraints: 11325 Sorted by residual: angle pdb=" C3' U C 54 " pdb=" O3' U C 54 " pdb=" P U C 55 " ideal model delta sigma weight residual 119.70 125.35 -5.65 1.20e+00 6.94e-01 2.22e+01 angle pdb=" O5' U C 44 " pdb=" C5' U C 44 " pdb=" C4' U C 44 " ideal model delta sigma weight residual 109.40 112.56 -3.16 8.00e-01 1.56e+00 1.56e+01 angle pdb=" O5' U C 55 " pdb=" C5' U C 55 " pdb=" C4' U C 55 " ideal model delta sigma weight residual 109.40 112.41 -3.01 8.00e-01 1.56e+00 1.41e+01 angle pdb=" O5' G C 51 " pdb=" C5' G C 51 " pdb=" C4' G C 51 " ideal model delta sigma weight residual 109.40 112.36 -2.96 8.00e-01 1.56e+00 1.37e+01 angle pdb=" O5' U C 56 " pdb=" C5' U C 56 " pdb=" C4' U C 56 " ideal model delta sigma weight residual 109.40 112.20 -2.80 8.00e-01 1.56e+00 1.23e+01 ... (remaining 11320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 4776 34.79 - 69.59: 334 69.59 - 104.38: 31 104.38 - 139.17: 1 139.17 - 173.97: 1 Dihedral angle restraints: 5143 sinusoidal: 2633 harmonic: 2510 Sorted by residual: dihedral pdb=" O4' U C 54 " pdb=" C1' U C 54 " pdb=" N1 U C 54 " pdb=" C2 U C 54 " ideal model delta sinusoidal sigma weight residual -128.00 45.97 -173.97 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" C4' U C 54 " pdb=" C3' U C 54 " pdb=" O3' U C 54 " pdb=" P U C 55 " ideal model delta sinusoidal sigma weight residual -110.00 25.11 -135.11 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" CA PHE B 55 " pdb=" C PHE B 55 " pdb=" N ASN B 56 " pdb=" CA ASN B 56 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 916 0.039 - 0.077: 282 0.077 - 0.116: 65 0.116 - 0.155: 46 0.155 - 0.194: 1 Chirality restraints: 1310 Sorted by residual: chirality pdb=" C3' U C 54 " pdb=" C4' U C 54 " pdb=" O3' U C 54 " pdb=" C2' U C 54 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" CB ILE B 272 " pdb=" CA ILE B 272 " pdb=" CG1 ILE B 272 " pdb=" CG2 ILE B 272 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ILE B 259 " pdb=" N ILE B 259 " pdb=" C ILE B 259 " pdb=" CB ILE B 259 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 1307 not shown) Planarity restraints: 1253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 290 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ASN B 290 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN B 290 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN B 291 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 63 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C THR B 63 " 0.026 2.00e-02 2.50e+03 pdb=" O THR B 63 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP B 64 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 60 " 0.110 9.50e-02 1.11e+02 4.96e-02 2.03e+00 pdb=" NE ARG B 60 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 60 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 60 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 60 " -0.000 2.00e-02 2.50e+03 ... (remaining 1250 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 552 2.73 - 3.28: 8067 3.28 - 3.82: 13792 3.82 - 4.36: 17391 4.36 - 4.90: 27343 Nonbonded interactions: 67145 Sorted by model distance: nonbonded pdb=" N GLU B 281 " pdb=" OE1 GLU B 281 " model vdw 2.192 3.120 nonbonded pdb=" OE2 GLU A 241 " pdb=" OG SER A 265 " model vdw 2.200 3.040 nonbonded pdb=" NZ LYS A 362 " pdb=" OD2 ASP A 528 " model vdw 2.209 3.120 nonbonded pdb=" OE1 GLN A 7 " pdb=" OG1 THR A 472 " model vdw 2.225 3.040 nonbonded pdb=" O SER A 380 " pdb=" NE2 GLN A 383 " model vdw 2.238 3.120 ... (remaining 67140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.630 Find NCS groups from input model: 0.030 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.004 0.045 8241 Z= 0.178 Angle : 0.628 6.935 11325 Z= 0.382 Chirality : 0.045 0.194 1310 Planarity : 0.004 0.050 1253 Dihedral : 20.777 173.967 3511 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.79 % Allowed : 36.07 % Favored : 61.