Starting phenix.real_space_refine on Sun Nov 17 22:11:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/11_2024/8t2t_40987.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/11_2024/8t2t_40987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/11_2024/8t2t_40987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/11_2024/8t2t_40987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/11_2024/8t2t_40987.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2t_40987/11_2024/8t2t_40987.cif" } resolution = 3.0 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= 0.016 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 546 5.49 5 Mg 10 5.21 5 S 21 5.16 5 C 7226 2.51 5 N 2738 2.21 5 O 4335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14876 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 183 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 5} Chain: "B" Number of atoms: 11548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 11548 Classifications: {'RNA': 537} Modifications used: {'rna2p_pur': 37, 'rna2p_pyr': 11, 'rna3p_pur': 287, 'rna3p_pyr': 202} Link IDs: {'rna2p': 47, 'rna3p': 489} Chain breaks: 5 Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3133 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 9, 'NH4': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 10.12, per 1000 atoms: 0.68 Number of scatterers: 14876 At special positions: 0 Unit cell: (103.168, 133.12, 161.408, 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 546 15.00 Mg 10 11.99 O 4335 8.00 N 2738 7.00 C 7226 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: 3.48 Conformation dependent library (CDL) restraints added in 674.5 milliseconds 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 70.5% alpha, 5.7% beta 172 base pairs and 301 stacking pairs defined. Time for finding SS restraints: 7.40 Creating SS restraints... Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.661A pdb=" N GLN D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 131 removed outlier: 3.754A pdb=" N ALA D 122 " --> pdb=" O CYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.607A pdb=" N ASP D 147 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 148 " --> pdb=" O PHE D 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 148' Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.672A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.635A pdb=" N ILE D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 207 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 234 through 252 Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.803A pdb=" N LEU D 270 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 313 through 332 Processing helix chain 'D' and resid 337 through 361 removed outlier: 3.555A pdb=" N LYS D 361 " --> pdb=" O TRP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 373 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 389 through 396 removed outlier: 4.161A pdb=" N LYS D 396 " --> pdb=" O TYR D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 404 through 412 Processing helix chain 'D' and resid 415 through 424 removed outlier: 3.607A pdb=" N TYR D 419 " --> pdb=" O SER D 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 223 removed outlier: 4.030A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS D 228 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP D 265 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 275 through 279 183 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 416 hydrogen bonds 648 hydrogen bond angles 0 basepair planarities 172 basepair parallelities 301 stacking parallelities Total time for adding SS restraints: 7.83 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2323 1.33 - 1.46: 7393 1.46 - 1.58: 5495 1.58 - 1.70: 1081 1.70 - 1.83: 35 Bond restraints: 16327 Sorted by residual: bond pdb=" CG1 ILE D 325 " pdb=" CD1 ILE D 325 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.27e+00 bond pdb=" C3' A B 204 " pdb=" O3' A B 204 " ideal model delta sigma