Starting phenix.real_space_refine on Thu Jul 2 09:54:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfa_49360/07_2026/9nfa_49360.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfa_49360/07_2026/9nfa_49360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nfa_49360/07_2026/9nfa_49360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfa_49360/07_2026/9nfa_49360.map" model { file = "/net/cci-nas-00/data/ceres_data/9nfa_49360/07_2026/9nfa_49360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfa_49360/07_2026/9nfa_49360.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 4881 2.51 5 N 1371 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8001 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4196 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 17, 'TRANS': 514} Chain: "B" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2712 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 322} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1092 Inner-chain residues flagged as termini: ['pdbres=" C C 26 "'] Classifications: {'RNA': 52} Modifications used: {'5*END': 2, 'rna2p_pur': 2, 'rna2p_pyr': 13, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 14, 'rna3p': 37} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.37, per 1000 atoms: 0.17 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: 0.46 Conformation dependent library (CDL) restraints added in 322.3 milliseconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 59.9% alpha, 7.5% beta 11 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.67 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: 0.97 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2086 1.33 - 1.45: 1606 1.45 - 1.57: 4385 1.57 - 1.69: 98 1.69 - 1.81: 66 Bond restraints: 8241 Sorted by residual: bond pdb=" CG LEU A 273 " pdb=" CD1 LEU A 273 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.82e+00 bond pdb=" N9 A C 11 " pdb=" C4 A C 11 " ideal model delta sigma weight residual 1.374 1.382 -0.008 6.00e-03 2.78e+04 1.58e+00 bond pdb=" CB ASN B 290 " pdb=" CG ASN B 290 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" N3 C C 26 " pdb=" C4 C C 26 " ideal model delta sigma weight residual 1.335 1.328 0.007 7.00e-03 2.04e+04 1.12e+00 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 ... (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: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.290 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8241 Z= 0.170 Angle : 0.572 6.935 11325 Z= 0.320 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/Z covalent geometry : bond 0.00349 / 0.17 ( 8241) covalent geometry : angle 0.57234 / 0.32 (11325) hydrogen bonds : bond 0.24330 / 15.72 ( 395) hydrogen bonds : angle 8.03492 / 5.74 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.176 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: 0.5227 time to fit residues: 116.9852 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 : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 301 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109855 restraints weight = 12228.110| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.81 r_work: 0.3277 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8241 Z= 0.227 Angle : 0.630 7.455 11325 Z= 0.341 Chirality : 0.044 0.267 1310 Planarity : 0.004 0.033 1253 Dihedral : 18.240 156.766 1759 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.04 % Allowed : 31.03 % 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: -0.07 (0.29), residues: 858 helix: 0.96 (0.24), residues: 484 sheet: -1.06 (0.56), residues: 70 loop : -1.41 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 60 TYR 0.018 0.002 TYR A 46 PHE 0.017 0.002 PHE B 253 TRP 0.007 0.002 TRP B 329 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 ( 8241) covalent geometry : angle 0.62981 / 0.34 (11325) hydrogen bonds : bond 0.06264 / 4.08 ( 395) hydrogen bonds : angle 5.48357 / 3.85 ( 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 250 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8281 (ttt180) REVERT: A 85 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7487 (mtm-85) REVERT: A 117 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8142 (pt0) REVERT: A 162 MET cc_start: 0.8635 (tpt) cc_final: 0.8260 (tpp) REVERT: A 201 TYR cc_start: 0.8639 (t80) cc_final: 0.8368 (t80) REVERT: A 223 GLU cc_start: 0.8018 (tp30) cc_final: 0.7808 (tp30) REVERT: A 241 GLU cc_start: 0.7316 (tt0) cc_final: 0.7075 (tt0) REVERT: A 256 GLU cc_start: 0.7874 (mp0) cc_final: 0.7652 (mp0) REVERT: A 275 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8155 (mm-30) REVERT: A 362 LYS cc_start: 0.7665 (mtpm) cc_final: 0.7347 (ttpt) REVERT: A 528 ASP cc_start: 0.8017 (m-30) cc_final: 0.7704 (m-30) REVERT: B 44 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 54 LYS cc_start: 0.6559 (mptt) cc_final: 0.5734 (mttp) REVERT: B 82 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6195 (mm) REVERT: B 134 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7351 (mptt) REVERT: B 216 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8230 (pmtt) REVERT: B 218 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: B 219 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: B 223 MET cc_start: 0.7808 (mmm) cc_final: 0.7433 (mmm) REVERT: B 224 LYS cc_start: 0.7920 (mttt) cc_final: 0.7659 (mttt) REVERT: B 241 ASP cc_start: 0.7576 (p0) cc_final: 0.7326 (p0) REVERT: B 287 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7390 (mmpt) REVERT: B 321 ASP cc_start: 0.7632 (m-30) cc_final: 0.7121 (m-30) REVERT: B 324 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7711 (mm-30) outliers start: 38 outliers final: 15 residues processed: 233 average time/residue: 0.5701 time to fit residues: 139.1012 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 : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 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 275 PHE Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 322 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110609 restraints weight = 12168.369| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.80 r_work: 0.3290 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8241 Z= 0.175 Angle : 0.590 8.507 11325 Z= 0.314 Chirality : 0.042 0.256 1310 Planarity : 0.004 0.041 1253 Dihedral : 18.162 158.787 1736 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.44 % Allowed : 29.58 % Favored : 64.99 % 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: 0.05 (0.29), residues: 858 helix: 1.13 (0.24), residues: 484 sheet: -1.06 (0.57), residues: 70 loop : -1.45 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 384 TYR 0.017 0.001 TYR A 46 PHE 0.012 0.002 PHE B 236 TRP 0.007 0.001 TRP A 144 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 8241) covalent geometry : angle 0.58965 / 0.31 (11325) hydrogen bonds : bond 0.04809 / 3.13 ( 395) hydrogen bonds : angle 5.05794 / 3.54 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8251 (ttt180) REVERT: A 85 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7510 (mtm-85) REVERT: A 117 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: A 162 MET cc_start: 0.8614 (tpt) cc_final: 0.8256 (mmp) REVERT: A 201 TYR cc_start: 0.8629 (t80) cc_final: 0.8360 (t80) REVERT: A 241 GLU cc_start: 0.7258 (tt0) cc_final: 0.7012 (tt0) REVERT: A 243 GLU cc_start: 0.7930 (tp30) cc_final: 0.7645 (tm-30) REVERT: A 347 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7234 (mp0) REVERT: A 351 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8532 (ttmt) REVERT: A 362 LYS cc_start: 0.7605 (mtpm) cc_final: 0.7226 (ttpt) REVERT: A 528 ASP cc_start: 0.8039 (m-30) cc_final: 0.7661 (m-30) REVERT: B 44 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7038 (tm-30) REVERT: B 54 LYS cc_start: 0.6555 (mptt) cc_final: 0.5702 (mttp) REVERT: B 128 LYS cc_start: 0.7709 (mttm) cc_final: 0.7459 (mptm) REVERT: B 134 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7319 (mppt) REVERT: B 216 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8272 (pmtt) REVERT: B 218 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: B 219 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 223 MET cc_start: 0.7848 (mmm) cc_final: 0.7459 (mmm) REVERT: B 224 LYS cc_start: 0.7923 (mttt) cc_final: 0.7662 (mttt) REVERT: B 241 ASP cc_start: 0.7674 (p0) cc_final: 0.7410 (p0) REVERT: B 261 TRP cc_start: 0.8247 (OUTLIER) cc_final: 0.7503 (t60) REVERT: B 277 GLU cc_start: 0.6908 (pp20) cc_final: 0.6706 (pp20) REVERT: B 287 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7415 (mmpt) REVERT: B 321 ASP cc_start: 0.7621 (m-30) cc_final: 0.7090 (m-30) REVERT: B 324 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7720 (mm-30) outliers start: 41 outliers final: 18 residues processed: 227 average time/residue: 0.5343 time to fit residues: 127.4088 Evaluate side-chains 223 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 322 