Starting phenix.real_space_refine on Tue Aug 4 23:14:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8k34_36843/08_2026/8k34_36843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k34_36843/08_2026/8k34_36843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8k34_36843/08_2026/8k34_36843.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8k34_36843/08_2026/8k34_36843.cif" model { file = "/net/cci-nas-00/data/ceres_data/8k34_36843/08_2026/8k34_36843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k34_36843/08_2026/8k34_36843.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k34_36843/08_2026/8k34_36843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k34_36843/08_2026/8k34_36843.map" } resolution = 2.81 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= 0.000 sd= 0.044 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 4 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 4650 2.51 5 N 1196 2.21 5 O 1315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7187 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3597 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 13, 'TRANS': 415} Chain breaks: 4 Chain: "B" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3503 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 409} Chain breaks: 3 Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Classifications: {'RNAv2': 4} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2} Link IDs: {'rna2p': 1, 'rna3p': 2} Chain: "B" 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: 0.19 Number of scatterers: 7187 At special positions: 0 Unit cell: (75.9, 81.4, 130.9, 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 21 16.00 P 4 15.00 Mg 1 11.99 O 1315 8.00 N 1196 7.00 C 4650 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: 0.47 Conformation dependent library (CDL) restraints added in 281.3 milliseconds 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 39.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.544A pdb=" N LYS A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.113A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.805A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.690A pdb=" N PHE A 223 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.587A pdb=" N ARG A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 365 removed outlier: 3.724A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 384 Processing helix chain 'A' and resid 420 through 438 removed outlier: 3.824A pdb=" N LEU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.744A pdb=" N LYS B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 115 through 132 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.860A pdb=" N LYS B 336 " --> pdb=" O PRO B 332 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.699A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 477 through 482 removed outlier: 4.596A pdb=" N PHE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 4.043A pdb=" N SER B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 5.832A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS A 4 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE A 60 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 6 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE A 62 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER A 8 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 165 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 394 Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 6 removed outlier: 5.712A pdb=" N ILE B 412 " --> pdb=" O PHE B 419 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE B 419 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.775A pdb=" N GLN B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 270 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 91 through 95 removed outlier: 3.608A pdb=" N GLY B 45 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B 141 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB3, first strand: chain 'B' and resid 425 through 426 293 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2203 1.34 - 1.46: 1336 1.46 - 1.58: 3792 1.58 - 1.70: 7 1.70 - 1.82: 31 Bond restraints: 7369 Sorted by residual: bond pdb=" CG PRO B 319 " pdb=" CD PRO B 319 " ideal model delta sigma weight residual 1.503 1.384 0.119 3.40e-02 8.65e+02 1.22e+01 bond pdb=" CG LEU B 13 " pdb=" CD1 LEU B 13 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 bond