weight residual 1.427 1.454 -0.027 1.50e-02 4.44e+03 3.16e+00 bond pdb=" CG LEU D 16 " pdb=" CD2 LEU D 16 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.09e+00 bond pdb=" CB CYS D 341 " pdb=" SG CYS D 341 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CA ASP D 265 " pdb=" CB ASP D 265 " ideal model delta sigma weight residual 1.532 1.558 -0.026 1.68e-02 3.54e+03 2.31e+00 ... (remaining 16322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 23986 2.39 - 4.79: 639 4.79 - 7.18: 103 7.18 - 9.57: 23 9.57 - 11.96: 5 Bond angle restraints: 24756 Sorted by residual: angle pdb=" C3' A B 204 " pdb=" O3' A B 204 " pdb=" P A B 205 " ideal model delta sigma weight residual 120.20 128.70 -8.50 1.50e+00 4.44e-01 3.21e+01 angle pdb=" O3' A B 204 " pdb=" C3' A B 204 " pdb=" C2' A B 204 " ideal model delta sigma weight residual 109.50 117.63 -8.13 1.50e+00 4.44e-01 2.94e+01 angle pdb=" O3' G B 123 " pdb=" C3' G B 123 " pdb=" C2' G B 123 " ideal model delta sigma weight residual 113.70 121.70 -8.00 1.50e+00 4.44e-01 2.84e+01 angle pdb=" C3' U B 89 " pdb=" O3' U B 89 " pdb=" P A B 90 " ideal model delta sigma weight residual 120.20 127.41 -7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" CA ILE D 325 " pdb=" CB ILE D 325 " pdb=" CG1 ILE D 325 " ideal model delta sigma weight residual 110.40 118.14 -7.74 1.70e+00 3.46e-01 2.07e+01 ... (remaining 24751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8873 35.49 - 70.98: 1308 70.98 - 106.48: 143 106.48 - 141.97: 4 141.97 - 177.46: 10 Dihedral angle restraints: 10338 sinusoidal: 9214 harmonic: 1124 Sorted by residual: dihedral pdb=" C4' C B 206 " pdb=" C3' C B 206 " pdb=" C2' C B 206 " pdb=" C1' C B 206 " ideal model delta sinusoidal sigma weight residual -35.00 29.06 -64.06 1 8.00e+00 1.56e-02 8.44e+01 dihedral pdb=" C5' C B 206 " pdb=" C4' C B 206 " pdb=" C3' C B 206 " pdb=" O3' C B 206 " ideal model delta sinusoidal sigma weight residual 147.00 84.54 62.46 1 8.00e+00 1.56e-02 8.06e+01 dihedral pdb=" O4' U B 2 " pdb=" C1' U B 2 " pdb=" N1 U B 2 " pdb=" C2 U B 2 " ideal model delta sinusoidal sigma weight residual 200.00 51.41 148.59 1 1.50e+01 4.44e-03 7.91e+01 ... (remaining 10335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2979 0.082 - 0.163: 192 0.163 - 0.245: 13 0.245 - 0.326: 3 0.326 - 0.408: 8 Chirality restraints: 3195 Sorted by residual: chirality pdb=" C1' A B 370 " pdb=" O4' A B 370 " pdb=" C2' A B 370 " pdb=" N9 A B 370 " both_signs ideal model delta sigma weight residual False 2.46 2.05 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C3' C B 206 " pdb=" C4' C B 206 " pdb=" O3' C B 206 " pdb=" C2' C B 206 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C3' G B 123 " pdb=" C4' G B 123 " pdb=" O3' G B 123 " pdb=" C2' G B 123 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 3192 not shown) Planarity restraints: 1089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 289 " 0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO D 290 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 290 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 290 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 102 " -0.019 2.00e-02 2.50e+03 2.04e-02 8.35e+00 pdb=" CG TYR D 102 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 102 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR D 102 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR D 102 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR D 102 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR D 102 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 102 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 99 " -0.044 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO D 100 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.038 5.00e-02 4.00e+02 ... (remaining 1086 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 142 2.57 - 3.15: 10129 3.15 - 3.73: 31199 3.73 - 4.32: 40526 4.32 - 4.90: 52341 Nonbonded interactions: 134337 Sorted by model distance: nonbonded pdb=" OP1 C B 581 " pdb="MG MG B 701 " model vdw 1.982 2.170 nonbonded pdb=" O2' U B 638 " pdb="MG MG B 701 " model vdw 2.005 2.170 nonbonded pdb=" OP2 G B 136 " pdb="MG MG B 709 " model vdw 2.013 2.170 nonbonded pdb=" OP2 G B 578 " pdb="MG MG B 708 " model vdw 2.020 2.170 nonbonded pdb=" O3' U B 638 " pdb="MG MG B 701 " model vdw 2.036 2.170 ... (remaining 134332 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=0.00 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: 4.100 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: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 41.