Starting phenix.real_space_refine on Wed Mar 12 06:22:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k34_36843/03_2025/8k34_36843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k34_36843/03_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_36843/03_2025/8k34_36843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k34_36843/03_2025/8k34_36843.map" model { file = "/net/cci-nas-00/data/ceres_data/8k34_36843/03_2025/8k34_36843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k34_36843/03_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-5624/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: 4.61, per 1000 atoms: 0.64 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: 1.69 Conformation dependent library (CDL) restraints added in 899.7 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: 0.85 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: 2.28 Time building geometry restraints manager: 2.02 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: 1.210 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.370 Find NCS groups from input model: 0.120 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:14.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.910 ------------------------------------------------------------------------------- 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 : 0.827 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: 0.7321 time to fit residues: 89.8715 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 : 0.904 ------------------------------------------------------------------------------- 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 = 38)----------------| | 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 : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7921 (m) cc_final: 0.7537 (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: 0.7866 (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: 0.6500 (OUTLIER) cc_final: 0.6200 (m-30) REVERT: A 394 ASN cc_start: 0.5498 (OUTLIER) cc_final: 0.5177 (p0) REVERT: B 305 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7640 (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: 0.9344 time to fit residues: 135.6609 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 : 0.869 ------------------------------------------------------------------------------- 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: 0.8980 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.178481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.145153 restraints weight = 10255.347| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 3.53 r_work: 0.4035 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.1242 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= 0.219 Angle : 0.585 7.551 9965 Z= 0.308 Chirality : 0.043 0.157 1076 Planarity : 0.004 0.051 1242 Dihedral : 7.497 73.558 980 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.56 % Allowed : 24.84 % Favored : 69.60 % 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: -0.19 (0.28), residues: 845 helix: 0.78 (0.30), residues: 292 sheet: -0.17 (0.42), residues: 140 loop : -0.71 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 139 HIS 0.004 0.001 HIS A 320 PHE 0.021 0.001 PHE A 343 TYR 0.009 0.001 TYR B 397 ARG 0.010 0.001 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: 43 poor density : 106 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.5760 (OUTLIER) cc_final: 0.5451 (m-30) REVERT: A 18 THR cc_start: 0.7836 (m) cc_final: 0.7467 (m) REVERT: A 31 GLU cc_start: 0.6769 (tp30) cc_final: 0.6486 (tp30) REVERT: A 41 LYS cc_start: 0.6032 (OUTLIER) cc_final: 0.5575 (pptt) REVERT: A 89 GLN cc_start: 0.8104 (mp10) cc_final: 0.7879 (pm20) REVERT: A 119 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7991 (p0) REVERT: A 305 PHE cc_start: 0.7536 (t80) cc_final: 0.7290 (t80) REVERT: A 345 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6513 (ppp) REVERT: A 346 ASP cc_start: 0.7845 (m-30) cc_final: 0.7526 (m-30) REVERT: A 371 ASP cc_start: 0.6445 (OUTLIER) cc_final: 0.6122 (m-30) REVERT: A 417 VAL cc_start: 0.7475 (t) cc_final: 0.7211 (t) REVERT: B 305 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7654 (mm) REVERT: B 350 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7529 (t0) REVERT: B 371 ASN cc_start: 0.7156 (m-40) cc_final: 0.6797 (m-40) REVERT: B 474 ASP cc_start: 0.7078 (t0) cc_final: 0.6847 (t0) outliers start: 43 outliers final: 16 residues processed: 131 average time/residue: 0.7210 time to fit residues: 103.1568 Evaluate side-chains 122 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP 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 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 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 377 THR Chi-restraints excluded: chain B residue 389 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: 3.