pdb=" CB LYS B 48 " pdb=" CG LYS B 48 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.28e+00 bond pdb=" CG LYS B 48 " pdb=" CD LYS B 48 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CG LEU B 57 " pdb=" CD2 LEU B 57 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.00e+00 ... (remaining 7364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 9807 2.58 - 5.17: 133 5.17 - 7.75: 16 7.75 - 10.33: 7 10.33 - 12.92: 2 Bond angle restraints: 9965 Sorted by residual: angle pdb=" CA LYS A 315 " pdb=" CB LYS A 315 " pdb=" CG LYS A 315 " ideal model delta sigma weight residual 114.10 127.02 -12.92 2.00e+00 2.50e-01 4.17e+01 angle pdb=" CA PRO B 319 " pdb=" N PRO B 319 " pdb=" CD PRO B 319 " ideal model delta sigma weight residual 112.00 103.09 8.91 1.40e+00 5.10e-01 4.05e+01 angle pdb=" N PRO B 319 " pdb=" CD PRO B 319 " pdb=" CG PRO B 319 " ideal model delta sigma weight residual 103.20 93.83 9.37 1.50e+00 4.44e-01 3.90e+01 angle pdb=" CB LYS B 48 " pdb=" CG LYS B 48 " pdb=" CD LYS B 48 " ideal model delta sigma weight residual 111.30 121.94 -10.64 2.30e+00 1.89e-01 2.14e+01 angle pdb=" CA GLN B 295 " pdb=" CB GLN B 295 " pdb=" CG GLN B 295 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 ... (remaining 9960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3664 16.42 - 32.83: 504 32.83 - 49.25: 172 49.25 - 65.67: 56 65.67 - 82.09: 11 Dihedral angle restraints: 4407 sinusoidal: 1875 harmonic: 2532 Sorted by residual: dihedral pdb=" C4' A C 1 " pdb=" C3' A C 1 " pdb=" C2' A C 1 " pdb=" C1' A C 1 " ideal model delta sinusoidal sigma weight residual 36.34 -36.41 72.75 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' C C 4 " pdb=" C3' C C 4 " pdb=" C2' C C 4 " pdb=" C1' C C 4 " ideal model delta sinusoidal sigma weight residual 36.35 -35.17 71.52 1 3.10e+00 1.04e-01 6.82e+02 dihedral pdb=" O4' C C 4 " pdb=" C4' C C 4 " pdb=" C3' C C 4 " pdb=" C2' C C 4 " ideal model delta sinusoidal sigma weight residual -35.15 24.45 -59.60 1 4.00e+00 6.25e-02 2.96e+02 ... (remaining 4404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 882 0.055 - 0.111: 159 0.111 - 0.166: 27 0.166 - 0.222: 2 0.222 - 0.277: 6 Chirality restraints: 1076 Sorted by residual: chirality pdb=" C2' A C 1 " pdb=" C3' A C 1 " pdb=" O2' A C 1 " pdb=" C1' A C 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' C C 4 " pdb=" C3' C C 4 " pdb=" O2' C C 4 " pdb=" C1' C C 4 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' A C 1 " pdb=" C4' A C 1 " pdb=" O3' A C 1 " pdb=" C2' A C 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.75 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1073 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 318 " 0.079 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 319 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 319 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 319 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 295 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C GLN B 295 " 0.037 2.00e-02 2.50e+03 pdb=" O GLN B 295 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 296 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 394 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C ASN A 394 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 394 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 395 " -0.012 2.00e-02 2.50e+03 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 80 2.58 - 3.16: 5839 3.16 - 3.74: 11725 3.74 - 4.32: 16273 4.32 - 4.90: 26684 Nonbonded interactions: 60601 Sorted by model distance: nonbonded pdb=" OD1 ASN B 468 " pdb="MG MG B 601 " model vdw 2.000 2.170 nonbonded pdb=" OP1 A C 3 " pdb="MG MG B 601 " model vdw 2.008 2.170 nonbonded pdb=" OP2 A C 1 " pdb="MG MG B 601 " model vdw 2.023 2.170 nonbonded pdb=" OXT ILE B 507 " pdb="MG MG B 601 " model vdw 2.088 2.170 nonbonded pdb=" O TRP B 269 " pdb=" OH TYR B 467 " model vdw 2.144 3.040 ... (remaining 60596 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: 1.290 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.890 Find NCS groups from input model: 0.040 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 7369 Z= 0.168 Angle : 0.752 12.915 9965 Z= 0.400 Chirality : 0.049 0.277 1076 Planarity : 0.005 0.113 1242 Dihedral : 18.097 82.086 2767 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.07 % Allowed : 31.05 % Favored : 66.88 % 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: -0.23 (0.28), residues: 845 