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0531 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 : 0.006 0.090 16327 Z= 0.351 Angle : 0.975 11.964 24756 Z= 0.481 Chirality : 0.047 0.408 3195 Planarity : 0.007 0.081 1089 Dihedral : 24.844 177.461 9614 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.46 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 24.93 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.78 (0.39), residues: 381 helix: -0.91 (0.29), residues: 244 sheet: -0.56 (1.06), residues: 28 loop : -1.59 (0.54), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 328 HIS 0.011 0.003 HIS D 151 PHE 0.027 0.003 PHE D 89 TYR 0.045 0.004 TYR D 102 ARG 0.014 0.001 ARG D 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6329 (mttp) cc_final: 0.5684 (mtpp) REVERT: D 37 TYR cc_start: 0.4045 (p90) cc_final: 0.3790 (p90) REVERT: D 241 VAL cc_start: 0.2833 (t) cc_final: 0.2266 (p) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 1.3988 time to fit residues: 116.3054 Evaluate side-chains 35 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 107 HIS D 121 GLN D 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2259 moved from start: 0.7098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 16327 Z= 0.390 Angle : 1.292 11.847 24756 Z= 0.634 Chirality : 0.062 0.413 3195 Planarity : 0.009 0.096 1089 Dihedral : 26.109 176.881 8809 Min Nonbonded Distance : 1.259 Molprobity Statistics. All-atom Clashscore : 35.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.51 % Favored : 94.23 % Rotamer: Outliers : 8.50 % Allowed : 26.69 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -1.87 (0.37), residues: 381 helix: -0.75 (0.29), residues: 238 sheet: 0.91 (1.63), residues: 14 loop : -2.27 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP D 328 HIS 0.009 0.004 HIS D 107 PHE 0.030 0.005 PHE D 145 TYR 0.024 0.003 TYR D 102 ARG 0.014 0.002 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 43 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6305 (mttp) cc_final: 0.5770 (tttm) REVERT: D 102 TYR cc_start: 0.2035 (OUTLIER) cc_final: 0.0789 (t80) REVERT: D 106 PHE cc_start: 0.1657 (OUTLIER) cc_final: 0.1380 (m-80) REVERT: D 236 MET cc_start: 0.4930 (mtt) cc_final: 0.0929 (ptm) REVERT: D 347 ARG cc_start: 0.2985 (OUTLIER) cc_final: 0.1591 (tpt170) REVERT: D 354 MET cc_start: -0.0500 (ptt) cc_final: -0.0705 (ptp) REVERT: D 424 CYS cc_start: -0.2463 (OUTLIER) cc_final: -0.2806 (p) outliers start: 29 outliers final: 3 residues processed: 68 average time/residue: 1.0378 time to fit residues: 79.5853 Evaluate side-chains 41 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 424 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2109 moved from start: 0.7601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 16327 Z= 0.213 Angle : 0.770 8.986 24756 Z= 0.390 Chirality : 0.041 0.283 3195 Planarity : 0.006 0.080 1089 Dihedral : 25.483 178.434 8809 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.46 % Favored : 95.28 % Rotamer: Outliers : 6.45 % Allowed : 30.50 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.00 (0.40), residues: 381 helix: 0.16 (0.31), residues: 239 sheet: -0.47 (1.10), residues: 29 loop : -2.38 (0.49), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 328 HIS 0.007 0.002 HIS D 284 PHE 0.029 0.003 PHE D 411 TYR 0.011 0.002 TYR D 272 ARG 0.008 0.001 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6413 (mttp) cc_final: 0.5853 (tttm) REVERT: D 102 TYR cc_start: 0.2187 (OUTLIER) cc_final: 0.1633 (t80) REVERT: D 206 MET cc_start: -0.0000 (OUTLIER) cc_final: -0.0272 (ttm) REVERT: D 253 LEU cc_start: 0.2064 (OUTLIER) cc_final: 0.1638 (tt) REVERT: D 354 MET cc_start: -0.1053 (ptt) cc_final: -0.1484 (ppp) outliers start: 22 outliers final: 6 residues processed: 54 average time/residue: 1.0993 time to fit residues: 66.7109 Evaluate side-chains 43 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 395 ASN Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3672 moved from start: 1.