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110515 restraints weight = 12456.696| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.82 r_work: 0.3289 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1460 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= 0.185 Angle : 0.586 7.044 11325 Z= 0.313 Chirality : 0.042 0.255 1310 Planarity : 0.004 0.037 1253 Dihedral : 18.140 158.487 1736 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.70 % Allowed : 29.58 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.29), residues: 858 helix: 1.18 (0.24), residues: 484 sheet: -1.00 (0.58), residues: 70 loop : -1.38 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 60 TYR 0.017 0.001 TYR A 46 PHE 0.014 0.002 PHE B 253 TRP 0.007 0.001 TRP A 144 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 8241) covalent geometry : angle 0.58554 / 0.31 (11325) hydrogen bonds : bond 0.04433 / 2.87 ( 395) hydrogen bonds : angle 4.90351 / 3.42 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8253 (ttt180) REVERT: A 85 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7528 (mtm-85) REVERT: A 117 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: A 162 MET cc_start: 0.8600 (tpt) cc_final: 0.8271 (mmp) REVERT: A 201 TYR cc_start: 0.8643 (t80) cc_final: 0.8383 (t80) REVERT: A 241 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: A 298 ASN cc_start: 0.7221 (t0) cc_final: 0.7000 (t0) REVERT: A 347 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7244 (mp0) REVERT: A 351 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8478 (ttmt) REVERT: A 362 LYS cc_start: 0.7631 (mtpm) cc_final: 0.7203 (ttpt) REVERT: A 528 ASP cc_start: 0.8024 (m-30) cc_final: 0.7673 (m-30) REVERT: B 44 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7078 (tm-30) REVERT: B 54 LYS cc_start: 0.6569 (mptt) cc_final: 0.5705 (mttp) REVERT: B 128 LYS cc_start: 0.7756 (mttm) cc_final: 0.7485 (mptm) REVERT: B 134 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7360 (mptt) REVERT: B 216 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8301 (pmtt) REVERT: B 218 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: B 219 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: B 223 MET cc_start: 0.7841 (mmm) cc_final: 0.7462 (mmm) REVERT: B 224 LYS cc_start: 0.7920 (mttt) cc_final: 0.7637 (mttt) REVERT: B 241 ASP cc_start: 0.7730 (p0) cc_final: 0.7464 (p0) REVERT: B 261 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7456 (t60) REVERT: B 287 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7447 (mmpt) REVERT: B 321 ASP cc_start: 0.7630 (m-30) cc_final: 0.7085 (m-30) REVERT: B 324 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7726 (mm-30) outliers start: 43 outliers final: 18 residues processed: 229 average time/residue: 0.5279 time to fit residues: 126.8877 Evaluate side-chains 226 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 241 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain 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 208 LYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.140876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110669 restraints weight = 12372.666| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.82 r_work: 0.3287 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1592 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= 0.182 Angle : 0.598 7.398 11325 Z= 0.318 Chirality : 0.042 0.246 1310 Planarity : 0.004 0.047 1253 Dihedral : 18.146 158.638 1736 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: 0.19 (0.29), residues: 858 helix: 1.21 (0.24), residues: 484 sheet: -1.01 (0.57), residues: 72 loop : -1.34 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 60 TYR 0.017 0.001 TYR A 46 PHE 0.014 0.001 PHE B 236 TRP 0.007 0.001 TRP A 144 HIS 0.003 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 8241) covalent geometry : angle 0.59805 / 0.32 (11325) hydrogen bonds : bond 0.04231 / 2.74 ( 395) hydrogen bonds : angle 4.76178 / 3.33 ( 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 251 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8249 (ttt180) REVERT: A 61 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 85 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7523 (mtm-85) REVERT: A 117 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: A 162 MET cc_start: 0.8593 (tpt) cc_final: 0.8315 (mmp) REVERT: A 201 TYR cc_start: 0.8637 (t80) cc_final: 0.8374 (t80) REVERT: A 241 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6996 (tt0) REVERT: A 243 GLU cc_start: 0.8100 (tt0) cc_final: 0.7889 (tt0) REVERT: A 307 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8315 (mttp) REVERT: A 351 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8432 (ttmt) REVERT: A 418 GLU cc_start: 0.8081 (pm20) cc_final: 0.7827 (pt0) REVERT: B 33 ASP cc_start: 0.6464 (t0) cc_final: 0.6159 (m-30) REVERT: B 43 ASP cc_start: 0.7750 (t0) cc_final: 0.7537 (t0) REVERT: B 44 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7178 (tm-30) REVERT: B 54 LYS cc_start: 0.6544 (mptt) cc_final: 0.5668 (mttp) REVERT: B 128 LYS cc_start: 0.7767 (mttm) cc_final: 0.7561 (mptm) REVERT: B 134 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7372 (mptt) REVERT: B 216 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8324 (pmtt) REVERT: B 218 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: B 219 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: B 223 MET cc_start: 0.7973 (mmm) cc_final: 0.7611 (mmm) REVERT: B 224 LYS cc_start: 0.7911 (mttt) cc_final: 0.7649 (mttt) REVERT: B 241 ASP cc_start: 0.7729 (p0) cc_final: 0.7473 (p0) REVERT: B 260 LYS cc_start: 0.7593 (pptt) cc_final: 0.7285 (pmtt) REVERT: B 261 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7402 (t60) REVERT: B 287 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7466 (mmpt) REVERT: B 321 ASP cc_start: 0.7626 (m-30) cc_final: 0.7091 (m-30) REVERT: B 324 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7744 (mm-30) outliers start: 44 outliers final: 16 residues processed: 232 average time/residue: 0.5499 time to fit residues: 134.1864 Evaluate side-chains 230 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 307 LYS 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 502 THR Chi-restraints excluded: chain A residue 517 LEU 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 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.140215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110121 restraints weight = 12175.959| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.81 r_work: 0.3277 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8241 Z= 0.211 Angle : 0.616 7.849 11325 Z= 0.325 Chirality : 0.043 0.260 1310 Planarity : 0.004 0.032 1253 Dihedral : 18.154 159.085 1736 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.57 % Allowed : 30.77 % 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: 0.18 (0.29), residues: 858 helix: 1.19 (0.24), residues: 483 sheet: -0.95 (0.58), residues: 72 loop : -1.33 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 60 TYR 0.020 0.001 TYR A 46 PHE 0.015 0.002 PHE B 236 TRP 0.007 0.002 TRP B 261 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 8241) covalent geometry : angle 0.61591 / 0.33 (11325) hydrogen bonds : bond 0.04297 / 2.78 ( 395) hydrogen bonds : angle 4.75845 / 3.34 ( 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 240 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8270 (ttt180) REVERT: A 61 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8417 (tt) REVERT: A 85 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7500 (mtm-85) REVERT: A 117 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8226 (pt0) REVERT: A 162 MET cc_start: 0.8610 (tpt) cc_final: 0.8169 (tpp) REVERT: A 201 TYR cc_start: 0.8657 (t80) cc_final: 0.8369 (t80) REVERT: A 241 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: A 307 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8335 (mttp) REVERT: A 351 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8452 (ttmt) REVERT: A 418 GLU cc_start: 0.8101 (pm20) cc_final: 0.7856 (pt0) REVERT: B 33 ASP cc_start: 0.6483 (t0) cc_final: 0.6175 (m-30) REVERT: B 44 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7216 (tm-30) REVERT: B 54 LYS cc_start: 0.6600 (mptt) cc_final: 0.5681 (mttp) REVERT: B 134 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7364 (mptt) REVERT: B 216 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8208 (pmtt) REVERT: B 219 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: B 223 MET cc_start: 0.7968 (mmm) cc_final: 0.7606 (mmm) REVERT: B 224 LYS cc_start: 0.7924 (mttt) cc_final: 0.7616 (mttt) REVERT: B 241 ASP cc_start: 0.7810 (p0) cc_final: 0.7532 (p0) REVERT: B 261 TRP cc_start: 0.8231 (OUTLIER) cc_final: 0.7385 (t60) REVERT: B 287 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7460 (mmpt) REVERT: B 321 ASP cc_start: 0.7664 (m-30) cc_final: 0.7126 (m-30) REVERT: B 324 