Starting phenix.real_space_refine on Tue Mar 3 19:10:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfa_49360/03_2026/9nfa_49360.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfa_49360/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/9nfa_49360/03_2026/9nfa_49360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfa_49360/03_2026/9nfa_49360.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nfa_49360/03_2026/9nfa_49360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfa_49360/03_2026/9nfa_49360.map" } 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-dev-5986/lib/python3.9/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: 2.06, per 1000 atoms: 0.26 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: 0.56 Conformation dependent library (CDL) restraints added in 191.6 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: 1.02 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: 1.41 Time building geometry restraints manager: 0.75 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=" 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=" CB GLN B 295 " pdb=" CG GLN B 295 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" C3' U C 54 " pdb=" O3' U C 54 " ideal model delta sigma weight residual 1.427 1.442 -0.015 1.50e-02 4.44e+03 9.77e-01 bond pdb=" CB GLU A 13 " pdb=" CG GLU A 13 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.72e-01 ... (remaining 8236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 10982 1.39 - 2.77: 255 2.77 - 4.16: 63 4.16 - 5.55: 16 5.55 - 6.94: 9 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 120.20 125.35 -5.15 1.50e+00 4.44e-01 1.18e+01 angle pdb=" CA GLU A 243 " pdb=" CB GLU A 243 " pdb=" CG GLU A 243 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.31e+00 angle pdb=" C4' U C 54 " pdb=" C3' U C 54 " pdb=" O3' U C 54 " ideal model delta sigma weight residual 109.40 113.61 -4.21 1.50e+00 4.44e-01 7.87e+00 angle pdb=" CA ASN B 290 " pdb=" CB ASN B 290 " pdb=" CG ASN B 290 " ideal model delta sigma weight residual 112.60 115.38 -2.78 1.00e+00 1.00e+00 7.71e+00 angle pdb=" CG LYS A 224 " pdb=" CD LYS A 224 " pdb=" CE LYS A 224 " ideal model delta sigma weight residual 111.30 117.55 -6.25 2.30e+00 1.89e-01 7.39e+00 ... (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: 968 0.039 - 0.077: 280 0.077 - 0.116: 52 0.116 - 0.155: 9 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: 8.240 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.003 0.045 8241 Z= 0.148 Angle : 0.572 6.935 11325 Z= 0.298 Chirality : 0.038 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 covalent geometry : bond 0.00349 ( 8241) covalent geometry : angle 0.57229 (11325) hydrogen bonds : bond 0.24330 ( 395) hydrogen bonds : angle 8.03492 ( 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 : 0.197 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: 0.8094 (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: 0.7507 (ptpt) REVERT: B 44 GLU cc_start: 0.7292 (tm-30) cc_final: 0.7048 (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: 0.6755 time to fit residues: 150.5937 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 : 0.286 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109249 restraints weight = 12235.904| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.81 r_work: 0.3272 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8241 Z= 0.226 Angle : 0.637 7.605 11325 Z= 0.332 Chirality : 0.043 0.283 1310 Planarity : 0.004 0.031 1253 Dihedral : 18.223 156.919 1759 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.31 % Allowed : 29.44 % Favored : 65.25 % 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: 0.11 (0.29), residues: 858 helix: 1.10 (0.24), residues: 481 sheet: -0.93 (0.57), residues: 70 loop : -1.29 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 60 TYR 0.018 0.002 TYR A 46 PHE 0.017 0.002 PHE B 253 TRP 0.008 0.002 TRP B 329 HIS 0.003 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 8241) covalent geometry : angle 0.63677 (11325) hydrogen bonds : bond 0.05234 ( 395) hydrogen bonds : angle 5.25462 ( 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 257 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8249 (ttt180) REVERT: A 85 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7487 (mtm-85) REVERT: A 117 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: A 162 MET cc_start: 0.8638 (tpt) cc_final: 0.8252 (mmp) REVERT: A 201 TYR cc_start: 0.8646 (t80) cc_final: 0.8342 (t80) REVERT: A 241 GLU cc_start: 0.7381 (tt0) cc_final: 0.7093 (tt0) REVERT: A 347 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7215 (mp0) REVERT: A 362 LYS cc_start: 0.7658 (mtpm) cc_final: 0.7249 (ttpt) REVERT: A 528 ASP cc_start: 0.8029 (m-30) cc_final: 0.7717 (m-30) REVERT: B 44 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7062 (tm-30) REVERT: B 54 LYS cc_start: 0.6633 (mptt) cc_final: 0.5750 (mttp) REVERT: B 128 LYS cc_start: 0.7646 (mttm) cc_final: 0.7440 (mptm) REVERT: B 134 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7331 (mptt) REVERT: B 216 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8283 (pmtt) REVERT: B 218 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: B 219 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: B 223 MET cc_start: 0.7831 (mmm) cc_final: 0.7420 (mmm) REVERT: B 241 ASP cc_start: 0.7632 (p0) cc_final: 0.7197 (p0) REVERT: B 287 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7448 (mmpt) REVERT: B 313 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7359 (mt-10) REVERT: B 321 ASP cc_start: 0.7670 (m-30) cc_final: 0.7146 (m-30) REVERT: B 324 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7737 (mm-30) outliers start: 40 outliers final: 14 residues processed: 237 average time/residue: 0.6533 time to fit residues: 162.3129 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 : 0.270 ------------------------------------------------------------------------------- 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 242 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 SER 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 53 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 80 MET 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 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 287 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3909 r_free = 0.3909 target = 0.141242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111411 restraints weight = 12186.631| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.81 r_work: 0.3303 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8241 Z= 0.158 Angle : 0.585 7.246 11325 Z= 0.302 Chirality : 0.040 0.234 1310 Planarity : 0.004 0.035 1253 Dihedral : 18.087 156.240 1737 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.91 % Allowed : 30.90 % 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: 0.34 (0.29), residues: 858 helix: 1.35 (0.24), residues: 482 sheet: -0.84 (0.58), residues: 72 loop : -1.34 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 60 TYR 0.016 0.001 TYR A 46 PHE 0.013 0.001 PHE B 236 TRP 0.007 0.001 TRP A 144 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8241) covalent geometry : angle 0.58488 (11325) hydrogen bonds : bond 0.04020 ( 395) hydrogen bonds : angle 4.76122 ( 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 254 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8256 (ttt180) REVERT: A 61 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8402 (tt) REVERT: A 85 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7549 (mtm-85) REVERT: A 117 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: A 162 MET cc_start: 0.8613 (tpt) cc_final: 0.8264 (mmp) REVERT: A 201 TYR cc_start: 0.8613 (t80) cc_final: 0.8352 (t80) REVERT: A 241 GLU cc_start: 0.7296 (tt0) cc_final: 0.7047 (tt0) REVERT: A 252 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7790 (mtt180) REVERT: A 347 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7247 (mp0) REVERT: A 351 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8414 (ttmt) REVERT: B 44 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7174 (tm-30) REVERT: B 54 LYS cc_start: 0.6550 (mptt) cc_final: 0.5653 (mttp) REVERT: B 128 LYS cc_start: 0.7625 (mttm) cc_final: 0.7341 (mptm) REVERT: B 134 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7364 (mppt) REVERT: B 216 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8311 (pmtt) REVERT: B 218 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: B 219 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: B 223 MET cc_start: 0.7958 (mmm) cc_final: 0.7593 (mmm) REVERT: B 224 LYS cc_start: 0.7953 (mttt) cc_final: 0.7680 (mttt) REVERT: B 241 ASP cc_start: 0.7691 (p0) cc_final: 0.7368 (p0) REVERT: B 287 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7424 (mmpt) REVERT: B 321 ASP cc_start: 0.7664 (m-30) cc_final: 0.7140 (m-30) REVERT: B 324 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7728 (mm-30) outliers start: 37 outliers final: 13 residues processed: 238 average time/residue: 0.6565 time to fit residues: 163.7283 Evaluate side-chains 226 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 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 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 A residue 524 THR 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 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3911 r_free = 0.3911 target = 0.141369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.111057 restraints weight = 12404.644| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.84 r_work: 0.3296 