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 364 GLN A 394 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.179477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.146460 restraints weight = 10257.309| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 3.51 r_work: 0.4040 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.1510 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= 0.202 Angle : 0.557 7.618 9965 Z= 0.292 Chirality : 0.043 0.144 1076 Planarity : 0.004 0.041 1242 Dihedral : 7.433 73.549 980 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.30 % Allowed : 26.78 % 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: -0.16 (0.28), residues: 845 helix: 0.88 (0.30), residues: 292 sheet: -0.23 (0.41), residues: 140 loop : -0.73 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 369 HIS 0.003 0.001 HIS A 320 PHE 0.021 0.001 PHE A 343 TYR 0.009 0.001 TYR B 506 ARG 0.010 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 154 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7817 (m) cc_final: 0.7456 (m) REVERT: A 31 GLU cc_start: 0.6773 (tp30) cc_final: 0.6463 (tp30) REVERT: A 41 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5445 (pptt) REVERT: A 89 GLN cc_start: 0.8112 (mp10) cc_final: 0.7886 (pm20) REVERT: A 108 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8082 (mp) REVERT: A 119 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8007 (p0) REVERT: A 267 GLN cc_start: 0.6969 (mp10) cc_final: 0.6738 (mp10) REVERT: A 305 PHE cc_start: 0.7599 (t80) cc_final: 0.7361 (t80) REVERT: A 345 MET cc_start: 0.7124 (ppp) cc_final: 0.6380 (ppp) REVERT: A 346 ASP cc_start: 0.7925 (m-30) cc_final: 0.7584 (m-30) REVERT: A 358 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7586 (m-70) REVERT: A 371 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.6135 (m-30) REVERT: B 286 LYS cc_start: 0.8024 (tppt) cc_final: 0.7447 (mptt) REVERT: B 302 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6404 (mp10) REVERT: B 305 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7651 (mm) REVERT: B 367 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7664 (t0) REVERT: B 371 ASN cc_start: 0.7181 (m-40) cc_final: 0.6732 (m-40) outliers start: 41 outliers final: 15 residues processed: 137 average time/residue: 1.0080 time to fit residues: 149.0939 Evaluate side-chains 122 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 108 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 358 HIS 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4554 r_free = 0.4554 target = 0.176430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.143744 restraints weight = 10275.278| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 3.48 r_work: 0.4004 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.1673 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= 0.264 Angle : 0.590 7.998 9965 Z= 0.307 Chirality : 0.043 0.147 1076 Planarity : 0.004 0.059 1242 Dihedral : 7.542 73.613 980 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.69 % Allowed : 26.78 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.28), residues: 845 helix: 0.76 (0.30), residues: 293 sheet: -0.42 (0.38), residues: 154 loop : -0.77 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 PHE 0.020 0.002 PHE A 343 TYR 0.012 0.001 TYR B 506 ARG 0.005 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 153 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.7948 (m) cc_final: 0.7601 (m) REVERT: A 41 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5523 (pptt) REVERT: A 89 GLN cc_start: 0.8104 (mp10) cc_final: 0.7878 (pm20) REVERT: A 99 ILE cc_start: 0.7712 (pt) cc_final: 0.7462 (pt) REVERT: A 108 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8189 (mp) REVERT: A 119 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8019 (p0) REVERT: A 277 MET cc_start: 0.7240 (mmp) cc_final: 0.6721 (mmp) REVERT: A 281 ASN cc_start: 0.8437 (t0) cc_final: 0.8074 (p0) REVERT: A 315 LYS cc_start: 0.9291 (tmtt) cc_final: 0.9022 (tmmt) REVERT: A 345 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6354 (ppp) REVERT: A 346 ASP cc_start: 0.7994 (m-30) cc_final: 0.7620 (m-30) REVERT: A 371 ASP cc_start: 0.6302 (OUTLIER) cc_final: 0.5937 (m-30) REVERT: B 286 LYS cc_start: 0.8025 (tppt) cc_final: 0.7489 (mptt) REVERT: B 305 