Starting phenix.real_space_refine on Wed Feb 12 06:22:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k34_36843/02_2025/8k34_36843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k34_36843/02_2025/8k34_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k34_36843/02_2025/8k34_36843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k34_36843/02_2025/8k34_36843.map" model { file = "/net/cci-nas-00/data/ceres_data/8k34_36843/02_2025/8k34_36843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k34_36843/02_2025/8k34_36843.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'RNA': 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: 4.40, per 1000 atoms: 0.61 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: 1.68 Conformation dependent library (CDL) restraints added in 905.6 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: 0.72 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: 2.00 Time building geometry restraints manager: 1.96 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: 9820 2.58 - 5.17: 120 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: 3676 16.42 - 32.83: 503 32.83 - 49.25: 169 49.25 - 65.67: 49 65.67 - 82.09: 10 Dihedral angle restraints: 4407 sinusoidal: 1875 harmonic: 2532 Sorted by residual: dihedral pdb=" CA PRO B 393 " pdb=" C PRO B 393 " pdb=" N LEU B 394 " pdb=" CA LEU B 394 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA SER A 173 " pdb=" C SER A 173 " pdb=" N ASN A 174 " pdb=" CA ASN A 174 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA THR A 216 " pdb=" C THR A 216 " pdb=" N PHE A 217 " pdb=" CA PHE A 217 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 640 0.031 - 0.062: 286 0.062 - 0.093: 87 0.093 - 0.124: 50 0.124 - 0.155: 13 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CA LEU B 57 " pdb=" N LEU B 57 " pdb=" C LEU B 57 " pdb=" CB LEU B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CB ILE B 486 " pdb=" CA ILE B 486 " pdb=" CG1 ILE B 486 " pdb=" CG2 ILE B 486 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE A 391 " pdb=" N ILE A 391 " pdb=" C ILE A 391 " pdb=" CB ILE A 391 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (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: 0.760 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:14.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 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= 0.275 Angle : 0.737 12.915 9965 Z= 0.396 Chirality : 0.044 0.155 1076 Planarity : 0.005 0.113 1242 Dihedral : 17.750 82.086 2767 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (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 TRP 0.026 0.002 TRP A 46 HIS 0.005 0.001 HIS A 358 PHE 0.027 0.002 PHE A 305 TYR 0.021 0.001 TYR B 506 ARG 0.008 0.000 ARG B 72 *********************** 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 : 0.861 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: 0.7732 (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: 0.7983 time to fit residues: 97.3831 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 : 0.784 ------------------------------------------------------------------------------- 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 71 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4572 r_free = 0.4572 target = 0.178782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.145764 restraints weight = 10068.337| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.46 r_work: 0.4054 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7369 Z= 0.223 Angle : 0.587 6.948 9965 Z= 0.308 Chirality : 0.043 0.139 1076 Planarity : 0.004 0.065 1242 Dihedral : 8.169 75.488 993 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.43 % Allowed : 25.36 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 845 helix: 0.75 (0.30), residues: 290 sheet: -0.02 (0.42), residues: 149 loop : -0.63 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 46 HIS 0.003 0.001 HIS A 320 PHE 0.023 0.002 PHE A 343 TYR 0.011 0.001 TYR A 190 ARG 0.006 0.001 ARG B 72 *********************** 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 152 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7922 (m) cc_final: 0.7539 (m) REVERT: A 31 GLU cc_start: 0.6701 (tp30) cc_final: 0.6457 (tp30) REVERT: A 89 GLN cc_start: 0.8095 (mp10) cc_final: 0.7865 (pm20) REVERT: A 165 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6331 (pt) REVERT: A 346 ASP cc_start: 0.7907 (m-30) cc_final: 0.7596 (m-30) REVERT: A 371 ASP cc_start: 0.6501 (OUTLIER) cc_final: 0.6200 (m-30) REVERT: A 394 ASN cc_start: 0.5498 (OUTLIER) cc_final: 0.5178 (p0) REVERT: B 305 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7641 (mm) REVERT: B 371 ASN cc_start: 0.7056 (m-40) cc_final: 0.6681 (m110) outliers start: 42 outliers final: 12 residues processed: 135 average time/residue: 0.9398 time to fit residues: 136.5223 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 : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 179 ILE 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 20 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 63 optimal weight: 0.0370 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 40 optimal weight: 0.0570 chunk 74 optimal weight: 0.0970 overall best weight: 0.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B 350 ASN B 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.184319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.151772 restraints weight = 10103.604| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 3.48 r_work: 0.4113 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7369 Z= 0.160 Angle : 0.552 7.551 9965 Z= 0.292 Chirality : 0.042 0.151 1076 Planarity : 0.004 0.049 1242 Dihedral : 7.316 73.460 980 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.53 % Allowed : 26.26 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.28), residues: 845 helix: 0.98 (0.31), residues: 292 sheet: 0.05 (0.43), residues: 135 loop : -0.65 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 139 HIS 0.004 0.001 HIS B 207 PHE 0.018 0.001 PHE A 343 TYR 0.010 0.001 TYR B 397 ARG 0.010 0.000 ARG A 189 *********************** 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 149 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7761 (m) cc_final: 0.7402 (m) REVERT: A 31 GLU cc_start: 0.6719 (tp30) cc_final: 0.6474 (tp30) REVERT: A 41 LYS cc_start: 0.5641 (OUTLIER) cc_final: 0.5256 (pptt) REVERT: A 89 GLN cc_start: 0.8110 (mp10) cc_final: 0.7888 (pm20) REVERT: A 305 PHE cc_start: 0.7498 (t80) cc_final: 0.7154 (t80) REVERT: A 345 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6361 (ppp) REVERT: A 346 ASP cc_start: 0.7876 (m-30) cc_final: 0.7574 (m-30) REVERT: A 371 ASP cc_start: 0.6493 (OUTLIER) cc_final: 0.6207 (m-30) REVERT: B 305 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7693 (mm) REVERT: B 350 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7447 (t0) REVERT: B 371 ASN cc_start: 0.7166 (m-40) cc_final: 0.6826 (m-40) outliers start: 35 outliers final: 11 residues processed: 134 average time/residue: 0.9091 time to fit residues: 131.1749 Evaluate side-chains 116 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 179 ILE Chi-restraints excluded: chain A residue 234 ASN 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 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.0020 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4624 r_free = 0.4624 target = 0.182521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.149768 restraints weight = 10208.145| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 3.51 r_work: 0.4086 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1679 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= 0.175 Angle : 0.541 7.454 9965 Z= 0.284 Chirality : 0.043 0.138 1076 Planarity : 0.004 0.038 1242 Dihedral : 7.217 73.530 978 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.14 % Allowed : 27.