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8241 Z= 0.161 Angle : 0.579 6.955 11325 Z= 0.300 Chirality : 0.040 0.215 1310 Planarity : 0.004 0.029 1253 Dihedral : 18.034 156.917 1737 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.44 % Allowed : 30.24 % 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: 0.39 (0.29), residues: 858 helix: 1.43 (0.24), residues: 481 sheet: -0.86 (0.59), residues: 72 loop : -1.35 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.016 0.001 TYR A 46 PHE 0.013 0.001 PHE B 236 TRP 0.007 0.001 TRP A 144 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8241) covalent geometry : angle 0.57897 (11325) hydrogen bonds : bond 0.03803 ( 395) hydrogen bonds : angle 4.59763 ( 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 255 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8256 (ttt180) REVERT: A 61 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8354 (tt) REVERT: A 85 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7532 (mtm-85) REVERT: A 117 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: A 162 MET cc_start: 0.8590 (tpt) cc_final: 0.8338 (mmp) REVERT: A 201 TYR cc_start: 0.8624 (t80) cc_final: 0.8348 (t80) REVERT: A 241 GLU cc_start: 0.7279 (tt0) cc_final: 0.7005 (tt0) REVERT: A 243 GLU cc_start: 0.8248 (tt0) cc_final: 0.8022 (tp30) REVERT: A 252 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7758 (mtt180) REVERT: A 275 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7738 (mm-30) REVERT: A 351 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8418 (ttmt) REVERT: B 33 ASP cc_start: 0.6467 (t0) cc_final: 0.6147 (m-30) REVERT: B 44 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7175 (tm-30) REVERT: B 54 LYS cc_start: 0.6469 (mptt) cc_final: 0.5540 (mttp) REVERT: B 128 LYS cc_start: 0.7630 (mttm) cc_final: 0.7403 (mptm) REVERT: B 134 LYS cc_start: 0.7802 (mmtt) cc_final: 0.7377 (mppt) REVERT: B 216 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8276 (pmtt) REVERT: B 219 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: B 223 MET cc_start: 0.8022 (mmm) cc_final: 0.7650 (mmm) REVERT: B 224 LYS cc_start: 0.7930 (mttt) cc_final: 0.7637 (mttt) REVERT: B 241 ASP cc_start: 0.7739 (p0) cc_final: 0.7383 (p0) REVERT: B 283 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6266 (tm) REVERT: B 321 ASP cc_start: 0.7645 (m-30) cc_final: 0.7137 (m-30) REVERT: B 324 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7718 (mm-30) outliers start: 41 outliers final: 12 residues processed: 235 average time/residue: 0.6462 time to fit residues: 159.2148 Evaluate side-chains 236 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 351 LYS 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 A residue 524 THR 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 219 GLU Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.140728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110235 restraints weight = 12310.633| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.84 r_work: 0.3287 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1890 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= 0.183 Angle : 0.605 7.525 11325 Z= 0.312 Chirality : 0.042 0.228 1310 Planarity : 0.004 0.031 1253 Dihedral : 17.999 156.937 1736 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.84 % Allowed : 30.24 % Favored : 63.93 % 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: 0.32 (0.29), residues: 858 helix: 1.36 (0.24), residues: 484 sheet: -0.84 (0.59), residues: 72 loop : -1.40 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 384 TYR 0.017 0.001 TYR A 46 PHE 0.014 0.001 PHE B 236 TRP 0.008 0.001 TRP B 303 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8241) covalent geometry : angle 0.60541 (11325) hydrogen bonds : bond 0.03895 ( 395) hydrogen bonds : angle 4.57870 ( 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 256 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8286 (ttt180) REVERT: A 61 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8321 (tt) REVERT: A 85 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7485 (mtm-85) REVERT: A 162 MET cc_start: 0.8598 (tpt) cc_final: 0.8140 (tpp) REVERT: A 201 TYR cc_start: 0.8654 (t80) cc_final: 0.8343 (t80) REVERT: A 234 LYS cc_start: 0.8605 (tttt) cc_final: 0.8404 (ttmt) REVERT: A 241 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: A 252 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7783 (mtt180) REVERT: A 275 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7850 (mm-30) REVERT: A 351 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8399 (ttmt) REVERT: B 33 ASP cc_start: 0.6458 (t0) cc_final: 0.6196 (m-30) REVERT: B 54 LYS cc_start: 0.6529 (mptt) cc_final: 0.5583 (mttp) REVERT: B 128 LYS cc_start: 0.7634 (mttt) cc_final: 0.7427 (mptm) REVERT: B 134 