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.29), residues: 858 helix: 0.46 (0.24), residues: 462 sheet: -0.90 (0.56), residues: 75 loop : -1.09 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 60 TYR 0.014 0.001 TYR A 46 PHE 0.010 0.001 PHE B 275 TRP 0.006 0.001 TRP B 261 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 8241) covalent geometry : angle 0.62788 / 0.38 (11325) hydrogen bonds : bond 0.24330 / 15.72 ( 395) hydrogen bonds : angle 8.03492 / 5.74 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.7590 (mtm-85) REVERT: A 117 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8093 (pt0) REVERT: A 162 MET cc_start: 0.8731 (tpt) cc_final: 0.8418 (mmp) REVERT: A 311 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 347 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7138 (mp0) REVERT: A 362 LYS cc_start: 0.7805 (mtpm) cc_final: 0.7506 (ptpt) REVERT: B 44 GLU cc_start: 0.7292 (tm-30) cc_final: 0.7049 (tm-30) REVERT: B 54 LYS cc_start: 0.6511 (mptt) cc_final: 0.5694 (mttp) REVERT: B 128 LYS cc_start: 0.7602 (mttm) cc_final: 0.7380 (mptm) REVERT: B 134 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7310 (mptt) REVERT: B 158 PHE cc_start: 0.6833 (m-10) cc_final: 0.6550 (m-10) REVERT: B 223 MET cc_start: 0.7716 (mmm) cc_final: 0.7335 (mmm) REVERT: B 261 TRP cc_start: 0.8127 (OUTLIER) cc_final: 0.7217 (t60) REVERT: B 320 GLU cc_start: 0.7882 (tt0) cc_final: 0.7619 (tt0) REVERT: B 324 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7676 (mm-30) outliers start: 21 outliers final: 15 residues processed: 213 average time/residue: 0.5821 time to fit residues: 130.1298 Evaluate side-chains 221 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.139665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109552 restraints weight = 12248.174| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.82 r_work: 0.3276 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8241 Z= 0.224 Angle : 0.643 7.954 11325 Z= 0.345 Chirality : 0.046 0.481 1310 Planarity : 0.004 0.033 1253 Dihedral : 18.229 156.081 1759 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.17 % Allowed : 30.64 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.29), residues: 858 helix: 0.95 (0.24), residues: 484 sheet: -1.07 (0.57), residues: 70 loop : -1.41 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 384 TYR 0.019 0.002 TYR A 46 PHE 0.016 0.002 PHE B 253 TRP 0.008 0.002 TRP B 329 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 8241) covalent geometry : angle 0.64309 / 0.35 (11325) hydrogen bonds : bond 0.05929 / 3.85 ( 395) hydrogen bonds : angle 5.43216 / 3.81 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8275 (ttt180) REVERT: A 85 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7490 (mtm-85) REVERT: A 117 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8150 (pt0) REVERT: A 162 MET cc_start: 0.8622 (tpt) cc_final: 0.8251 (tpp) REVERT: A 201 TYR cc_start: 0.8638 (t80) cc_final: 0.8376 (t80) REVERT: A 223 GLU cc_start: 0.8001 (tp30) cc_final: 0.7787 (tp30) REVERT: A 241 GLU cc_start: 0.7280 (tt0) cc_final: 0.7038 (tt0) REVERT: A 256 GLU cc_start: 0.7896 (mp0) cc_final: 0.7677 (mp0) REVERT: A 362 LYS cc_start: 0.7661 (mtpm) cc_final: 0.7284 (ttpt) REVERT: A 528 ASP cc_start: 0.8020 (m-30) cc_final: 0.7609 (m-30) REVERT: B 44 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6977 (tm-30) REVERT: B 54 LYS cc_start: 0.6561 (mptt) cc_final: 0.5725 (mttp) REVERT: B 82 ILE cc_start: 0.6436 (OUTLIER) cc_final: 0.6226 (mm) REVERT: B 134 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7335 (mptt) REVERT: B 158 PHE cc_start: 0.6920 (m-10) cc_final: 0.6697 (m-10) REVERT: B 216 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8245 (pmtt) REVERT: B 218 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: B 219 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: B 223 MET cc_start: 0.7819 (mmm) cc_final: 0.7440 (mmm) REVERT: B 224 LYS cc_start: 0.7910 (mttt) cc_final: 0.7648 (mttt) REVERT: B 241 ASP cc_start: 0.7634 (p0) cc_final: 0.7376 (p0) REVERT: B 287 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7396 (mmpt) REVERT: B 321 ASP cc_start: 0.7641 (m-30) cc_final: 0.7125 (m-30) REVERT: B 324 