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 845 helix: 1.09 (0.31), residues: 292 sheet: -0.26 (0.41), residues: 149 loop : -0.60 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 369 HIS 0.003 0.001 HIS A 320 PHE 0.019 0.001 PHE A 343 TYR 0.012 0.001 TYR B 397 ARG 0.009 0.000 ARG A 189 *********************** 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 131 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7833 (m) cc_final: 0.7479 (m) REVERT: A 31 GLU cc_start: 0.6715 (tp30) cc_final: 0.6447 (tp30) REVERT: A 41 LYS cc_start: 0.5865 (OUTLIER) cc_final: 0.5430 (pptt) REVERT: A 89 GLN cc_start: 0.8037 (mp10) cc_final: 0.7813 (pm20) REVERT: A 277 MET cc_start: 0.7170 (mmp) cc_final: 0.6777 (mmp) REVERT: A 281 ASN cc_start: 0.8403 (t0) cc_final: 0.8086 (p0) REVERT: A 345 MET cc_start: 0.7034 (ppp) cc_final: 0.6221 (ppp) REVERT: A 346 ASP cc_start: 0.7932 (m-30) cc_final: 0.7563 (m-30) REVERT: A 371 ASP cc_start: 0.6484 (OUTLIER) cc_final: 0.6149 (m-30) REVERT: B 286 LYS cc_start: 0.7978 (tppt) cc_final: 0.7421 (mptt) REVERT: B 371 ASN cc_start: 0.7067 (m-40) cc_final: 0.6698 (m-40) REVERT: B 474 ASP cc_start: 0.7106 (t0) cc_final: 0.6873 (t0) outliers start: 32 outliers final: 12 residues processed: 118 average time/residue: 0.8147 time to fit residues: 104.5768 Evaluate side-chains 106 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 233 TYR Chi-restraints excluded: chain A residue 256 ILE 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 437 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.0570 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 72 optimal weight: 0.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4594 r_free = 0.4594 target = 0.179908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.147210 restraints weight = 10239.188| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 3.50 r_work: 0.4054 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7369 Z= 0.198 Angle : 0.539 6.735 9965 Z= 0.281 Chirality : 0.043 0.145 1076 Planarity : 0.004 0.038 1242 Dihedral : 7.202 73.549 976 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.66 % Allowed : 27.17 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.28), residues: 845 helix: 1.07 (0.30), residues: 292 sheet: -0.29 (0.41), residues: 147 loop : -0.59 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 PHE 0.019 0.002 PHE A 305 TYR 0.013 0.001 TYR A 190 ARG 0.010 0.000 ARG A 189 *********************** 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: 36 poor density : 112 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7748 (m-30) cc_final: 0.6879 (m-30) REVERT: A 18 THR cc_start: 0.7895 (m) cc_final: 0.7540 (m) REVERT: A 41 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5395 (pptt) REVERT: A 277 MET cc_start: 0.7093 (mmp) cc_final: 0.6584 (mmp) REVERT: A 281 ASN cc_start: 0.8390 (t0) cc_final: 0.8094 (p0) REVERT: A 345 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6247 (ppp) REVERT: A 346 ASP cc_start: 0.7964 (m-30) cc_final: 0.7574 (m-30) REVERT: A 358 HIS cc_start: 0.7913 (m-70) cc_final: 0.7637 (m-70) REVERT: A 371 ASP cc_start: 0.6347 (OUTLIER) cc_final: 0.6026 (m-30) REVERT: B 286 LYS cc_start: 0.7948 (tppt) cc_final: 0.7388 (mptt) REVERT: B 302 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6176 (mp-120) REVERT: B 350 ASN cc_start: 0.7781 (t0) cc_final: 0.7546 (t0) REVERT: B 371 ASN cc_start: 0.7086 (m-40) cc_final: 0.6712 (m-40) REVERT: B 453 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: B 474 ASP cc_start: 0.7143 (t0) cc_final: 0.6892 (t0) outliers start: 36 outliers final: 17 residues processed: 132 average time/residue: 0.8952 time to fit residues: 127.0626 Evaluate side-chains 122 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 179 ILE Chi-restraints excluded: chain A residue 223 PHE 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 63 optimal weight: 0.0370 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.0870 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.181134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.148642 restraints weight = 10221.138| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 3.48 r_work: 0.4077 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7369 Z= 0.188 Angle : 0.563 8.194 9965 Z= 0.294 Chirality : 0.043 0.141 1076 Planarity : 0.004 0.041 1242 Dihedral : 7.166 73.529 976 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.53 % Allowed : 27.43 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.28), residues: 845 helix: 1.10 (0.30), residues: 292 sheet: -0.30 (0.39), residues: 156 loop : -0.64 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 PHE 0.016 0.001 PHE A 343 TYR 0.010 0.001 TYR B 506 ARG 0.008 0.000 ARG A 189 *********************** 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 143 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7715 (m-30) cc_final: 0.6859 (m-30) REVERT: A 18 THR cc_start: 0.7887 (m) cc_final: 0.7542 (m) REVERT: A 31 GLU cc_start: 0.6806 (tp30) cc_final: 0.6360 (tp30) REVERT: A 41 LYS cc_start: 0.5894 (OUTLIER) cc_final: 0.5399 (pptt) REVERT: A 107 ASP cc_start: 0.8874 (t0) cc_final: 0.8528 (m-30) REVERT: A 277 MET cc_start: 0.7185 (mmp) cc_final: 0.6539 (mmp) REVERT: A 281 ASN cc_start: 0.8346 (t0) cc_final: 0.8079 (p0) REVERT: A 305 PHE cc_start: 0.7528 (t80) cc_final: 0.7253 (t80) REVERT: A 315 LYS cc_start: 0.9255 (tmtt) cc_final: 0.9052 (ttpp) REVERT: A 345 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6181 (ppp) REVERT: A 346 ASP cc_start: 0.7948 (m-30) cc_final: 0.7565 (m-30) REVERT: A 371 ASP cc_start: 0.6183 (OUTLIER) cc_final: 0.5858 (m-30) REVERT: B 243 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7987 (ttp-110) REVERT: B 286 LYS cc_start: 0.7883 (tppt) cc_final: 0.7388 (mptt) REVERT: B 350 ASN cc_start: 0.7803 (t0) cc_final: 0.7550 (t0) REVERT: B 371 ASN cc_start: 0.7070 (m-40) cc_final: 0.6712 (m-40) REVERT: B 453 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: B 474 ASP cc_start: 0.7086 (t0) cc_final: 0.6832 (t0) outliers start: 35 outliers final: 16 residues processed: 129 average time/residue: 0.9167 time to fit residues: 127.3025 Evaluate side-chains 117 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 HIS ** 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 = 0.4572 r_free = 0.4572 target = 0.177400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.145220 restraints weight = 10134.910| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 3.44 r_work: 0.4038 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7369 Z= 0.221 Angle : 0.575 7.953 9965 Z= 0.299 Chirality : 0.043 0.139 1076 Planarity : 0.004 0.037 1242 Dihedral : 7.251 73.572 976 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.40 % Allowed : 27.94 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 845 helix: 1.04 (0.30), residues: 294 sheet: -0.49 (0.40), residues: 152 loop : -0.62 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 369 HIS 0.006 0.001 HIS A 320 PHE 0.020 0.002 PHE A 343 TYR 0.014 0.001 TYR A 190 ARG 0.007 0.001 ARG A 362 *********************** 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 143 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7784 (m-30) cc_final: 0.6980 (m-30) REVERT: A 18 THR cc_start: 0.7981 (m) cc_final: 0.7638 (m) REVERT: A 41 LYS cc_start: 0.6069 (OUTLIER) cc_final: 0.5521 (pptt) REVERT: A 107 ASP cc_start: 0.8833 (t0) cc_final: 0.8520 (m-30) REVERT: A 119 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8028 (p0) REVERT: A 277 MET cc_start: 0.7374 (mmp) cc_final: 0.6753 (mmp) REVERT: A 345 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6230 (ppp) REVERT: A 346 ASP cc_start: 0.8038 (m-30) cc_final: 0.7667 (m-30) REVERT: A 358 HIS cc_start: 0.7793 (m-70) cc_final: 0.7443 (m-70) REVERT: A 371 ASP cc_start: 0.6421 (OUTLIER) cc_final: 0.6033 (m-30) REVERT: B 229 LEU cc_start: 0.7431 (mm) cc_final: 0.6864 (mt) REVERT: B 243 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7674 (ttp-170) REVERT: B 350 ASN cc_start: 0.7854 (t0) cc_final: 0.7580 (t0) REVERT: B 371 ASN cc_start: 0.7052 (m-40) cc_final: 0.6710 (m-40) REVERT: B 453 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7140 (mp10) REVERT: B 474 ASP cc_start: 0.7209 (t0) cc_final: 0.6929 (t0) outliers start: 34 outliers final: 15 residues processed: 131 average time/residue: 0.9033 time to fit residues: 127.3129 Evaluate side-chains 117 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.178945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.145910 restraints weight = 10290.558| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 3.51 r_work: 0.4041 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2195 