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7420 (mptt) REVERT: B 138 LEU cc_start: 0.8922 (mp) cc_final: 0.8679 (mp) REVERT: B 158 PHE cc_start: 0.7033 (m-10) cc_final: 0.6795 (m-10) REVERT: B 216 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8431 (pmtt) REVERT: B 223 MET cc_start: 0.8036 (mmm) cc_final: 0.7648 (mmm) REVERT: B 241 ASP cc_start: 0.7800 (p0) cc_final: 0.7493 (p0) REVERT: B 253 PHE cc_start: 0.8202 (m-80) cc_final: 0.7954 (m-80) REVERT: B 321 ASP cc_start: 0.7648 (m-30) cc_final: 0.7136 (m-30) REVERT: B 324 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7734 (mm-30) REVERT: B 336 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5621 (p90) outliers start: 44 outliers final: 22 residues processed: 238 average time/residue: 0.6237 time to fit residues: 155.6425 Evaluate side-chains 229 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 76 GLU 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 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 242 LEU 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 A residue 517 LEU Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 LYS 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 336 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 8 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3916 r_free = 0.3916 target = 0.141623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111423 restraints weight = 12138.950| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.81 r_work: 0.3306 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8241 Z= 0.153 Angle : 0.601 9.329 11325 Z= 0.309 Chirality : 0.040 0.194 1310 Planarity : 0.004 0.034 1253 Dihedral : 17.951 157.829 1736 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.44 % Allowed : 30.90 % Favored : 63.66 % 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: 0.44 (0.29), residues: 858 helix: 1.46 (0.24), residues: 482 sheet: -0.77 (0.60), residues: 72 loop : -1.35 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 60 TYR 0.016 0.001 TYR A 46 PHE 0.013 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 covalent geometry : bond 0.00352 ( 8241) covalent geometry : angle 0.60137 (11325) hydrogen bonds : bond 0.03584 ( 395) hydrogen bonds : angle 4.47175 ( 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 252 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8239 (ttt180) REVERT: A 61 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8264 (tt) REVERT: A 72 GLU cc_start: 0.7994 (tt0) cc_final: 0.7726 (tt0) REVERT: A 85 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7562 (mtm-85) REVERT: A 162 MET cc_start: 0.8596 (tpt) cc_final: 0.8361 (mmp) REVERT: A 201 TYR cc_start: 0.8641 (t80) cc_final: 0.8386 (t80) REVERT: A 241 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7005 (tt0) REVERT: A 252 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7823 (mtt180) REVERT: A 256 GLU cc_start: 0.7907 (mp0) cc_final: 0.7683 (mp0) REVERT: A 275 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 306 GLU cc_start: 0.8013 (tp30) cc_final: 0.7731 (tp30) REVERT: A 351 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8415 (mttm) REVERT: B 33 ASP cc_start: 0.6423 (t0) cc_final: 0.6155 (m-30) REVERT: B 44 GLU cc_start: 0.7285 (pp20) cc_final: 0.7079 (tm-30) REVERT: B 54 LYS cc_start: 0.6499 (mptt) cc_final: 0.5574 (mttp) REVERT: B 128 LYS cc_start: 0.7646 (mttt) cc_final: 0.7370 (mptm) REVERT: B 134 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7402 (mptt) REVERT: B 138 LEU cc_start: 0.8897 (mp) cc_final: 0.8674 (mp) REVERT: B 158 PHE cc_start: 0.6946 (m-10) cc_final: 0.6743 (m-10) REVERT: B 216 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8402 (pmtt) REVERT: B 223 MET cc_start: 0.8054 (mmm) cc_final: 0.7675 (mmm) REVERT: B 224 LYS cc_start: 0.7914 (mttt) cc_final: 0.7609 (mttt) REVERT: B 241 ASP cc_start: 0.7776 (p0) cc_final: 0.7455 (p0) REVERT: B 253 PHE cc_start: 0.8174 (m-80) cc_final: 0.7870 (m-80) REVERT: B 260 LYS cc_start: 0.7439 (pptt) cc_final: 0.7133 (pmtt) REVERT: B 321 ASP cc_start: 0.7645 (m-30) cc_final: 0.7138 (m-30) REVERT: B 324 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7762 (mm-30) REVERT: B 336 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.5586 (p90) outliers start: 41 outliers final: 20 residues processed: 235 average time/residue: 0.6368 time to fit residues: 156.7938 Evaluate side-chains 233 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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 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 A residue 517 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 83 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 219 GLU Chi-restraints excluded: chain B residue 336 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.0570 