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7712 (mm-30) outliers start: 39 outliers final: 17 residues processed: 234 average time/residue: 0.6793 time to fit residues: 166.6279 Evaluate side-chains 227 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 322 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110816 restraints weight = 12211.390| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.80 r_work: 0.3295 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8241 Z= 0.175 Angle : 0.596 8.164 11325 Z= 0.315 Chirality : 0.043 0.461 1310 Planarity : 0.004 0.040 1253 Dihedral : 18.153 159.670 1737 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.57 % Allowed : 30.11 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.29), residues: 858 helix: 1.11 (0.24), residues: 485 sheet: -1.02 (0.57), residues: 70 loop : -1.43 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 384 TYR 0.017 0.001 TYR A 46 PHE 0.013 0.001 PHE B 65 TRP 0.007 0.001 TRP A 144 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 8241) covalent geometry : angle 0.59613 / 0.32 (11325) hydrogen bonds : bond 0.04871 / 3.17 ( 395) hydrogen bonds : angle 5.06150 / 3.54 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8247 (ttt180) REVERT: A 85 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7522 (mtm-85) REVERT: A 117 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: A 162 MET cc_start: 0.8618 (tpt) cc_final: 0.8246 (mmp) REVERT: A 201 TYR cc_start: 0.8639 (t80) cc_final: 0.8376 (t80) REVERT: A 241 GLU cc_start: 0.7248 (tt0) cc_final: 0.7004 (tt0) REVERT: A 243 GLU cc_start: 0.7922 (tp30) cc_final: 0.7648 (tm-30) REVERT: A 347 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7234 (mp0) REVERT: A 351 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8528 (ttmt) REVERT: A 362 LYS cc_start: 0.7609 (mtpm) cc_final: 0.7218 (ttpt) REVERT: A 528 ASP cc_start: 0.8033 (m-30) cc_final: 0.7643 (m-30) REVERT: B 44 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7037 (tm-30) REVERT: B 54 LYS cc_start: 0.6571 (mptt) cc_final: 0.5730 (mttp) REVERT: B 134 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7325 (mptt) REVERT: B 216 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8271 (pmtt) REVERT: B 218 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: B 219 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 223 MET cc_start: 0.7859 (mmm) cc_final: 0.7465 (mmm) REVERT: B 224 LYS cc_start: 0.7925 (mttt) cc_final: 0.7666 (mttt) REVERT: B 241 ASP cc_start: 0.7683 (p0) cc_final: 0.7419 (p0) REVERT: B 261 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7504 (t60) REVERT: B 277 GLU cc_start: 0.6907 (pp20) cc_final: 0.6706 (pp20) REVERT: B 287 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7439 (mmpt) REVERT: B 321 ASP cc_start: 0.7623 (m-30) cc_final: 0.7079 (m-30) REVERT: B 324 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7732 (mm-30) outliers start: 42 outliers final: 20 residues processed: 226 average time/residue: 0.6232 time to fit residues: 147.8854 Evaluate side-chains 224 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 322 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 88 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.140842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110788 restraints weight = 12450.397| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.81 r_work: 0.3293 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8241 Z= 0.178 Angle : 0.589 8.164 11325 Z= 0.311 Chirality : 0.043 0.461 1310 Planarity : 0.004 0.041 1253 Dihedral : 18.138 159.357 1737 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.84 % Allowed : 29.71 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.29), residues: 858 helix: 1.19 (0.24), residues: 484 sheet: -0.99 (0.57), residues: 70 loop : -1.39 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 60 TYR 0.018 0.001 TYR A 46 PHE 0.014 0.001 PHE B 253 TRP 0.007 0.001 TRP A 144 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 8241) covalent geometry : angle 0.58924 / 0.31 (11325) hydrogen bonds : bond 0.04451 / 2.88 ( 395) hydrogen bonds : angle 4.89919 / 3.42 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8249 (ttt180) REVERT: A 85 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7521 (mtm-85) REVERT: A 117 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: A 162 MET cc_start: 0.8585 (tpt) cc_final: 0.8253 (mmp) REVERT: A 201 TYR cc_start: 0.8640 (t80) cc_final: 0.8396 (t80) REVERT: A 241 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6976 (tt0) REVERT: A 298 ASN cc_start: 0.7327 (t0) cc_final: 0.6810 (t0) REVERT: A 300 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: A 347 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7253 (mp0) REVERT: A 351 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8495 (ttmt) REVERT: B 44 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7080 (tm-30) REVERT: B 54 LYS cc_start: 0.6579 (mptt) cc_final: 0.5721 (mttp) REVERT: B 134 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7248 (mppt) REVERT: B 216 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8288 (pmtt) REVERT: B 218 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: B 219 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: B 223 MET cc_start: 0.7868 (mmm) cc_final: 0.7493 (mmm) REVERT: B 224 LYS cc_start: 0.7914 (mttt) cc_final: 0.7629 (mttt) REVERT: B 241 ASP cc_start: 0.7726 (p0) cc_final: 0.7454 (p0) REVERT: B 261 TRP cc_start: 0.8260 (OUTLIER) cc_final: 0.7443 (t60) REVERT: B 287 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7474 (mmpt) REVERT: B 321 ASP cc_start: 0.7622 (m-30) cc_final: 0.7069 (m-30) REVERT: B 324 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7714 (mm-30) outliers start: 44 outliers final: 17 residues processed: 229 average time/residue: 0.5681 time to fit residues: 136.8288 Evaluate side-chains 227 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.137339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106596 restraints weight = 12339.274| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.83 r_work: 0.3289 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8241 Z= 0.212 Angle : 0.623 8.192 11325 Z= 0.327 Chirality : 0.045 0.487 1310 Planarity : 0.004 0.046 1253 Dihedral : 18.154 159.613 1737 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.70 % Allowed : 29.58 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.29), residues: 858 helix: 1.15 (0.24), residues: 484 sheet: -1.01 (0.57), residues: 72 loop : -1.34 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 60 TYR 0.020 0.001 TYR A 46 PHE 0.015 0.002 PHE B 236 TRP 0.007 0.002 TRP A 144 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 ( 8241) covalent geometry : angle 0.62263 / 0.33 (11325) hydrogen bonds : bond 0.04463 / 2.89 ( 395) hydrogen bonds : angle 4.82630 / 3.38 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8261 (ttt180) REVERT: A 61 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8427 (tt) REVERT: A 85 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7505 (mtm-85) REVERT: A 117 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8219 (pt0) REVERT: A 162 MET cc_start: 0.8586 (tpt) cc_final: 0.8231 (tpp) REVERT: A 201 TYR cc_start: 0.8644 (t80) cc_final: 0.8379 (t80) REVERT: A 241 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: A 298 ASN cc_start: 0.7314 (t0) cc_final: 0.6646 (t0) REVERT: A 300 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: A 347 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7228 (mp0) REVERT: A 351 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8452 (ttmt) REVERT: A 418 GLU cc_start: 0.8077 (pm20) cc_final: 0.7833 (pt0) REVERT: B 33 ASP cc_start: 0.6485 (t0) cc_final: 0.6159 (m-30) REVERT: B 44 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 54 LYS cc_start: 0.6572 (mptt) cc_final: 0.5670 (mttp) REVERT: B 134 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7237 (mppt) REVERT: B 216 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8328 (pmtt) REVERT: B 218 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 