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= 0.218 Angle : 0.613 9.569 9965 Z= 0.317 Chirality : 0.044 0.154 1076 Planarity : 0.004 0.037 1242 Dihedral : 7.256 73.560 976 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.01 % Allowed : 28.85 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.28), residues: 845 helix: 1.06 (0.30), residues: 294 sheet: -0.53 (0.40), residues: 152 loop : -0.65 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 369 HIS 0.006 0.001 HIS A 320 PHE 0.020 0.002 PHE A 343 TYR 0.016 0.001 TYR A 190 ARG 0.006 0.000 ARG B 72 *********************** 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: 31 poor density : 109 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7613 (m-30) cc_final: 0.6780 (m-30) REVERT: A 18 THR cc_start: 0.7900 (m) cc_final: 0.7559 (m) REVERT: A 31 GLU cc_start: 0.6751 (tp30) cc_final: 0.6287 (tp30) REVERT: A 41 LYS cc_start: 0.6016 (OUTLIER) cc_final: 0.5472 (pptt) REVERT: A 107 ASP cc_start: 0.8853 (t0) cc_final: 0.8520 (m-30) REVERT: A 108 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8078 (mp) REVERT: A 277 MET cc_start: 0.7308 (mmp) cc_final: 0.6678 (mmp) REVERT: A 345 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6256 (ppp) REVERT: A 346 ASP cc_start: 0.8059 (m-30) cc_final: 0.7696 (m-30) REVERT: A 371 ASP cc_start: 0.6271 (OUTLIER) cc_final: 0.5586 (m-30) REVERT: B 229 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6838 (mt) REVERT: B 243 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7688 (ttp-170) REVERT: B 350 ASN cc_start: 0.7797 (t0) cc_final: 0.7516 (t0) REVERT: B 371 ASN cc_start: 0.7090 (m-40) cc_final: 0.6750 (m-40) REVERT: B 453 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: B 474 ASP cc_start: 0.7140 (t0) cc_final: 0.6869 (t0) outliers start: 31 outliers final: 16 residues processed: 128 average time/residue: 0.8326 time to fit residues: 115.5253 Evaluate side-chains 121 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 234 ASN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 82 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 49 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.179867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.147272 restraints weight = 10384.872| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 3.52 r_work: 0.4066 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7369 Z= 0.199 Angle : 0.620 11.205 9965 Z= 0.320 Chirality : 0.044 0.144 1076 Planarity : 0.004 0.037 1242 Dihedral : 7.205 73.521 976 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.14 % Allowed : 28.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.28), residues: 845 helix: 0.94 (0.30), residues: 300 sheet: -0.52 (0.41), residues: 150 loop : -0.67 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 369 HIS 0.007 0.001 HIS A 358 PHE 0.023 0.001 PHE A 305 TYR 0.016 0.001 TYR B 506 ARG 0.006 0.000 ARG B 72 *********************** 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 145 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7492 (m-30) cc_final: 0.6720 (m-30) REVERT: A 18 THR cc_start: 0.7861 (m) cc_final: 0.7531 (m) REVERT: A 31 GLU cc_start: 0.6771 (tp30) cc_final: 0.6310 (tp30) REVERT: A 41 LYS cc_start: 0.6165 (OUTLIER) cc_final: 0.5653 (pptt) REVERT: A 107 ASP cc_start: 0.8870 (t0) cc_final: 0.8553 (m-30) REVERT: A 108 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 277 MET cc_start: 0.7208 (mmp) cc_final: 0.6711 (mmp) REVERT: A 313 LYS cc_start: 0.9306 (tptm) cc_final: 0.9001 (tppp) REVERT: A 345 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6220 (ppp) REVERT: A 346 ASP cc_start: 0.8061 (m-30) cc_final: 0.7736 (m-30) REVERT: A 371 ASP cc_start: 0.5779 (OUTLIER) cc_final: 0.5467 (m-30) REVERT: B 229 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6886 (mt) REVERT: B 243 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7633 (ttp-170) REVERT: B 302 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.5991 (mp-120) REVERT: B 350 ASN cc_start: 0.7801 (t0) cc_final: 0.7509 (t0) REVERT: B 371 ASN cc_start: 0.7064 (m-40) cc_final: 0.6724 (m-40) REVERT: B 453 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: B 474 ASP cc_start: 0.7102 (t0) cc_final: 0.6851 (t0) outliers start: 32 outliers final: 17 residues processed: 131 average time/residue: 0.8644 time to fit residues: 122.3158 Evaluate side-chains 123 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 108 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 246 ILE 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 229 LEU 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: 1.