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3898 r_free = 0.3898 target = 0.140350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110034 restraints weight = 12230.609| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.82 r_work: 0.3284 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2021 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= 0.203 Angle : 0.637 8.043 11325 Z= 0.328 Chirality : 0.043 0.229 1310 Planarity : 0.004 0.036 1253 Dihedral : 17.965 156.810 1733 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.04 % Allowed : 30.77 % 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: 0.31 (0.29), residues: 858 helix: 1.35 (0.24), residues: 485 sheet: -0.87 (0.59), residues: 72 loop : -1.42 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 60 TYR 0.018 0.001 TYR A 46 PHE 0.014 0.002 PHE B 275 TRP 0.008 0.001 TRP A 144 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8241) covalent geometry : angle 0.63694 (11325) hydrogen bonds : bond 0.03953 ( 395) hydrogen bonds : angle 4.54818 ( 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 245 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8272 (ttt180) REVERT: A 61 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8291 (tt) REVERT: A 72 GLU cc_start: 0.8002 (tt0) cc_final: 0.7717 (tt0) REVERT: A 79 SER cc_start: 0.8274 (m) cc_final: 0.7880 (t) REVERT: A 85 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7544 (mtm-85) REVERT: A 162 MET cc_start: 0.8618 (tpt) cc_final: 0.8237 (tpp) REVERT: A 201 TYR cc_start: 0.8669 (t80) cc_final: 0.8390 (t80) REVERT: A 241 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: A 256 GLU cc_start: 0.7907 (mp0) cc_final: 0.7705 (mp0) REVERT: A 306 GLU cc_start: 0.8025 (tp30) cc_final: 0.7743 (tp30) REVERT: A 351 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8408 (ttmt) REVERT: A 362 LYS cc_start: 0.7843 (ttpt) cc_final: 0.7419 (ttpt) REVERT: B 33 ASP cc_start: 0.6513 (t0) cc_final: 0.6231 (m-30) REVERT: B 37 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7680 (mmmt) REVERT: B 54 LYS cc_start: 0.6508 (mptt) cc_final: 0.5557 (mttp) REVERT: B 134 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7409 (mptt) REVERT: B 138 LEU cc_start: 0.8916 (mp) cc_final: 0.8693 (mp) REVERT: B 158 PHE cc_start: 0.7088 (m-10) cc_final: 0.6839 (m-10) REVERT: B 216 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8400 (pmtt) REVERT: B 223 MET cc_start: 0.8042 (mmm) cc_final: 0.7676 (mmm) REVERT: B 241 ASP cc_start: 0.7825 (p0) cc_final: 0.7525 (p0) REVERT: B 253 PHE cc_start: 0.8226 (m-80) cc_final: 0.7916 (m-80) REVERT: B 321 ASP cc_start: 0.7661 (m-30) cc_final: 0.7162 (m-30) REVERT: B 324 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7751 (mm-30) REVERT: B 336 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.5652 (p90) outliers start: 38 outliers final: 25 residues processed: 231 average time/residue: 0.6419 time to fit residues: 155.5051 Evaluate side-chains 228 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 76 GLU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 123 THR 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 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 520 CYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 83 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 336 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3890 r_free = 0.3890 target = 0.139701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109583 restraints weight = 12284.992| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.81 r_work: 0.3272 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8241 Z= 0.237 Angle : 0.671 7.378 11325 Z= 0.344 Chirality : 0.045 0.264 1310 Planarity : 0.004 0.041 1253 Dihedral : 18.034 155.733 1733 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 6.10 % Allowed : 30.11 % Favored : 63.79 % 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: 1.28 (0.24), residues: 484 sheet: -1.01 (0.59), residues: 72 loop : -1.42 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 60 TYR 0.020 0.002 TYR A 46 PHE 0.015 0.002 PHE B 275 TRP 0.008 0.002 TRP A 144 HIS 0.003 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 8241) covalent geometry : angle 0.67135 (11325) hydrogen bonds : bond 0.04126 ( 395) hydrogen bonds : angle 4.64284 ( 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 250 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8293 (ttt180) REVERT: A 61 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8302 (tt) REVERT: A 72 GLU cc_start: 0.8024 (tt0) cc_final: 0.7760 (tt0) REVERT: A 78 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8069 (mmmm) REVERT: A 79 SER cc_start: 0.8433 (m) cc_final: 0.8057 (t) REVERT: A 85 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7561 (mtm-85) REVERT: A 117 