219 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: B 223 MET cc_start: 0.7987 (mmm) cc_final: 0.7609 (mmm) REVERT: B 224 LYS cc_start: 0.7913 (mttt) cc_final: 0.7635 (mttt) REVERT: B 241 ASP cc_start: 0.7737 (p0) cc_final: 0.7474 (p0) REVERT: B 261 TRP cc_start: 0.8253 (OUTLIER) cc_final: 0.7366 (t60) REVERT: B 287 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7466 (mmpt) REVERT: B 321 ASP cc_start: 0.7636 (m-30) cc_final: 0.7086 (m-30) REVERT: B 324 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7693 (mm-30) outliers start: 43 outliers final: 18 residues processed: 229 average time/residue: 0.5599 time to fit residues: 134.9743 Evaluate side-chains 236 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.137923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107235 restraints weight = 12173.239| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.82 r_work: 0.3301 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8241 Z= 0.170 Angle : 0.607 8.180 11325 Z= 0.318 Chirality : 0.043 0.447 1310 Planarity : 0.004 0.033 1253 Dihedral : 18.148 159.125 1737 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.70 % Allowed : 30.77 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.29), residues: 858 helix: 1.26 (0.24), residues: 483 sheet: -0.97 (0.58), residues: 72 loop : -1.34 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 60 TYR 0.018 0.001 TYR A 46 PHE 0.015 0.001 PHE B 253 TRP 0.007 0.001 TRP B 261 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 8241) covalent geometry : angle 0.60745 / 0.32 (11325) hydrogen bonds : bond 0.04105 / 2.66 ( 395) hydrogen bonds : angle 4.71456 / 3.30 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8262 (ttt180) REVERT: A 61 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8407 (tt) REVERT: A 85 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7509 (mtm-85) REVERT: A 117 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8235 (pt0) REVERT: A 162 MET cc_start: 0.8569 (tpt) cc_final: 0.8195 (tpp) REVERT: A 201 TYR cc_start: 0.8629 (t80) cc_final: 0.8378 (t80) REVERT: A 241 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: A 298 ASN cc_start: 0.7275 (t0) cc_final: 0.6627 (t0) REVERT: A 300 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: A 347 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7232 (mp0) REVERT: A 351 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8423 (ttmt) REVERT: A 418 GLU cc_start: 0.8077 (pm20) cc_final: 0.7819 (pt0) REVERT: B 33 ASP cc_start: 0.6453 (t0) cc_final: 0.6095 (m-30) REVERT: B 44 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7192 (tm-30) REVERT: B 54 LYS cc_start: 0.6547 (mptt) cc_final: 0.5661 (mttp) REVERT: B 134 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7255 (mptt) REVERT: B 138 LEU cc_start: 0.8860 (mp) cc_final: 0.8594 (mp) REVERT: B 216 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8135 (pmtt) REVERT: B 219 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: B 223 MET cc_start: 0.7998 (mmm) cc_final: 0.7605 (mmm) REVERT: B 224 LYS cc_start: 0.7908 (mttt) cc_final: 0.7648 (mttt) REVERT: B 241 ASP cc_start: 0.7783 (p0) cc_final: 0.7508 (p0) REVERT: B 260 LYS cc_start: 0.7519 (pptt) cc_final: 0.7215 (pmtt) REVERT: B 261 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7381 (t60) REVERT: B 287 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7471 (mmpt) REVERT: B 321 ASP cc_start: 0.7618 (m-30) cc_final: 0.7072 (m-30) REVERT: B 324 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7700 (mm-30) outliers start: 43 outliers final: 18 residues processed: 233 average time/residue: 0.5550 time to fit residues: 136.2668 Evaluate side-chains 227 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 0.0010 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.137398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106685 restraints weight = 12258.965| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.83 r_work: 0.3293 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8241 Z= 0.201 Angle : 0.628 