helix: 0.61 (0.31), residues: 280 sheet: -0.17 (0.41), residues: 153 loop : -0.60 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 72 TYR 0.021 0.001 TYR B 506 PHE 0.027 0.002 PHE A 305 TRP 0.026 0.002 TRP A 46 HIS 0.005 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 7369) covalent geometry : angle 0.75216 / 0.40 ( 9965) hydrogen bonds : bond 0.14013 / 9.45 ( 293) hydrogen bonds : angle 6.70087 / 4.54 ( 816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.6775 (mp10) cc_final: 0.6572 (mp10) REVERT: A 346 ASP cc_start: 0.7995 (m-30) cc_final: 0.7735 (m-30) REVERT: B 356 GLU cc_start: 0.7885 (mp0) cc_final: 0.7657 (mp0) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.2922 time to fit residues: 35.8581 Evaluate side-chains 102 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 311 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 434 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.178415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.145129 restraints weight = 10220.651| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.51 r_work: 0.4039 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7369 Z= 0.152 Angle : 0.611 6.981 9965 Z= 0.317 Chirality : 0.046 0.339 1076 Planarity : 0.004 0.063 1242 Dihedral : 8.070 80.689 993 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.56 % Allowed : 25.10 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.28), residues: 845 helix: 0.76 (0.30), residues: 290 sheet: -0.03 (0.42), residues: 149 loop : -0.63 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 72 TYR 0.011 0.001 TYR B 397 PHE 0.023 0.002 PHE A 343 TRP 0.015 0.002 TRP A 46 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 7369) covalent geometry : angle 0.61112 / 0.32 ( 9965) hydrogen bonds : bond 0.04031 / 2.58 ( 293) hydrogen bonds : angle 5.67093 / 3.86 ( 816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7958 (m) cc_final: 0.7578 (m) REVERT: A 31 GLU cc_start: 0.6735 (tp30) cc_final: 0.6495 (tp30) REVERT: A 89 GLN cc_start: 0.8111 (mp10) cc_final: 0.7886 (pm20) REVERT: A 345 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6510 (ppp) REVERT: A 346 ASP cc_start: 0.7917 (m-30) cc_final: 0.7539 (m-30) REVERT: A 371 ASP cc_start: 0.6564 (OUTLIER) cc_final: 0.6269 (m-30) REVERT: A 394 ASN cc_start: 0.5505 (OUTLIER) cc_final: 0.5189 (p0) REVERT: B 371 ASN cc_start: 0.7154 (m-40) cc_final: 0.6784 (m110) outliers start: 43 outliers final: 15 residues processed: 138 average time/residue: 0.3804 time to fit residues: 56.3294 Evaluate side-chains 117 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.172118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.139358 restraints weight = 10307.131| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 3.44 r_work: 0.3977 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7369 Z= 0.255 Angle : 0.696 7.684 9965 Z= 0.362 Chirality : 0.048 0.272 1076 Planarity : 0.005 0.054 1242 Dihedral : 7.673 79.203 980 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 6.47 % Allowed : 23.67 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.50 (0.28), residues: 845 helix: 0.33 (0.30), residues: 297 sheet: -0.28 (0.41), residues: 146 loop : -0.77 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 189 TYR 0.013 0.002 TYR A 213 PHE 0.031 0.002 PHE A 343 TRP 0.016 0.003 TRP B 139 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.26 ( 7369) covalent geometry : angle 0.69608 / 0.36 ( 9965) hydrogen bonds : bond 0.04408 / 2.84 ( 293) hydrogen bonds : angle 5.64882 / 3.89 ( 816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 100 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.6394 (OUTLIER) cc_final: 0.5805 (pptt) REVERT: A 89 GLN cc_start: 0.8081 (mp10) cc_final: 0.7864 (pm20) REVERT: A 99 ILE cc_start: 0.7848 (pt) cc_final: 0.7601 (pt) REVERT: A 119 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8045 (p0) REVERT: A 346 ASP cc_start: 0.8126 (m-30) cc_final: 0.7665 (m-30) REVERT: A 371 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6255 (m-30) REVERT: B 350 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7701 (t0) REVERT: B 371 ASN cc_start: 0.7195 (m-40) cc_final: 0.6716 (m110) REVERT: B 474 ASP cc_start: 0.7291 (t0) cc_final: 0.7082 (t0) outliers start: 50 outliers final: 17 residues processed: 133 average time/residue: 0.3279 time to fit residues: 47.3267 Evaluate side-chains 120 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 44 