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.148 16327 Z= 0.490 Angle : 1.529 17.103 24756 Z= 0.773 Chirality : 0.078 0.632 3195 Planarity : 0.011 0.118 1089 Dihedral : 27.351 178.784 8809 Min Nonbonded Distance : 1.058 Molprobity Statistics. All-atom Clashscore : 44.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.82 % Favored : 92.91 % Rotamer: Outliers : 11.14 % Allowed : 30.50 % Favored : 58.36 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.14 (0.37), residues: 381 helix: -1.65 (0.28), residues: 235 sheet: -1.24 (1.44), residues: 14 loop : -2.77 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP D 328 HIS 0.108 0.013 HIS D 43 PHE 0.044 0.007 PHE D 298 TYR 0.040 0.004 TYR D 419 ARG 0.018 0.003 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 53 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6651 (mttp) cc_final: 0.6081 (mtpp) REVERT: D 40 LEU cc_start: 0.1891 (OUTLIER) cc_final: 0.1383 (mp) REVERT: D 41 LYS cc_start: 0.4296 (OUTLIER) cc_final: 0.3796 (tptt) REVERT: D 130 MET cc_start: 0.5766 (ptt) cc_final: 0.5392 (ptt) REVERT: D 206 MET cc_start: 0.2011 (OUTLIER) cc_final: 0.0048 (mmt) REVERT: D 236 MET cc_start: 0.4705 (OUTLIER) cc_final: 0.1432 (ptm) REVERT: D 242 MET cc_start: 0.6852 (mmm) cc_final: 0.6462 (mmp) REVERT: D 310 TRP cc_start: 0.0762 (OUTLIER) cc_final: -0.0252 (m-10) REVERT: D 354 MET cc_start: 0.0693 (OUTLIER) cc_final: -0.0236 (ppp) outliers start: 38 outliers final: 10 residues processed: 81 average time/residue: 1.1029 time to fit residues: 100.3095 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 395 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3773 moved from start: 1.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 16327 Z= 0.304 Angle : 1.040 13.093 24756 Z= 0.521 Chirality : 0.054 0.561 3195 Planarity : 0.007 0.084 1089 Dihedral : 26.626 177.609 8809 Min Nonbonded Distance : 1.007 Molprobity Statistics. All-atom Clashscore : 28.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.25 % Favored : 94.49 % Rotamer: Outliers : 7.33 % Allowed : 35.48 % Favored : 57.18 % 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: -2.19 (0.38), residues: 381 helix: -0.85 (0.29), residues: 239 sheet: -1.50 (1.08), residues: 24 loop : -2.48 (0.52), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP D 328 HIS 0.006 0.002 HIS D 109 PHE 0.035 0.004 PHE D 89 TYR 0.024 0.003 TYR D 111 ARG 0.013 0.001 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6966 (mttp) cc_final: 0.6485 (tttm) REVERT: D 54 GLN cc_start: 0.3516 (OUTLIER) cc_final: 0.3274 (tp-100) REVERT: D 89 PHE cc_start: 0.8422 (t80) cc_final: 0.7875 (t80) REVERT: D 94 ILE cc_start: 0.8058 (tt) cc_final: 0.7822 (pp) REVERT: D 154 LEU cc_start: 0.4746 (OUTLIER) cc_final: 0.4536 (OUTLIER) REVERT: D 206 MET cc_start: 0.3193 (OUTLIER) cc_final: 0.1110 (mmt) REVERT: D 236 MET cc_start: 0.5511 (OUTLIER) cc_final: 0.1905 (ptt) REVERT: D 289 LYS cc_start: 0.7605 (pttt) cc_final: 0.7338 (ptmt) REVERT: D 302 MET cc_start: 0.4298 (OUTLIER) cc_final: 0.3787 (tmm) REVERT: D 310 TRP cc_start: 0.0851 (OUTLIER) cc_final: -0.0558 (m-10) REVERT: D 354 MET cc_start: 0.0530 (ptt) cc_final: -0.0706 (ppp) outliers start: 25 outliers final: 9 residues processed: 68 average time/residue: 1.1264 time to fit residues: 85.7981 Evaluate side-chains 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 424 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN D 395 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4930 moved from start: 2.