8.162 11325 Z= 0.327 Chirality : 0.045 0.475 1310 Planarity : 0.004 0.032 1253 Dihedral : 18.143 159.694 1737 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.44 % Allowed : 31.43 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.29), residues: 858 helix: 1.25 (0.24), residues: 483 sheet: -0.93 (0.58), residues: 72 loop : -1.37 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.020 0.001 TYR A 46 PHE 0.016 0.002 PHE B 236 TRP 0.007 0.002 TRP B 261 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 8241) covalent geometry : angle 0.62816 / 0.33 (11325) hydrogen bonds : bond 0.04207 / 2.74 ( 395) hydrogen bonds : angle 4.74345 / 3.32 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8260 (ttt180) REVERT: A 61 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8400 (tt) REVERT: A 85 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7497 (mtm-85) REVERT: A 162 MET cc_start: 0.8589 (tpt) cc_final: 0.8149 (tpp) REVERT: A 201 TYR cc_start: 0.8649 (t80) cc_final: 0.8380 (t80) REVERT: A 241 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: A 298 ASN cc_start: 0.7295 (t0) cc_final: 0.6662 (t0) REVERT: A 300 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 347 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7245 (mp0) REVERT: A 351 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8453 (ttmt) REVERT: A 418 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: B 33 ASP cc_start: 0.6454 (t0) cc_final: 0.6152 (m-30) REVERT: B 44 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: B 54 LYS cc_start: 0.6597 (mptt) cc_final: 0.5670 (mttp) REVERT: B 134 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7283 (mptt) REVERT: B 138 LEU cc_start: 0.8862 (mp) cc_final: 0.8582 (mp) REVERT: B 216 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8119 (pmtt) REVERT: B 219 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: B 223 MET cc_start: 0.8038 (mmm) cc_final: 0.7640 (mmm) REVERT: B 224 LYS cc_start: 0.7868 (mttt) cc_final: 0.7598 (mttt) REVERT: B 241 ASP cc_start: 0.7810 (p0) cc_final: 0.7540 (p0) REVERT: B 261 TRP cc_start: 0.8229 (OUTLIER) cc_final: 0.7358 (t60) REVERT: B 287 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7485 (mmpt) REVERT: B 321 ASP cc_start: 0.7652 (m-30) cc_final: 0.7101 (m-30) REVERT: B 324 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7731 (mm-30) outliers start: 41 outliers final: 21 residues processed: 216 average time/residue: 0.5527 time to fit residues: 125.4226 Evaluate side-chains 223 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.137452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106833 restraints weight = 12280.317| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.83 r_work: 0.3295 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8241 Z= 0.189 Angle : 0.621 8.170 11325 Z= 0.325 Chirality : 0.044 0.462 1310 Planarity : 0.004 0.031 1253 Dihedral : 18.058 159.419 1733 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.31 % Allowed : 31.83 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.29), residues: 858 helix: 1.26 (0.24), residues: 483 sheet: -0.98 (0.58), residues: 72 loop : -1.33 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 384 TYR 0.019 0.001 TYR A 46 PHE 0.015 0.001 PHE B 236 TRP 0.009 0.001 TRP B 261 HIS 0.003 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 8241) covalent geometry : angle 0.62118 / 0.33 (11325) hydrogen bonds : bond 0.04109 / 2.68 ( 395) hydrogen bonds : angle 4.69713 / 3.29 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8275 (ttt180) REVERT: A 61 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8372 (tt) REVERT: A 85 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7489 (mtm-85) REVERT: A 162 MET cc_start: 0.8578 (tpt) cc_final: 0.8141 (tpp) REVERT: A 201 TYR cc_start: 0.8640 (t80) cc_final: 0.8360 (t80) REVERT: A 241 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: A 298 ASN cc_start: 0.7301 (t0) cc_final: 0.6675 (t0) REVERT: A 300 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: A 347 