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: A 162 MET cc_start: 0.8612 (tpt) cc_final: 0.8277 (tpp) REVERT: A 201 TYR cc_start: 0.8678 (t80) cc_final: 0.8403 (t80) REVERT: A 241 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: A 256 GLU cc_start: 0.7909 (mp0) cc_final: 0.7677 (mp0) REVERT: A 351 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8429 (ttmt) REVERT: B 33 ASP cc_start: 0.6537 (t0) cc_final: 0.6245 (m-30) REVERT: B 37 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7702 (mmmt) REVERT: B 54 LYS cc_start: 0.6612 (mptt) cc_final: 0.5615 (mttp) REVERT: B 134 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7411 (mptt) REVERT: B 138 LEU cc_start: 0.8926 (mp) cc_final: 0.8706 (mp) REVERT: B 158 PHE cc_start: 0.7090 (m-10) cc_final: 0.6842 (m-10) REVERT: B 216 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8402 (pmtt) REVERT: B 218 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: B 223 MET cc_start: 0.8035 (mmm) cc_final: 0.7661 (mmm) REVERT: B 241 ASP cc_start: 0.7845 (p0) cc_final: 0.7557 (p0) REVERT: B 253 PHE cc_start: 0.8284 (m-80) cc_final: 0.7945 (m-80) REVERT: B 260 LYS cc_start: 0.7508 (pptt) cc_final: 0.7233 (pmtt) REVERT: B 321 ASP cc_start: 0.7665 (m-30) cc_final: 0.7170 (m-30) REVERT: B 324 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 336 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.5656 (p90) outliers start: 46 outliers final: 24 residues processed: 230 average time/residue: 0.6188 time to fit residues: 149.3626 Evaluate side-chains 231 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 76 GLU Chi-restraints excluded: chain A residue 78 LYS 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 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 273 LEU 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 418 GLU 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 520 CYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 83 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 336 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 27 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.140952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110875 restraints weight = 12181.082| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.80 r_work: 0.3297 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8241 Z= 0.179 Angle : 0.654 10.021 11325 Z= 0.333 Chirality : 0.042 0.224 1310 Planarity : 0.004 0.044 1253 Dihedral : 17.999 156.972 1733 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.77 % Allowed : 31.70 % 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: 0.33 (0.29), residues: 858 helix: 1.38 (0.24), residues: 485 sheet: -0.78 (0.61), residues: 72 loop : -1.45 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 60 TYR 0.019 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 covalent geometry : bond 0.00417 ( 8241) covalent geometry : angle 0.65413 (11325) hydrogen bonds : bond 0.03740 ( 395) hydrogen bonds : angle 4.49814 ( 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 239 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8274 (ttt180) REVERT: A 61 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8260 (tt) REVERT: A 72 GLU cc_start: 0.8031 (tt0) cc_final: 0.7752 (tt0) REVERT: A 85 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7584 (mtm-85) REVERT: A 162 MET cc_start: 0.8595 (tpt) cc_final: 0.8211 (tpp) REVERT: A 201 TYR cc_start: 0.8648 (t80) cc_final: 0.8379 (t80) REVERT: A 241 GLU cc_start: 0.7321 (tt0) cc_final: 0.7058 (tt0) REVERT: A 306 GLU cc_start: 0.8005 (tp30) cc_final: 0.7760 (tp30) REVERT: A 351 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8391 (ttmt) REVERT: B 33 ASP cc_start: 0.6497 (t0) cc_final: 0.6206 (m-30) REVERT: B 37 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7573 (mmmt) REVERT: B 44 GLU cc_start: 0.7212 (pp20) cc_final: 0.6989 (pp20) REVERT: B 54 LYS cc_start: 0.6509 (mptt) cc_final: 0.5526 (mttp) REVERT: B 134 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7383 (mptt) REVERT: B 138 LEU cc_start: 0.8910 (mp) cc_final: 0.8699 (mp) REVERT: B 158 PHE cc_start: 0.7062 (m-10) cc_final: 0.6798 (m-10) REVERT: B 216 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8414 (pmtt) REVERT: B 223 MET cc_start: 0.7998 (mmm) cc_final: 0.7644 (mmm) REVERT: B 241 ASP cc_start: 0.7808 (p0) cc_final: 0.7513 (p0) REVERT: B 253 PHE cc_start: 0.8182 (m-80) cc_final: 0.7845 (m-80) REVERT: B 260 LYS cc_start: 0.7499 (pptt) cc_final: 0.7204 (pmtt) REVERT: B 321 ASP cc_start: 0.7639 (m-30) cc_final: 0.7133 (m-30) REVERT: B 324 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 336 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.5636 (p90) outliers start: 36 outliers final: 22 residues processed: 226 average time/residue: 0.6345 time to fit residues: 150.3820 Evaluate