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 16327 Z= 0.455 Angle : 1.446 12.406 24756 Z= 0.705 Chirality : 0.067 0.381 3195 Planarity : 0.010 0.090 1089 Dihedral : 27.480 175.707 8809 Min Nonbonded Distance : 1.186 Molprobity Statistics. All-atom Clashscore : 40.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 8.80 % Allowed : 36.07 % Favored : 55.13 % 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: -2.39 (0.39), residues: 381 helix: -0.82 (0.31), residues: 234 sheet: -2.33 (1.06), residues: 24 loop : -2.73 (0.49), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.006 TRP D 136 HIS 0.008 0.003 HIS D 284 PHE 0.049 0.008 PHE D 248 TYR 0.032 0.005 TYR D 224 ARG 0.030 0.002 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 LEU cc_start: 0.4011 (OUTLIER) cc_final: 0.3628 (mt) REVERT: D 89 PHE cc_start: 0.8308 (t80) cc_final: 0.7796 (t80) REVERT: D 94 ILE cc_start: 0.8347 (tt) cc_final: 0.8123 (pp) REVERT: D 236 MET cc_start: 0.4858 (OUTLIER) cc_final: 0.3122 (ptt) REVERT: D 302 MET cc_start: 0.5301 (OUTLIER) cc_final: 0.4770 (tmm) REVERT: D 354 MET cc_start: 0.0677 (OUTLIER) cc_final: -0.0747 (ppp) REVERT: D 424 CYS cc_start: 0.5724 (OUTLIER) cc_final: 0.5487 (t) outliers start: 30 outliers final: 6 residues processed: 82 average time/residue: 1.1504 time to fit residues: 105.5013 Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 424 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN D 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5241 moved from start: 2.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 16327 Z= 0.358 Angle : 1.116 16.731 24756 Z= 0.543 Chirality : 0.055 0.436 3195 Planarity : 0.008 0.106 1089 Dihedral : 26.967 175.425 8809 Min Nonbonded Distance : 1.446 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 6.16 % Allowed : 39.88 % Favored : 53.96 % 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: -1.89 (0.40), residues: 381 helix: -0.53 (0.31), residues: 238 sheet: -2.16 (1.64), residues: 10 loop : -2.40 (0.49), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP D 310 HIS 0.007 0.002 HIS D 291 PHE 0.036 0.005 PHE D 275 TYR 0.020 0.003 TYR D 60 ARG 0.010 0.001 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: D 13 SER cc_start: 0.4694 (OUTLIER) cc_final: 0.4370 (p) REVERT: D 89 PHE cc_start: 0.8443 (t80) cc_final: 0.7835 (t80) REVERT: D 90 ILE cc_start: 0.6807 (pt) cc_final: 0.6481 (pp) REVERT: D 236 MET cc_start: 0.4837 (OUTLIER) cc_final: 0.3525 (ptt) REVERT: D 271 LYS cc_start: 0.8382 (tttt) cc_final: 0.8174 (tttt) REVERT: D 354 MET cc_start: 0.2888 (ptt) cc_final: 0.1320 (tmt) REVERT: D 356 ILE cc_start: 0.5601 (OUTLIER) cc_final: 0.5356 (mt) REVERT: D 364 GLN cc_start: 0.6260 (tp-100) cc_final: 0.5875 (tp-100) outliers start: 21 outliers final: 5 residues processed: 72 average time/residue: 1.2683 time to fit residues: 101.6890 Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN D 208 ASN ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5450 moved from start: 2.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16327 Z= 0.254 Angle : 0.927 11.331 24756 Z= 0.454 Chirality : 0.045 0.351 3195 Planarity : 0.007 0.097 1089 Dihedral : 26.577 173.483 8809 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.57 % Allowed : 41.64 % Favored : 52.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.45 (0.40), residues: 381 helix: -0.20 (0.31), residues: 236 sheet: -0.16 (1.08), residues: 24 loop : -2.58 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP D 328 HIS 0.005 0.002 HIS D 151 PHE 0.045 0.005 PHE D 277 TYR 0.024 0.003 TYR D 278 ARG 0.007 0.001 ARG D 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.670 Fit side-chains REVERT: D 7 MET cc_start: 0.0935 (OUTLIER) cc_final: 0.0332 (ttt) REVERT: D 42 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6538 (mp0) REVERT: D 89 PHE cc_start: 0.8304 (t80) cc_final: 0.7888 (t80) REVERT: D 90 ILE cc_start: 0.6921 (pt) cc_final: 0.6696 (pp) REVERT: D 102 TYR cc_start: 0.3528 (OUTLIER) cc_final: 0.3198 (t80) REVERT: D 136 TRP cc_start: 0.8324 (m100) cc_final: 0.8124 (m100) outliers start: 19 outliers final: 5 residues processed: 67 average time/residue: 1.1275 time to fit residues: 84.6215 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5373 moved from start: 2.