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7232 (mp0) REVERT: A 351 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8430 (ttmt) REVERT: A 418 GLU cc_start: 0.8086 (pm20) cc_final: 0.7838 (pt0) REVERT: B 33 ASP cc_start: 0.6430 (t0) cc_final: 0.6104 (m-30) REVERT: B 44 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: B 54 LYS cc_start: 0.6577 (mptt) cc_final: 0.5667 (mttp) REVERT: B 134 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7278 (mptt) REVERT: B 138 LEU cc_start: 0.8863 (mp) cc_final: 0.8583 (mp) REVERT: B 216 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8283 (pmtt) REVERT: B 218 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: B 219 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: B 223 MET cc_start: 0.8009 (mmm) cc_final: 0.7612 (mmm) REVERT: B 224 LYS cc_start: 0.7890 (mttt) cc_final: 0.7613 (mttt) REVERT: B 241 ASP cc_start: 0.7801 (p0) cc_final: 0.7528 (p0) REVERT: B 261 TRP cc_start: 0.8232 (OUTLIER) cc_final: 0.7396 (t60) REVERT: B 287 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7482 (mmpt) REVERT: B 321 ASP cc_start: 0.7639 (m-30) cc_final: 0.7090 (m-30) REVERT: B 324 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7711 (mm-30) outliers start: 40 outliers final: 23 residues processed: 224 average time/residue: 0.6189 time to fit residues: 145.8025 Evaluate side-chains 216 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.137820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.107154 restraints weight = 12216.252| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.83 r_work: 0.3300 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8241 Z= 0.179 Angle : 0.636 8.126 11325 Z= 0.332 Chirality : 0.044 0.449 1310 Planarity : 0.004 0.034 1253 Dihedral : 18.049 159.495 1733 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.17 % Allowed : 32.49 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.29), residues: 858 helix: 1.31 (0.24), residues: 484 sheet: -0.96 (0.58), residues: 72 loop : -1.38 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 384 TYR 0.018 0.001 TYR A 46 PHE 0.015 0.001 PHE B 236 TRP 0.008 0.001 TRP B 261 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 8241) covalent geometry : angle 0.63644 / 0.33 (11325) hydrogen bonds : bond 0.04010 / 2.62 ( 395) hydrogen bonds : angle 4.68493 / 3.29 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8264 (ttt180) REVERT: A 61 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8373 (tt) REVERT: A 85 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7482 (mtm-85) REVERT: A 162 MET cc_start: 0.8575 (tpt) cc_final: 0.8135 (tpp) REVERT: A 201 TYR cc_start: 0.8633 (t80) cc_final: 0.8349 (t80) REVERT: A 241 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: A 347 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7236 (mp0) REVERT: A 351 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8428 (ttmt) REVERT: A 418 GLU cc_start: 0.8107 (pm20) cc_final: 0.7851 (pt0) REVERT: B 33 ASP cc_start: 0.6424 (t0) cc_final: 0.6116 (m-30) REVERT: B 44 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: B 54 LYS cc_start: 0.6584 (mptt) cc_final: 0.5666 (mttp) REVERT: B 134 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7287 (mptt) REVERT: B 138 LEU cc_start: 0.8864 (mp) cc_final: 0.8586 (mp) REVERT: B 216 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8282 (pmtt) REVERT: B 218 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: B 219 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: B 223 MET cc_start: 0.8065 (mmm) cc_final: 0.7664 (mmm) REVERT: B 224 LYS cc_start: 0.7875 (mttt) cc_final: 0.7607 (mttt) REVERT: B 241 ASP cc_start: 0.7793 (p0) cc_final: 0.7526 (p0) REVERT: B 261 TRP cc_start: 0.8229 (OUTLIER) cc_final: 0.7443 (t60) REVERT: B 287 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7400 (mmpt) REVERT: B 321 ASP cc_start: 0.7620 (m-30) cc_final: 0.7070 (m-30) REVERT: B 324 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7705 (mm-30) REVERT: B 336 PHE cc_start: 0.6445 (OUTLIER) cc_final: 0.5625 (p90) outliers start: 