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7675 (mm) REVERT: B 350 ASN cc_start: 0.7935 (t0) cc_final: 0.7613 (t0) REVERT: B 371 ASN cc_start: 0.7255 (m-40) cc_final: 0.6757 (m-40) REVERT: B 453 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7019 (mp10) REVERT: B 474 ASP cc_start: 0.7146 (t0) cc_final: 0.6887 (t0) outliers start: 44 outliers final: 19 residues processed: 133 average time/residue: 0.7817 time to fit residues: 112.9078 Evaluate side-chains 127 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 108 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 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 252 LEU Chi-restraints excluded: chain B residue 305 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 63 optimal weight: 0.0570 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 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 = 0.4586 r_free = 0.4586 target = 0.179305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.146949 restraints weight = 10240.642| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 3.47 r_work: 0.4041 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.1871 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= 0.186 Angle : 0.564 7.913 9965 Z= 0.295 Chirality : 0.042 0.143 1076 Planarity : 0.004 0.049 1242 Dihedral : 7.393 73.519 980 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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: -0.21 (0.28), residues: 845 helix: 0.92 (0.30), residues: 292 sheet: -0.59 (0.40), residues: 149 loop : -0.68 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 369 HIS 0.004 0.001 HIS A 320 PHE 0.016 0.001 PHE A 343 TYR 0.012 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 148 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7670 (m-30) cc_final: 0.6849 (m-30) REVERT: A 18 THR cc_start: 0.7832 (m) cc_final: 0.7503 (m) REVERT: A 31 GLU cc_start: 0.6860 (tp30) cc_final: 0.6403 (tp30) REVERT: A 41 LYS cc_start: 0.6029 (OUTLIER) cc_final: 0.5478 (pptt) REVERT: A 107 ASP cc_start: 0.8862 (t0) cc_final: 0.8518 (m-30) REVERT: A 108 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7965 (mp) REVERT: A 277 MET cc_start: 0.7100 (mmp) cc_final: 0.6513 (mmp) REVERT: A 281 ASN cc_start: 0.8294 (t0) cc_final: 0.8042 (p0) REVERT: A 305 PHE cc_start: 0.7569 (t80) cc_final: 0.7347 (t80) REVERT: A 345 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6214 (ppp) REVERT: A 346 ASP cc_start: 0.8004 (m-30) cc_final: 0.7622 (m-30) REVERT: A 358 HIS cc_start: 0.7819 (m-70) cc_final: 0.7557 (m-70) REVERT: A 371 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5911 (m-30) REVERT: B 302 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.6045 (mp-120) REVERT: B 350 ASN cc_start: 0.8000 (t0) cc_final: 0.7733 (t0) REVERT: B 371 ASN cc_start: 0.7238 (m-40) cc_final: 0.6848 (m110) REVERT: B 453 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7001 (mp10) REVERT: B 474 ASP cc_start: 0.7148 (t0) cc_final: 0.6893 (t0) outliers start: 35 outliers final: 15 residues processed: 132 average time/residue: 0.8119 time to fit residues: 116.1138 Evaluate side-chains 126 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 108 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 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 = 0.4576 r_free = 0.4576 target = 0.178332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.145932 restraints weight = 10214.305| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 3.45 r_work: 0.4032 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1935 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= 0.204 Angle : 0.590 8.894 9965 Z= 0.305 Chirality : 0.043 0.157 1076 Planarity : 0.004 0.047 1242 Dihedral : 7.381 73.550 980 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.79 % Allowed : 28.20 % Favored : 67.01 % 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: 0.98 (0.30), residues: 292 sheet: -0.62 (0.40), residues: 152 loop : -0.68 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 369 HIS 0.005 0.001 HIS A 320 PHE 0.018 0.001 PHE A 343 TYR 0.015 0.001 TYR B 506 ARG 0.005 0.000 ARG B 72 *********************** 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 149 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7687 (m-30) cc_final: 0.6836 (m-30) REVERT: A 18 THR cc_start: 0.7871 (m) cc_final: 0.7542 (m) REVERT: A 41 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5542 (pptt) REVERT: A 107 ASP cc_start: 0.8888 (t0) cc_final: 0.8567 (m-30) REVERT: A 108 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 277 MET cc_start: 0.7170 (mmp) cc_final: 0.6556 (mmp) REVERT: A 281 ASN cc_start: 0.8260 (t0) cc_final: 0.8044 (p0) REVERT: A 305 PHE cc_start: 0.7639 (t80) cc_final: 0.7376 (t80) REVERT: A 313 LYS cc_start: 0.9280 (tptm) cc_final: 0.8965 (tppp) REVERT: A 345 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6319 (ppp) REVERT: A 346 ASP cc_start: 0.8023 (m-30) cc_final: 0.7650 (m-30) REVERT: A 371 ASP cc_start: 0.6279 (OUTLIER) cc_final: 0.5917 (m-30) REVERT: B 229 LEU cc_start: 0.7370 (mm) cc_final: 0.6838 (mt) REVERT: B 302 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.6045 (mp-120) REVERT: B 350 ASN cc_start: 0.8005 (t0) cc_final: 0.7695 (t0) REVERT: B 371 ASN cc_start: 0.7318 (m-40) cc_final: 0.6965 (m-40) REVERT: B 453 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: B 474 ASP cc_start: 0.7148 (t0) cc_final: 0.6896 (t0) outliers start: 37 outliers final: 13 residues processed: 136 average time/residue: 0.8562 time to fit residues: 125.6567 Evaluate side-chains 120 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 426 VAL Chi-restraints excluded: chain B residue 453 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 72 optimal weight: 0.0570 chunk 28 optimal weight: 0.3980 chunk 53 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 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 = 0.4600 r_free = 0.4600 target = 0.180157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.147877 restraints weight = 10290.170| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 3.46 r_work: 0.4053 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.2106 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= 0.194 Angle : 0.609 9.601 9965 Z= 0.314 Chirality : 0.043 0.137 1076 Planarity : 0.004 0.044 1242 Dihedral : 7.278 73.516 979 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.88 % Allowed : 29.37 % Favored : 66.75 % 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: 1.04 (0.30), residues: 292 sheet: -0.60 (0.40), residues: 152 loop : -0.70 (0.30), residues: 401 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 0.022 0.001 PHE A 343 TYR 0.015 0.001 TYR B 506 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 145 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7583 (m-30) cc_final: 0.6753 (m-30) REVERT: A 18 THR cc_start: 0.7843 (m) cc_final: 0.7521 (m) REVERT: A 31 GLU cc_start: 0.6779 (tp30) cc_final: 0.6452 (tp30) REVERT: A 41 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5532 (pptt) REVERT: A 108 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8000 (mp) REVERT: A 277 MET cc_start: 0.7314 (mmp) cc_final: 0.6692 (mmp) REVERT: A 305 PHE cc_start: 0.7620 (t80) cc_final: 0.7346 (t80) REVERT: A 313 LYS cc_start: 0.9323 (tptm) cc_final: 0.9025 (tppp) REVERT: A 345 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6277 (ppp) REVERT: A 346 ASP cc_start: 0.8024 (m-30) cc_final: 0.7662 (m-30) REVERT: A 358 HIS cc_start: 0.7742 (m-70) cc_final: 0.7526 (m-70) REVERT: A 371 ASP cc_start: 0.6241 (OUTLIER) cc_final: 0.5552 (m-30) REVERT: B 350 ASN cc_start: 0.8001 (t0) cc_final: 0.7676 (t0) REVERT: B 371 ASN cc_start: 0.7408 (m-40) cc_final: 0.7073 (m-40) REVERT: B 453 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7073 (mp10) REVERT: B 474 ASP cc_start: 0.7137 (t0) cc_final: 0.6878 (t0) outliers start: 30 outliers final: 13 residues processed: 135 average time/residue: 0.8285 time to fit residues: 121.2911 Evaluate side-chains 125 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 82 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 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 = 0.4583 r_free = 0.4583 target = 0.178778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.146039 restraints weight = 10387.382| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.50 r_work: 0.4041 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7369 Z= 0.221 Angle : 0.636 11.145 9965 Z= 0.328 Chirality : 0.044 0.156 1076 Planarity : 0.004 0.043 1242 Dihedral : 7.255 73.540 977 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.49 % Allowed : 29.88 % Favored : 66.62 % 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: -0.19 (0.28), residues: 845 helix: 0.97 (0.30), residues: 292 sheet: -0.58 (0.41), residues: 152 loop : -0.70 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 369 HIS 0.005 0.001 HIS A 358 PHE 0.012 0.001 PHE A 176 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 139 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7577 (m-30) cc_final: 0.6755 (m-30) REVERT: A 18 THR cc_start: 0.7845 (m) cc_final: 0.7520 (m) REVERT: A 31 GLU cc_start: 0.6886 (tp30) cc_final: 0.6504 (tp30) REVERT: A 