side-chains 224 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 76 GLU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 123 THR 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 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 502 THR Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 83 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 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: 0.1980 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.141165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110970 restraints weight = 12303.411| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.81 r_work: 0.3296 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8241 Z= 0.177 Angle : 0.648 8.015 11325 Z= 0.332 Chirality : 0.042 0.269 1310 Planarity : 0.004 0.048 1253 Dihedral : 17.958 157.123 1733 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.91 % Allowed : 31.83 % Favored : 63.26 % 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: 0.32 (0.29), residues: 858 helix: 1.40 (0.24), residues: 486 sheet: -0.83 (0.60), residues: 72 loop : -1.51 (0.35), residues: 300 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 0.015 0.001 PHE B 236 TRP 0.010 0.001 TRP B 261 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8241) covalent geometry : angle 0.64781 (11325) hydrogen bonds : bond 0.03722 ( 395) hydrogen bonds : angle 4.48688 ( 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 234 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8273 (ttt180) REVERT: A 61 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8255 (tt) REVERT: A 72 GLU cc_start: 0.8025 (tt0) cc_final: 0.7743 (tt0) REVERT: A 79 SER cc_start: 0.8564 (m) cc_final: 0.8104 (t) REVERT: A 162 MET cc_start: 0.8593 (tpt) cc_final: 0.8219 (tpp) REVERT: A 201 TYR cc_start: 0.8645 (t80) cc_final: 0.8371 (t80) REVERT: A 241 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: A 306 GLU cc_start: 0.8013 (tp30) cc_final: 0.7737 (tp30) REVERT: A 351 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8392 (ttmt) REVERT: A 362 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7615 (tttt) REVERT: B 33 ASP cc_start: 0.6498 (t0) cc_final: 0.6232 (m-30) REVERT: B 37 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7594 (mmmt) REVERT: B 44 GLU cc_start: 0.7221 (pp20) cc_final: 0.7006 (pp20) REVERT: B 54 LYS cc_start: 0.6430 (mptt) cc_final: 0.5437 (mttp) REVERT: B 134 LYS cc_start: 0.7789 (mmtt) cc_final: 0.7390 (mptt) REVERT: B 138 LEU cc_start: 0.8911 (mp) cc_final: 0.8694 (mp) REVERT: B 158 PHE cc_start: 0.7032 (m-10) cc_final: 0.6796 (m-10) REVERT: B 216 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8386 (pmtt) REVERT: B 223 MET cc_start: 0.8009 (mmm) cc_final: 0.7663 (mmm) REVERT: B 241 ASP cc_start: 0.7781 (p0) cc_final: 0.7483 (p0) REVERT: B 253 PHE cc_start: 0.8200 (m-80) cc_final: 0.7849 (m-80) REVERT: B 321 ASP cc_start: 0.7628 (m-30) cc_final: 0.7137 (m-30) REVERT: B 324 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7771 (mm-30) REVERT: B 336 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.5631 (p90) outliers start: 37 outliers final: 24 residues processed: 219 average time/residue: 0.6412 time to fit residues: 147.3631 Evaluate side-chains 225 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 76 GLU Chi-restraints excluded: chain A residue 123 THR 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 265 SER 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 502 THR Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 83 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 219 GLU Chi-restraints excluded: chain B residue 295 GLN 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 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3912 r_free = 0.3912 target = 0.141340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111152 restraints weight = 12203.961| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.80 r_work: 0.3305 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8241 Z= 0.184 Angle : 0.658 7.988 11325 Z= 0.335 Chirality : 0.042 0.215 1310 Planarity : 0.004 0.059 1253 Dihedral : 17.952 157.118 1733 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.98 % Allowed : 32.49 % 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: 0.29 (0.29), residues: 858 helix: 1.37 (0.24), residues: 486 sheet: -0.82 (0.60), residues: 70 loop : -1.52 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 60 TYR 0.018 0.001 TYR A 213 PHE 0.014 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 covalent geometry : bond 0.00429 ( 8241) covalent geometry : angle 0.65845 (11325) hydrogen bonds : bond 0.03768 ( 395) hydrogen bonds : angle 4.47132 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4184.77 seconds wall clock time: 71 minutes 46.96 seconds (4306.96 seconds total)