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 HIS ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4602 r_free = 0.4602 target = 0.180552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.148092 restraints weight = 10498.179| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 3.52 r_work: 0.4059 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7369 Z= 0.215 Angle : 0.649 11.727 9965 Z= 0.333 Chirality : 0.044 0.148 1076 Planarity : 0.004 0.038 1242 Dihedral : 7.239 73.537 976 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.36 % Allowed : 30.66 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.28), residues: 845 helix: 0.91 (0.30), residues: 300 sheet: -0.42 (0.42), residues: 143 loop : -0.73 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 369 HIS 0.005 0.001 HIS A 358 PHE 0.025 0.002 PHE A 305 TYR 0.016 0.001 TYR B 506 ARG 0.007 0.000 ARG A 362 ********************** 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 130 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7483 (m-30) cc_final: 0.6753 (m-30) REVERT: A 18 THR cc_start: 0.7864 (m) cc_final: 0.7528 (m) REVERT: A 31 GLU cc_start: 0.6842 (tp30) cc_final: 0.6339 (tp30) REVERT: A 41 LYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5694 (pptt) REVERT: A 107 ASP cc_start: 0.8877 (t0) cc_final: 0.8558 (m-30) REVERT: A 108 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8135 (mp) REVERT: A 277 MET cc_start: 0.7167 (mmp) cc_final: 0.6675 (mmp) REVERT: A 313 LYS cc_start: 0.9300 (tptm) cc_final: 0.8937 (tppp) REVERT: A 345 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6195 (ppp) REVERT: A 346 ASP cc_start: 0.8049 (m-30) cc_final: 0.7719 (m-30) REVERT: A 371 ASP cc_start: 0.5830 (OUTLIER) cc_final: 0.5508 (m-30) REVERT: B 229 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6911 (mt) REVERT: B 243 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7568 (ttp-170) REVERT: B 302 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6017 (mp-120) REVERT: B 350 ASN cc_start: 0.7824 (t0) cc_final: 0.7532 (t0) REVERT: B 371 ASN cc_start: 0.7060 (m-40) cc_final: 0.6736 (m-40) REVERT: B 453 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7038 (mp10) REVERT: B 474 ASP cc_start: 0.7111 (t0) cc_final: 0.6857 (t0) outliers start: 26 outliers final: 17 residues processed: 120 average time/residue: 0.8644 time to fit residues: 112.0488 Evaluate side-chains 125 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 108 ILE Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 246 ILE 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 229 LEU 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 35 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN ** 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 = 0.4609 r_free = 0.4609 target = 0.181266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.149026 restraints weight = 10173.867| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 3.48 r_work: 0.4082 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7369 Z= 0.200 Angle : 0.632 10.529 9965 Z= 0.327 Chirality : 0.044 0.138 1076 Planarity : 0.004 0.041 1242 Dihedral : 7.205 73.518 976 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.10 % Allowed : 30.92 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.28), residues: 845 helix: 0.99 (0.30), residues: 297 sheet: -0.40 (0.43), residues: 143 loop : -0.68 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 369 HIS 0.005 0.001 HIS A 320 PHE 0.030 0.002 PHE A 343 TYR 0.013 0.001 TYR B 506 ARG 0.009 0.000 ARG B 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5482.46 seconds wall clock time: 97 minutes 33.18 seconds (5853.18 seconds total)