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.0050 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 61 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.178927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.146353 restraints weight = 10279.118| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.48 r_work: 0.4044 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7369 Z= 0.128 Angle : 0.581 7.400 9965 Z= 0.303 Chirality : 0.044 0.135 1076 Planarity : 0.004 0.046 1242 Dihedral : 7.143 76.711 980 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.92 % Allowed : 26.78 % Favored : 68.31 % 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 (0.28), residues: 845 helix: 0.73 (0.30), residues: 292 sheet: -0.31 (0.41), residues: 140 loop : -0.78 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 189 TYR 0.014 0.001 TYR A 293 PHE 0.020 0.001 PHE A 343 TRP 0.020 0.002 TRP A 369 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7369) covalent geometry : angle 0.58123 / 0.30 ( 9965) hydrogen bonds : bond 0.03668 / 2.36 ( 293) hydrogen bonds : angle 5.28321 / 3.64 ( 816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7940 (m) cc_final: 0.7563 (m) REVERT: A 41 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5493 (pptt) REVERT: A 89 GLN cc_start: 0.8111 (mp10) cc_final: 0.7869 (pm20) REVERT: A 277 MET cc_start: 0.7046 (mmp) cc_final: 0.6678 (mmp) REVERT: A 281 ASN cc_start: 0.8427 (t0) cc_final: 0.8086 (p0) REVERT: A 328 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7335 (tttt) REVERT: A 345 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6315 (ppp) REVERT: A 346 ASP cc_start: 0.7926 (m-30) cc_final: 0.7616 (m-30) REVERT: A 371 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.5992 (m-30) REVERT: A 394 ASN cc_start: 0.5615 (OUTLIER) cc_final: 0.5170 (p0) REVERT: B 302 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6176 (mp10) REVERT: B 305 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7594 (mm) REVERT: B 371 ASN cc_start: 0.7183 (m-40) cc_final: 0.6795 (m110) REVERT: B 453 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.6998 (mp10) outliers start: 38 outliers final: 14 residues processed: 137 average time/residue: 0.3898 time to fit residues: 57.4906 Evaluate side-chains 118 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.176417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.143962 restraints weight = 10342.576| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 3.46 r_work: 0.4013 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7369 Z= 0.160 Angle : 0.604 7.967 9965 Z= 0.313 Chirality : 0.044 0.158 1076 Planarity : 0.004 0.054 1242 Dihedral : 7.185 76.270 980 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.92 % Allowed : 27.17 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.28), residues: 845 helix: 0.78 (0.30), residues: 291 sheet: -0.60 (0.40), residues: 149 loop : -0.75 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 189 TYR 0.013 0.001 TYR A 190 PHE 0.022 0.002 PHE A 343 TRP 0.023 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 7369) covalent geometry : angle 0.60357 / 0.31 ( 9965) hydrogen bonds : bond 0.03724 / 2.39 ( 293) hydrogen bonds : angle 5.27233 / 3.64 ( 816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7949 (m) cc_final: 0.7567 (m) REVERT: A 41 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5520 (pptt) REVERT: A 99 ILE cc_start: 0.7709 (pt) cc_final: 0.7452 (pt) REVERT: A 119 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8009 (p0) REVERT: A 277 MET cc_start: 0.7006 (mmp) cc_final: 0.6614 (mmp) REVERT: A 281 ASN cc_start: 0.8428 (t0) cc_final: 0.8094 (p0) REVERT: A 315 LYS cc_start: 0.9263 (tmtt) cc_final: 0.9024 (tmmt) REVERT: A 345 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6274 (ppp) REVERT: A 346 ASP cc_start: 0.7991 (m-30) cc_final: 0.7653 (m-30) REVERT: A 358 HIS cc_start: 0.7861 (m-70) cc_final: 0.7571 (m-70) REVERT: A 371 ASP cc_start: 0.6302 (OUTLIER) cc_final: 0.5933 (m-30) REVERT: B 286 LYS cc_start: 0.8047 (tppt) cc_final: 0.7465 (mptt) REVERT: B 305 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7602 (mm) REVERT: B 350 ASN cc_start: 0.7933 (t0) cc_final: 0.7622 (t0) REVERT: B 365 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.5279 (m-80) REVERT: B 371 ASN cc_start: 0.7214 (m-40) cc_final: 0.6884 (m110) REVERT: B 453 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6994 (mp10) REVERT: B 474 ASP cc_start: 0.7197 (t0) cc_final: 0.6946 (t0) outliers start: 38 outliers final: 17 residues processed: 131 average time/residue: 0.3039 time to fit residues: 43.0839 Evaluate side-chains 129 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 0.3980 chunk 44 optimal weight: 0.0980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.180912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.148783 restraints weight = 10188.017| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 3.45 r_work: 0.4067 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7369 Z= 0.115 Angle : 0.559 7.733 9965 Z= 0.291 Chirality : 0.043 0.139 1076 Planarity : 0.004 0.050 1242 Dihedral : 6.880 74.349 980 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.79 % Allowed : 27.81 % Favored : 67.40 % 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: -0.17 (0.28), residues: 845 helix: 1.00 (0.31), residues: 292 sheet: -0.56 (0.41), residues: 149 loop : -0.70 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 189 TYR 0.011 0.001 TYR B 506 PHE 0.017 0.001 PHE A 343 TRP 0.030 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 7369) covalent geometry : angle 0.55853 / 0.29 ( 9965) hydrogen bonds : bond 0.03387 / 2.19 ( 293) hydrogen bonds : angle 5.08836 / 3.52 ( 816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7751 (m-30) cc_final: 0.6838 (m-30) REVERT: A 18 THR cc_start: 0.7841 (m) cc_final: 0.7479 (m) REVERT: A 31 GLU cc_start: 0.6821 (tp30) cc_final: 0.6354 (tp30) REVERT: A 41 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5471 (pptt) REVERT: A 107 ASP cc_start: 0.8835 (t0) cc_final: 0.8545 (m-30) REVERT: A 277 MET cc_start: 0.7040 (mmp) cc_final: 0.6631 (mmp) REVERT: A 315 LYS cc_start: 0.9297 (tmtt) cc_final: 0.9071 (tmmt) REVERT: A 345 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6284 (ppp) REVERT: A 346 ASP cc_start: 0.7943 (m-30) cc_final: 0.7627 (m-30) REVERT: A 371 ASP cc_start: 0.6344 (OUTLIER) cc_final: 0.6029 (m-30) REVERT: B 286 LYS cc_start: 0.7921 (tppt) cc_final: 0.7414 (mptt) REVERT: B 302 GLN cc_start: 0.6758 (OUTLIER) cc_final: 0.6051 (mp-120) REVERT: B 350 ASN cc_start: 0.7709 (t0) cc_final: 0.7504 (t0) REVERT: B 367 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7657 (t0) REVERT: B 371 ASN cc_start: 0.7241 (m-40) cc_final: 0.6883 (m-40) REVERT: B 453 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: B 474 ASP cc_start: 0.7197 (t0) cc_final: 0.6975 (t0) outliers start: 37 outliers final: 13 residues processed: 139 average time/residue: 0.3841 time to fit residues: 57.5605 Evaluate side-chains 123 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 chunk 54 optimal weight: 0.0970 chunk 63 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 207 HIS ** 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 = 0.4607 r_free = 0.4607 target = 0.181366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.148163 restraints weight = 10378.842| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.55 r_work: 0.4065 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7369 Z= 0.120 Angle : 0.585 8.871 9965 Z= 0.304 Chirality : 0.044 0.150 1076 Planarity : 0.004 0.051 1242 Dihedral : 6.751 73.582 977 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.62 % Allowed : 29.50 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.28), residues: 845 helix: 1.09 (0.31), residues: 292 sheet: -0.57 (0.40), residues: 152 loop : -0.71 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 72 TYR 0.014 0.001 TYR A 190 PHE 0.024 0.001 PHE A 305 TRP 0.024 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7369) covalent geometry : angle 0.58478 / 0.30 ( 9965) hydrogen bonds : bond 0.03453 / 2.25 ( 293) hydrogen bonds : angle 5.05517 / 3.50 ( 816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7749 (m-30) cc_final: 0.6860 (m-30) REVERT: A 18 THR cc_start: 0.7846 (m) cc_final: 0.7484 (m) REVERT: A 41 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5463 (pptt) REVERT: A 277 MET cc_start: 0.7056 (mmp) cc_final: 0.6659 (mmp) REVERT: A 345 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6249 (ppp) REVERT: A 346 ASP cc_start: 0.7940 (m-30) cc_final: 0.7618 (m-30) REVERT: A 358 HIS cc_start: 0.7836 (m-70) cc_final: 0.7618 (m-70) REVERT: A 371 ASP cc_start: 0.6189 (OUTLIER) cc_final: 0.5567 (m-30) REVERT: B 229 LEU cc_start: 0.7400 (mm) cc_final: 0.6898 (mt) REVERT: B 286 LYS cc_start: 0.7891 (tppt) cc_final: 0.7352 (mptt) REVERT: B 302 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6436 (mp10) REVERT: B 350 ASN cc_start: 0.7728 (t0) cc_final: 0.7472 (t0) REVERT: B 371 ASN cc_start: 0.7233 (m-40) cc_final: 0.6902 (m-40) REVERT: B 453 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: B 474 ASP cc_start: 0.7146 (t0) cc_final: 0.6856 (t0) outliers start: 28 outliers final: 13 residues processed: 130 average time/residue: 0.3596 time to fit residues: 50.5962 Evaluate side-chains 117 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 72 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 78 optimal weight: 0.0870 chunk 44 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.181149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.148382 restraints weight = 10387.783| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 3.51 r_work: 0.4053 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7369 Z= 0.138 Angle : 0.619 10.358 9965 Z= 0.320 Chirality : 0.044 0.142 1076 Planarity : 0.004 0.052 1242 Dihedral : 6.768 73.777 977 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.75 % Allowed : 30.14 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.28), residues: 845 helix: 1.05 (0.30), residues: 292 sheet: -0.57 (0.40), residues: 152 loop : -0.71 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 72 TYR 0.015 0.001 TYR B 506 PHE 0.021 0.002 PHE A 305 TRP 0.028 0.002 TRP A 33 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7369) covalent geometry : angle 0.61931 / 0.32 ( 9965) hydrogen bonds : bond 0.03462 / 2.26 ( 293) hydrogen bonds : angle 5.09737 / 3.52 ( 816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7663 (m-30) cc_final: 0.6796 (m-30) REVERT: A 18 THR cc_start: 0.7816 (m) cc_final: 0.7452 (m) REVERT: A 41 LYS cc_start: 0.6036 (OUTLIER) cc_final: 0.5493 (pptt) REVERT: A 100 ASP cc_start: 0.8220 (t0) cc_final: 0.8008 (t0) REVERT: A 107 ASP cc_start: 0.8849 (t0) cc_final: 0.8546 (m-30) REVERT: A 277 MET cc_start: 0.7028 (mmp) cc_final: 0.6587 (mmp) REVERT: A 345 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6257 (ppp) REVERT: A 346 ASP cc_start: 0.7968 (m-30) cc_final: 0.7645 (m-30) REVERT: A 358 HIS cc_start: 0.7827 (m-70) cc_final: 0.7601 (m-70) REVERT: A 364 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7507 (tp-100) REVERT: A 371 ASP cc_start: 0.5842 (OUTLIER) cc_final: 0.5506 (m-30) REVERT: B 229 LEU cc_start: 0.7333 (mm) cc_final: 0.6884 (mt) REVERT: B 286 LYS cc_start: 0.7921 (tppt) cc_final: 0.7553 (mptt) REVERT: B 302 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.6059 (mp-120) REVERT: B 350 ASN cc_start: 0.7759 (t0) cc_final: 0.7526 (t0) REVERT: B 371 ASN cc_start: 0.7235 (m-40) cc_final: 0.6910 (m-40) REVERT: B 453 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7092 (mp10) outliers start: 29 outliers final: 14 residues processed: 129 average time/residue: 0.3969 time to fit residues: 55.3007 Evaluate side-chains 122 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 79 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.178320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.145376 restraints weight = 10241.195| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 3.48 r_work: 0.4026 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7369 Z= 0.160 Angle : 0.660 11.163 9965 Z= 0.340 Chirality : 0.045 0.138 1076 Planarity : 0.004 0.057 1242 Dihedral : 6.901 74.433 977 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.62 % Allowed : 30.53 % Favored : 65.85 % 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: -0.25 (0.28), residues: 845 helix: 0.98 (0.30), residues: 292 sheet: -0.58 (0.38), residues: 161 loop : -0.79 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 72 TYR 0.017 0.001 TYR B 506 PHE 0.022 0.002 PHE A 343 TRP 0.030 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 7369) covalent geometry : angle 0.65979 / 0.34 ( 9965) hydrogen bonds : bond 0.03621 / 2.37 ( 293) hydrogen bonds : angle 5.14318 / 3.55 ( 816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7734 (m-30) cc_final: 0.6887 (m-30) REVERT: A 18 THR cc_start: 0.7953 (m) cc_final: 0.7589 (m) REVERT: A 31 GLU cc_start: 0.6851 (tp30) cc_final: 0.6305 (tp30) REVERT: A 41 LYS cc_start: 0.6466 (OUTLIER) cc_final: 0.5864 (pptt) REVERT: A 100 ASP cc_start: 0.8217 (t0) cc_final: 0.8016 (t0) REVERT: A 107 ASP cc_start: 0.8839 (t0) cc_final: 0.8549 (m-30) REVERT: A 277 MET cc_start: 0.7145 (mmp) cc_final: 0.6708 (mmp) REVERT: A 345 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6286 (ppp) REVERT: A 346 ASP cc_start: 0.7911 (m-30) cc_final: 0.7523 (m-30) REVERT: A 358 HIS cc_start: 0.7854 (m-70) cc_final: 0.7609 (m-70) REVERT: A 364 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7082 (tp-100) REVERT: A 368 TRP cc_start: 0.7811 (m-10) cc_final: 0.7269 (m100) REVERT: A 371 ASP cc_start: 0.6013 (OUTLIER) cc_final: 0.5661 (m-30) REVERT: B 51 GLN cc_start: 0.7515 (pp30) cc_final: 0.7314 (pp30) REVERT: B 229 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6990 (mt) REVERT: B 350 ASN cc_start: 0.7854 (t0) cc_final: 0.7631 (t0) REVERT: B 371 ASN cc_start: 0.7230 (m-40) cc_final: 0.6913 (m-40) REVERT: B 453 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7095 (mp10) outliers start: 28 outliers final: 15 residues processed: 126 average time/residue: 0.3455 time to fit residues: 47.1484 Evaluate side-chains 122 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.177827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.145749 restraints weight = 10244.752| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.38 r_work: 0.4036 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7369 Z= 0.167 Angle : 0.674 12.008 9965 Z= 0.346 Chirality : 0.045 0.149 1076 Planarity : 0.004 0.055 1242 Dihedral : 6.991 74.977 977 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.10 % Allowed : 31.31 % Favored : 65.59 % 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 (0.28), residues: 845 helix: 0.94 (0.31), residues: 292 sheet: -0.56 (0.41), residues: 145 loop : -0.85 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 72 TYR 0.017 0.001 TYR B 506 PHE 0.023 0.002 PHE A 343 TRP 0.032 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 7369) covalent geometry : angle 0.67363 / 0.35 ( 9965) hydrogen bonds : bond 0.03667 / 2.39 ( 293) hydrogen bonds : angle 5.21429 / 3.60 ( 816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7592 (m-30) cc_final: 0.7161 (m-30) REVERT: A 31 GLU cc_start: 0.6881 (tp30) cc_final: 0.6380 (tp30) REVERT: A 41 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.5896 (pptt) REVERT: A 107 ASP cc_start: 0.8775 (t0) cc_final: 0.8487 (m-30) REVERT: A 277 MET cc_start: 0.7050 (mmp) cc_final: 0.6627 (mmp) REVERT: A 345 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6334 (ppp) REVERT: A 346 ASP cc_start: 0.7974 (m-30) cc_final: 0.7589 (m-30) REVERT: A 358 HIS cc_start: 0.7869 (m-70) cc_final: 0.7604 (m-70) REVERT: A 364 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7179 (tp-100) REVERT: A 368 TRP cc_start: 0.7857 (m-10) cc_final: 0.7338 (m100) REVERT: A 371 ASP cc_start: 0.5924 (OUTLIER) cc_final: 0.5565 (m-30) REVERT: B 302 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6036 (mp-120) REVERT: B 350 ASN cc_start: 0.7872 (t0) cc_final: 0.7640 (t0) REVERT: B 371 ASN cc_start: 0.7237 (m-40) cc_final: 0.6918 (m-40) REVERT: B 453 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7094 (mp10) outliers start: 24 outliers final: 15 residues processed: 124 average time/residue: 0.3100 time to fit residues: 41.7002 Evaluate side-chains 128 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.0060 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 0.0270 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 0.0060 overall best weight: 0.2270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.181421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.148527 restraints weight = 10258.146| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 3.49 r_work: 0.4070 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7369 Z= 0.128 Angle : 0.656 11.926 9965 Z= 0.340 Chirality : 0.044 0.172 1076 Planarity : 0.004 0.054 1242 Dihedral : 6.827 74.294 977 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.46 % Allowed : 32.47 % Favored : 65.07 % 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: -0.28 (0.28), residues: 845 helix: 0.86 (0.30), residues: 298 sheet: -0.50 (0.42), residues: 143 loop : -0.81 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 72 TYR 0.013 0.001 TYR B 506 PHE 0.020 0.001 PHE A 60 TRP 0.029 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7369) covalent geometry : angle 0.65567 / 0.34 ( 9965) hydrogen bonds : bond 0.03540 / 2.35 ( 293) hydrogen bonds : angle 5.14294 / 3.55 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2365.69 seconds wall clock time: 41 minutes 2.28 seconds (2462.28 seconds total)