39 outliers final: 21 residues processed: 221 average time/residue: 0.6070 time to fit residues: 141.3125 Evaluate side-chains 221 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 336 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 77 optimal weight: 2.9990 chunk 44 optimal weight: 0.0030 chunk 34 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.142898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112763 restraints weight = 12407.928| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.82 r_work: 0.3327 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8241 Z= 0.130 Angle : 0.631 8.707 11325 Z= 0.325 Chirality : 0.042 0.364 1310 Planarity : 0.004 0.041 1253 Dihedral : 18.010 159.324 1733 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.71 % Allowed : 34.75 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.29), residues: 858 helix: 1.40 (0.24), residues: 485 sheet: -0.79 (0.60), residues: 72 loop : -1.44 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 384 TYR 0.013 0.001 TYR A 46 PHE 0.012 0.001 PHE B 236 TRP 0.011 0.001 TRP B 261 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8241) covalent geometry : angle 0.63124 / 0.32 (11325) hydrogen bonds : bond 0.03553 / 2.32 ( 395) hydrogen bonds : angle 4.57319 / 3.21 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8205 (ttt180) REVERT: A 61 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8340 (tt) REVERT: A 78 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8100 (mptp) REVERT: A 80 PHE cc_start: 0.8605 (m-80) cc_final: 0.8145 (m-80) REVERT: A 85 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7490 (mtm-85) REVERT: A 162 MET cc_start: 0.8532 (tpt) cc_final: 0.8320 (mmp) REVERT: A 201 TYR cc_start: 0.8612 (t80) cc_final: 0.8349 (t80) REVERT: A 241 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: A 351 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8408 (ttmt) REVERT: B 33 ASP cc_start: 0.6419 (t0) cc_final: 0.6116 (m-30) REVERT: B 54 LYS cc_start: 0.6470 (mptt) cc_final: 0.5596 (mttp) REVERT: B 134 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7278 (mppt) REVERT: B 138 LEU cc_start: 0.8856 (mp) cc_final: 0.8583 (mp) REVERT: B 216 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8372 (pmtt) REVERT: B 223 MET cc_start: 0.8040 (mmm) cc_final: 0.7646 (mmm) REVERT: B 224 LYS cc_start: 0.7887 (mttt) cc_final: 0.7615 (mttt) REVERT: B 241 ASP cc_start: 0.7777 (p0) cc_final: 0.7501 (p0) REVERT: B 260 LYS cc_start: 0.7439 (pptt) cc_final: 0.7167 (pmtt) REVERT: B 261 TRP cc_start: 0.8191 (OUTLIER) cc_final: 0.7231 (t60) REVERT: B 321 ASP cc_start: 0.7596 (m-30) cc_final: 0.7049 (m-30) REVERT: B 324 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7707 (mm-30) outliers start: 28 outliers final: 13 residues processed: 220 average time/residue: 0.6087 time to fit residues: 140.9830 Evaluate side-chains 208 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 261 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.138129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107440 restraints weight = 12220.730| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.82 r_work: 0.3307 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8241 Z= 0.190 Angle : 0.667 8.225 11325 Z= 0.345 Chirality : 0.045 0.431 1310 Planarity : 0.004 0.058 1253 Dihedral : 17.981 160.989 1733 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.71 % Allowed : 34.48 % Favored : 61.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.29), residues: 858 helix: 1.36 (0.24), residues: 484 sheet: -0.85 (0.59), residues: 72 loop : -1.46 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 60 TYR 0.018 0.001 TYR A 46 PHE 0.016 0.002 PHE B 253 TRP 0.011 0.002 TRP B 303 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 8241) covalent geometry : angle 0.66654 / 0.35 (11325) hydrogen bonds : bond 0.03948 / 2.57 ( 395) hydrogen bonds : angle 4.63406 / 3.25 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4043.75 seconds wall clock time: 69 minutes 13.76 seconds (4153.76 seconds total)