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7765 (mm-30) outliers start: 42 outliers final: 19 residues processed: 222 average time/residue: 0.5642 time to fit residues: 131.2952 Evaluate side-chains 215 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.140616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110290 restraints weight = 12231.637| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.81 r_work: 0.3286 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8241 Z= 0.189 Angle : 0.618 7.259 11325 Z= 0.326 Chirality : 0.042 0.247 1310 Planarity : 0.004 0.031 1253 Dihedral : 18.122 158.649 1735 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.70 % Allowed : 30.64 % 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: 0.24 (0.29), residues: 858 helix: 1.24 (0.24), residues: 483 sheet: -0.93 (0.59), residues: 72 loop : -1.30 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.018 0.001 TYR A 46 PHE 0.015 0.001 PHE B 253 TRP 0.007 0.001 TRP A 144 HIS 0.003 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 8241) covalent geometry : angle 0.61789 / 0.33 (11325) hydrogen bonds : bond 0.04101 / 2.67 ( 395) hydrogen bonds : angle 4.71428 / 3.30 ( 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 240 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8281 (ttt180) REVERT: A 61 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8383 (tt) REVERT: A 85 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7491 (mtm-85) REVERT: A 117 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: A 162 MET cc_start: 0.8592 (tpt) cc_final: 0.8135 (tpp) REVERT: A 201 TYR cc_start: 0.8650 (t80) cc_final: 0.8363 (t80) REVERT: A 241 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7009 (tt0) REVERT: A 351 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8424 (ttmt) REVERT: A 418 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7855 (pt0) REVERT: B 33 ASP cc_start: 0.6473 (t0) cc_final: 0.6154 (m-30) REVERT: B 44 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: B 54 LYS cc_start: 0.6566 (mptt) cc_final: 0.5646 (mttp) REVERT: B 134 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7344 (mptt) REVERT: B 138 LEU cc_start: 0.8922 (mp) cc_final: 0.8690 (mp) REVERT: B 216 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8223 (pmtt) REVERT: B 219 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: B 223 MET cc_start: 0.8003 (mmm) cc_final: 0.7627 (mmm) REVERT: B 224 LYS cc_start: 0.7914 (mttt) cc_final: 0.7634 (mttt) REVERT: B 241 ASP cc_start: 0.7802 (p0) cc_final: 0.7539 (p0) REVERT: B 261 TRP cc_start: 0.8248 (OUTLIER) cc_final: 0.7317 (t60) REVERT: B 287 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7470 (mmpt) REVERT: B 321 ASP cc_start: 0.7639 (m-30) cc_final: 0.7109 (m-30) REVERT: B 324 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7731 (mm-30) outliers start: 43 outliers final: 23 residues processed: 222 average time/residue: 0.5472 time to fit residues: 127.5828 Evaluate side-chains 228 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 265 SER Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110291 restraints weight = 12269.190| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.82 r_work: 0.3283 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8241 Z= 0.204 Angle : 0.623 7.106 11325 Z= 0.331 Chirality : 0.044 0.270 1310 Planarity : 0.004 0.032 1253 Dihedral : 18.115 158.999 1735 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.70 % Allowed : 31.30 % Favored : 63.00 % 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: 0.20 (0.29), residues: 858 helix: 1.21 (0.24), residues: 483 sheet: -0.99 (0.58), residues: 70 loop : -1.30 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 384 TYR 0.019 0.001 TYR A 46 PHE 0.013 0.001 PHE B 236 TRP 0.007 0.002 TRP A 144 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 8241) covalent geometry : angle 0.62300 / 0.33 (11325) hydrogen bonds : bond 0.04141 / 2.71 ( 395) hydrogen bonds : angle 4.72416 / 3.31 ( 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 241 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8267 (ttt180) REVERT: A 61 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8369 (tt) REVERT: A 85 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7501 (mtm-85) REVERT: A 162 MET cc_start: 0.8604 (tpt) cc_final: 0.8184 (tpp) REVERT: A 201 TYR cc_start: 0.8658 (t80) cc_final: 0.8347 (t80) REVERT: A 241 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: A 243 GLU cc_start: 0.8069 (tt0) cc_final: 0.7752 (tt0) REVERT: A 298 ASN cc_start: 0.7204 (t0) cc_final: 0.6989 (t0) REVERT: A 351 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8438 (ttmt) REVERT: A 418 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: B 33 ASP cc_start: 0.6467 (t0) cc_final: 0.6170 (m-30) REVERT: B 44 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: B 54 LYS cc_start: 0.6609 (mptt) cc_final: 0.5685 (mttp) REVERT: B 134 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7344 (mptt) REVERT: B 138 LEU cc_start: 0.8930 (mp) cc_final: 0.8700 (mp) REVERT: B 216 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8270 (pmtt) REVERT: B 218 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: B 219 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: B 223 MET cc_start: 0.7988 (mmm) cc_final: 0.7602 (mmm) REVERT: B 224 LYS cc_start: 0.7872 (mttt) cc_final: 0.7604 (mttt) REVERT: B 241 ASP cc_start: 0.7810 (p0) cc_final: 0.7549 (p0) REVERT: B 260 LYS cc_start: 0.7574 (pptt) cc_final: 0.7307 (pmtt) REVERT: B 261 TRP cc_start: 0.8261 (OUTLIER) cc_final: 0.7271 (t60) REVERT: B 275 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: B 277 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6975 (tm-30) REVERT: B 287 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7460 (mmpt) REVERT: B 321 ASP cc_start: 0.7651 (m-30) cc_final: 0.7101 (m-30) REVERT: B 324 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7740 (mm-30) outliers start: 43 outliers final: 22 residues processed: 221 average time/residue: 0.5496 time to fit residues: 127.2342 Evaluate side-chains 224 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.140201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109935 restraints weight = 12176.175| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.82 r_work: 0.3288 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8241 Z= 0.219 Angle : 0.645 8.223 11325 Z= 0.340 Chirality : 0.045 0.260 1310 Planarity : 0.004 0.032 1253 Dihedral : 18.077 158.871 1732 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.57 % Allowed : 31.96 % Favored : 62.47 % 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: 0.20 (0.29), residues: 858 helix: 1.18 (0.24), residues: 483 sheet: -0.90 (0.59), residues: 72 loop : -1.30 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 384 TYR 0.021 0.001 TYR A 46 PHE 0.015 0.002 PHE B 236 TRP 0.008 0.002 TRP A 144 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 ( 8241) covalent geometry : angle 0.64548 / 0.34 (11325) hydrogen bonds : bond 0.04221 / 2.76 ( 395) hydrogen bonds : angle 4.74184 / 3.33 ( 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 236 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8272 (ttt180) REVERT: A 61 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 85 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7491 (mtm-85) REVERT: A 162 MET cc_start: 0.8604 (tpt) cc_final: 0.8219 (tpp) REVERT: A 201 TYR cc_start: 0.8667 (t80) cc_final: 0.8406 (t80) REVERT: A 241 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: A 298 ASN cc_start: 0.7225 (t0) cc_final: 0.7011 (t0) REVERT: A 351 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8443 (ttmt) REVERT: A 418 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7867 (pt0) REVERT: B 33 ASP cc_start: 0.6450 (t0) cc_final: 0.6182 (m-30) REVERT: B 54 LYS cc_start: 0.6625 (mptt) cc_final: 0.5676 (mttp) REVERT: B 134 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7322 (mptt) REVERT: B 138 LEU cc_start: 0.8910 (mp) cc_final: 0.8669 (mp) REVERT: B 216 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8275 (pmtt) REVERT: B 218 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: B 219 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: B 223 MET cc_start: 0.7993 (mmm) cc_final: 0.7607 (mmm) REVERT: B 224 LYS cc_start: 0.7881 (mttt) cc_final: 0.7617 (mttt) REVERT: B 241 ASP cc_start: 0.7816 (p0) cc_final: 0.7560 (p0) REVERT: B 258 GLU cc_start: 0.7125 (pm20) cc_final: 0.6826 (pp20) REVERT: B 260 LYS cc_start: 0.7615 (pptt) cc_final: 0.7334 (pttm) REVERT: B 277 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6867 (tm-30) REVERT: B 321 ASP cc_start: 0.7643 (m-30) cc_final: 0.7132 (m-30) REVERT: B 324 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7736 (mm-30) REVERT: B 336 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.5697 (p90) outliers start: 42 outliers final: 20 residues processed: 219 average