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16327 Z= 0.186 Angle : 0.792 12.167 24756 Z= 0.389 Chirality : 0.040 0.332 3195 Planarity : 0.006 0.091 1089 Dihedral : 26.135 169.243 8809 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.93 % Allowed : 45.45 % Favored : 51.61 % 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: -1.31 (0.41), residues: 381 helix: -0.23 (0.32), residues: 238 sheet: None (None), residues: 0 loop : -1.87 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 328 HIS 0.004 0.001 HIS D 284 PHE 0.021 0.002 PHE D 248 TYR 0.017 0.002 TYR D 385 ARG 0.009 0.001 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: D 7 MET cc_start: 0.1041 (OUTLIER) cc_final: 0.0798 (ttt) REVERT: D 42 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6665 (mp0) REVERT: D 89 PHE cc_start: 0.8280 (t80) cc_final: 0.7855 (t80) REVERT: D 90 ILE cc_start: 0.7097 (pt) cc_final: 0.6895 (pp) REVERT: D 130 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7591 (pmm) REVERT: D 268 SER cc_start: 0.8203 (m) cc_final: 0.7900 (p) REVERT: D 330 ASN cc_start: 0.7914 (m-40) cc_final: 0.7674 (m110) REVERT: D 354 MET cc_start: 0.5141 (ptt) cc_final: 0.4604 (mtt) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 1.1134 time to fit residues: 72.9517 Evaluate side-chains 44 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 2.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16327 Z= 0.252 Angle : 0.904 12.486 24756 Z= 0.443 Chirality : 0.044 0.305 3195 Planarity : 0.007 0.097 1089 Dihedral : 26.237 170.265 8809 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.52 % Allowed : 47.51 % Favored : 48.97 % 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: -1.53 (0.41), residues: 381 helix: -0.36 (0.32), residues: 241 sheet: 0.96 (1.46), residues: 14 loop : -2.44 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 328 HIS 0.017 0.003 HIS D 284 PHE 0.031 0.003 PHE D 248 TYR 0.033 0.003 TYR D 102 ARG 0.014 0.001 ARG D 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: D 42 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6590 (mp0) REVERT: D 136 TRP cc_start: 0.8296 (m100) cc_final: 0.8067 (m100) REVERT: D 268 SER cc_start: 0.8339 (m) cc_final: 0.8085 (p) REVERT: D 271 LYS cc_start: 0.8316 (tttt) cc_final: 0.8000 (tptm) REVERT: D 388 LYS cc_start: 0.2889 (mptt) cc_final: 0.2491 (tptt) REVERT: D 390 ILE cc_start: 0.7250 (mt) cc_final: 0.6793 (mt) outliers start: 12 outliers final: 2 residues processed: 62 average time/residue: 1.4157 time to fit residues: 97.2253 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.134990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.114581 restraints weight = 53551.102| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 1.76 r_work: 0.4073 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 2.9279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 16327 Z= 0.394 Angle : 1.127 11.756 24756 Z= 0.544 Chirality : 0.053 0.345 3195 Planarity : 0.008 0.091 1089 Dihedral : 26.770 176.947 8809 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 28.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.93 % Allowed : 48.68 % Favored : 48.39 % 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: -2.26 (0.39), residues: 381 helix: -1.03 (0.30), residues: 238 sheet: 0.06 (1.13), residues: 24 loop : -2.56 (0.52), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP D 328 HIS 0.003 0.001 HIS D 109 PHE 0.050 0.005 PHE D 248 TYR 0.070 0.005 TYR D 316 ARG 0.013 0.002 ARG D 351 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3359.07 seconds wall clock time: 63 minutes 37.07 seconds (3817.07 seconds total)