41 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5529 (pptt) REVERT: A 107 ASP cc_start: 0.8892 (t0) cc_final: 0.8563 (m-30) REVERT: A 108 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 277 MET cc_start: 0.7239 (mmp) cc_final: 0.6620 (mmp) REVERT: A 305 PHE cc_start: 0.7644 (t80) cc_final: 0.7362 (t80) REVERT: A 313 LYS cc_start: 0.9257 (tptm) cc_final: 0.8950 (tppp) REVERT: A 345 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6266 (ppp) REVERT: A 346 ASP cc_start: 0.8049 (m-30) cc_final: 0.7719 (m-30) REVERT: A 371 ASP cc_start: 0.5868 (OUTLIER) cc_final: 0.5514 (m-30) REVERT: B 229 LEU cc_start: 0.7324 (mm) cc_final: 0.6792 (mt) REVERT: B 302 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6559 (mp-120) REVERT: B 350 ASN cc_start: 0.8025 (t0) cc_final: 0.7728 (t0) REVERT: B 371 ASN cc_start: 0.7332 (m-40) cc_final: 0.6991 (m-40) REVERT: B 453 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: B 474 ASP cc_start: 0.7052 (t0) cc_final: 0.6814 (t0) outliers start: 27 outliers final: 11 residues processed: 131 average time/residue: 0.8859 time to fit residues: 124.9067 Evaluate side-chains 120 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 41 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 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 = 0.4577 r_free = 0.4577 target = 0.178426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.145296 restraints weight = 10486.586| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 3.52 r_work: 0.4029 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7369 Z= 0.226 Angle : 0.663 11.742 9965 Z= 0.341 Chirality : 0.045 0.168 1076 Planarity : 0.004 0.043 1242 Dihedral : 7.314 73.549 977 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.85 % Allowed : 30.53 % Favored : 66.62 % 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: -0.24 (0.28), residues: 845 helix: 0.87 (0.30), residues: 292 sheet: -0.45 (0.42), residues: 145 loop : -0.76 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 369 HIS 0.005 0.001 HIS A 358 PHE 0.014 0.001 PHE A 38 TYR 0.014 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 125 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7572 (m-30) cc_final: 0.6732 (m-30) REVERT: A 18 THR cc_start: 0.7917 (m) cc_final: 0.7585 (m) REVERT: A 31 GLU cc_start: 0.6855 (tp30) cc_final: 0.6531 (tp30) REVERT: A 41 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.5796 (pptt) REVERT: A 107 ASP cc_start: 0.8877 (t0) cc_final: 0.8553 (m-30) REVERT: A 108 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8051 (mp) REVERT: A 277 MET cc_start: 0.7216 (mmp) cc_final: 0.6656 (mmp) REVERT: A 305 PHE cc_start: 0.7654 (t80) cc_final: 0.7408 (t80) REVERT: A 313 LYS cc_start: 0.9295 (tptm) cc_final: 0.8966 (tppp) REVERT: A 345 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6277 (ppp) REVERT: A 346 ASP cc_start: 0.8056 (m-30) cc_final: 0.7694 (m-30) REVERT: A 371 ASP cc_start: 0.5853 (OUTLIER) cc_final: 0.5506 (m-30) REVERT: B 229 LEU cc_start: 0.7320 (mm) cc_final: 0.6789 (mt) REVERT: B 302 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6255 (mp-120) REVERT: B 350 ASN cc_start: 0.8046 (t0) cc_final: 0.7749 (t0) REVERT: B 371 ASN cc_start: 0.7322 (m-40) cc_final: 0.6986 (m-40) REVERT: B 453 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7066 (mp10) REVERT: B 474 ASP cc_start: 0.7125 (t0) cc_final: 0.6884 (t0) outliers start: 22 outliers final: 11 residues processed: 119 average time/residue: 0.8320 time to fit residues: 107.2379 Evaluate side-chains 119 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** 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 61 GLN ** 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 = 0.4573 r_free = 0.4573 target = 0.177992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.144994 restraints weight = 10275.253| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 3.48 r_work: 0.4030 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7369 Z= 0.233 Angle : 0.661 10.701 9965 Z= 0.342 Chirality : 0.045 0.173 1076 Planarity : 0.004 0.057 1242 Dihedral : 7.345 73.560 977 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.23 % Allowed : 29.88 % 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: -0.38 (0.28), residues: 845 helix: 0.69 (0.30), residues: 298 sheet: -0.46 (0.42), residues: 145 loop : -0.83 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 369 HIS 0.006 0.001 HIS A 358 PHE 0.013 0.001 PHE A 176 TYR 0.017 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: 5630.41 seconds wall clock time: 96 minutes 40.91 seconds (5800.91 seconds total)