time/residue: 0.5380 time to fit residues: 123.7184 Evaluate side-chains 213 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 336 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 77 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.0370 chunk 81 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.142132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111796 restraints weight = 12316.498| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.83 r_work: 0.3314 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8241 Z= 0.134 Angle : 0.613 7.862 11325 Z= 0.322 Chirality : 0.040 0.214 1310 Planarity : 0.004 0.043 1253 Dihedral : 18.054 158.171 1732 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.85 % Allowed : 33.82 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.29), residues: 858 helix: 1.36 (0.24), residues: 484 sheet: -0.79 (0.60), residues: 72 loop : -1.33 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 384 TYR 0.014 0.001 TYR A 46 PHE 0.011 0.001 PHE B 236 TRP 0.014 0.001 TRP B 261 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8241) covalent geometry : angle 0.61343 / 0.32 (11325) hydrogen bonds : bond 0.03621 / 2.36 ( 395) hydrogen bonds : angle 4.58389 / 3.22 ( 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 232 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8214 (ttt180) REVERT: A 61 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8319 (tt) REVERT: A 85 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7519 (mtm-85) REVERT: A 162 MET cc_start: 0.8552 (tpt) cc_final: 0.8315 (mmp) REVERT: A 201 TYR cc_start: 0.8623 (t80) cc_final: 0.8384 (t80) REVERT: A 241 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: A 351 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8411 (ttmt) REVERT: A 418 GLU cc_start: 0.8095 (pm20) cc_final: 0.7820 (pt0) REVERT: B 8 GLU cc_start: 0.6996 (pm20) cc_final: 0.6254 (pm20) REVERT: B 33 ASP cc_start: 0.6445 (t0) cc_final: 0.6138 (m-30) REVERT: B 44 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: B 54 LYS cc_start: 0.6462 (mptt) cc_final: 0.5574 (mttp) REVERT: B 134 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7342 (mptt) REVERT: B 138 LEU cc_start: 0.8910 (mp) cc_final: 0.8647 (mp) REVERT: B 216 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8383 (pmtt) REVERT: B 223 MET cc_start: 0.7973 (mmm) cc_final: 0.7600 (mmm) REVERT: B 224 LYS cc_start: 0.7893 (mttt) cc_final: 0.7626 (mttt) REVERT: B 241 ASP cc_start: 0.7770 (p0) cc_final: 0.7485 (p0) REVERT: B 260 LYS cc_start: 0.7576 (pptt) cc_final: 0.7292 (pttm) REVERT: B 277 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6726 (tm-30) REVERT: B 321 ASP cc_start: 0.7616 (m-30) cc_final: 0.7121 (m-30) REVERT: B 324 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 336 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.5654 (p90) outliers start: 29 outliers final: 11 residues processed: 221 average time/residue: 0.5405 time to fit residues: 125.3173 Evaluate side-chains 212 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 435 MET Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 73 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=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: 0.9990 chunk 82 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN B 66 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.140933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110748 restraints weight = 12254.303| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.82 r_work: 0.3291 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1970 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= 0.187 Angle : 0.648 8.196 11325 Z= 0.341 Chirality : 0.043 0.223 1310 Planarity : 0.004 0.058 1253 Dihedral : 18.011 160.186 1732 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.71 % Allowed : 33.82 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.29), residues: 858 helix: 1.31 (0.24), residues: 484 sheet: -0.84 (0.60), residues: 72 loop : -1.34 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 60 TYR 0.018 0.001 TYR A 46 PHE 0.014 0.001 PHE B 236 TRP 0.013 0.002 TRP B 261 HIS 0.004 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 8241) covalent geometry : angle 0.64760 / 0.34 (11325) hydrogen bonds : bond 0.03950 / 2.58 ( 395) hydrogen bonds : angle 4.64064 / 3.26 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3488.66 seconds wall clock time: 59 minutes 54.72 seconds (3594.72 seconds total)